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

Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?

PubMed

Khedkar, Supriya; Seshasayee, Aswin Sai Narain

2016-06-01

Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences. Copyright © 2016 Khedkar and Seshasayee.

Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology?

PubMed Central

Khedkar, Supriya; Seshasayee, Aswin Sai Narain

2016-01-01

Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences. PMID:27172194

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

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

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

PubMed Central

Sale, Kenneth L.; Simmons, Blake A.; Popelier, Paul L. A.

2017-01-01

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:28857244

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

DOE PAGES

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.; ...

2017-08-31

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Robust PRNG based on homogeneously distributed chaotic dynamics

NASA Astrophysics Data System (ADS)

Garasym, Oleg; Lozi, René; Taralova, Ina

2016-02-01

This paper is devoted to the design of new chaotic Pseudo Random Number Generator (CPRNG). Exploring several topologies of network of 1-D coupled chaotic mapping, we focus first on two dimensional networks. Two topologically coupled maps are studied: TTL rc non-alternate, and TTL SC alternate. The primary idea of the novel maps has been based on an original coupling of the tent and logistic maps to achieve excellent random properties and homogeneous /uniform/ density in the phase plane, thus guaranteeing maximum security when used for chaos base cryptography. In this aim two new nonlinear CPRNG: MTTL 2 sc and NTTL 2 are proposed. The maps successfully passed numerous statistical, graphical and numerical tests, due to proposed ring coupling and injection mechanisms.

Canonical Representations of the Simple Map

NASA Astrophysics Data System (ADS)

Kerwin, Olivia; Punjabi, Alkesh; Ali, Halima; Boozer, Allen

2007-11-01

The simple map is the simplest map that has the topology of a divertor tokamak. The simple map has three canonical representations: (i) toroidal flux and poloidal angle (ψ,θ) as canonical coordinates, (ii) the physical variables (R,Z) or (X,Y) as canonical coordinates, and (iii) the action-angle (J,ζ) or magnetic variables (ψ,θ) as canonical coordinates. We give the derivation of the simple map in the (X,Y) representation. The simple map in this representation has been studied extensively (Ref. 1 and references therein). We calculate the magnetic coordinates for the simple map, construct the simple map in magnetic coordinates, and calculate generic topological effects of magnetic perturbations in divertor tokamaks using the map. We also construct the simple map in (ψ,θ) representation. Preliminary results of these studies will be presented. This work is supported by US DOE OFES DE-FG02-01ER54624 and DE-FG02-04ER54793. [1] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A 364 140--145 (2007).

Revealing Fermi arcs and Weyl nodes in MoTe2 by quasiparticle interference mapping

NASA Astrophysics Data System (ADS)

Deng, Peng; Xu, Zhilin; Deng, Ke; Zhang, Kenan; Wu, Yang; Zhang, Haijun; Zhou, Shuyun; Chen, Xi

2017-06-01

A Weyl semimetal exhibits unique properties with Weyl nodes in the bulk and Fermi arcs on the surface. Recently, MoTe2 was found to be a type-II Weyl semimetal, providing a platform for realizing these Weyl physics. Here, we report visualization of topological surface states on the surface of MoTe2 using a scanning tunneling microscope. Scattering between topological states forms quasiparticle interference (QPI) patterns in the Fourier transform of conductance maps. The complete existence of topological surface states in energy momentum space is revealed by d I /d V mapping. By comparing QPI results with a first-principles calculation, we further unveil the locations of Weyl nodes in the surface Brillouin zone. Our work provides spectroscopic information in the unoccupied states, especially those around the Weyl nodes energy, demonstrating the node-arc correlation in Weyl semimetals.

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

Application of sensitivity-analysis techniques to the calculation of topological quantities

NASA Astrophysics Data System (ADS)

Gilchrist, Stuart

2017-08-01

Magnetic reconnection in the corona occurs preferentially at sites where the magnetic connectivity is either discontinuous or has a large spatial gradient. Hence there is a general interest in computing quantities (like the squashing factor) that characterize the gradient in the field-line mapping function. Here we present an algorithm for calculating certain (quasi)topological quantities using mathematical techniques from the field of ``sensitivity-analysis''. The method is based on the calculation of a three dimensional field-line mapping Jacobian from which all the present topological quantities of interest can be derived. We will present the algorithm and the details of a publicly available set of libraries that implement the algorithm.

Topology and the Lay of the Land: A Mathematician on the Topographer's Turf.

ERIC Educational Resources Information Center

Shubin, Mikhail

1992-01-01

Presents a proof of Euler's Theorem on polyhedra by relating the theorem to the field of modern topology, specifically to the topology of relief maps. An analogous theorem involving the features of mountain summits, basins, and passes on a terrain is proved and related to the faces, vertices, and edges on a convex polyhedron. (MDH)

Topological T-duality, automorphisms and classifying spaces

NASA Astrophysics Data System (ADS)

Pande, Ashwin S.

2014-08-01

We extend the formalism of Topological T-duality to spaces which are the total space of a principal S1-bundle p:E→W with an H-flux in H3(E,Z) together with an automorphism of the continuous-trace algebra on E determined by H. The automorphism is a ‘topological approximation’ to a gerby gauge transformation of spacetime. We motivate this physically from Buscher’s Rules for T-duality. Using the Equivariant Brauer Group, we connect this problem to the C∗-algebraic formalism of Topological T-duality of Mathai and Rosenberg (2005). We show that the study of this problem leads to the study of a purely topological problem, namely, Topological T-duality of triples (p,b,H) consisting of isomorphism classes of a principal circle bundle p:X→B and classes b∈H2(X,Z) and H∈H3(X,Z). We construct a classifying space R for triples in a manner similar to the work of Bunke and Schick (2005). We characterize R up to homotopy and study some of its properties. We show that it possesses a natural self-map which induces T-duality for triples. We study some properties of this map.

The topology of geology 1: Topological analysis

NASA Astrophysics Data System (ADS)

Thiele, Samuel T.; Jessell, Mark W.; Lindsay, Mark; Ogarko, Vitaliy; Wellmann, J. Florian; Pakyuz-Charrier, Evren

2016-10-01

Topology has been used to characterise and quantify the properties of complex systems in a diverse range of scientific domains. This study explores the concept and applications of topological analysis in geology. We have developed an automatic system for extracting first order 2D topological information from geological maps, and 3D topological information from models built with the Noddy kinematic modelling system, and equivalent analyses should be possible for other implicit modelling systems. A method is presented for describing the spatial and temporal topology of geological models using a set of adjacency relationships that can be expressed as a topology network, thematic adjacency matrix or hive diagram. We define three types of spatial topology (cellular, structural and lithological) that allow us to analyse different aspects of the geology, and then apply them to investigate the geology of the Hamersley Basin, Western Australia.

Cosmic Topology: Studying The Shape And Size Of Our Universe

NASA Astrophysics Data System (ADS)

Yzaguirre, Amelia; Hajian, A.

2010-01-01

The question of the size and the shape of our universe is a very old problem that has received considerable attention over the past few years. The simplest cosmological model predicts that the mean density of the universe is very close to the critical density, admitting a local geometry of the universe that is flat. Current results from different cosmological observations confirm this to the percent level accuracy. General Relativity (being a local theory) only determines local geometry, which allows for the possibility of a multiply connected universe with a zero (or small) curvature. To study the global shape, or topology, of the universe, one can use cosmological observations on large scales. In this project we investigate the possibility of a ``small universe'', that is, a compact finite space, by searching for planar symmetries in the CMB anisotropy maps provided by the five-year WMAP observations in two foreground cleaned maps (WMAP ILC map and the Tegmark, et al. (TOH) map ). Our results strongly suggest that the small universe model is not a viable topology for the universe.

Interactive Spacecraft Trajectory Design Strategies Featuring Poincare Map Topology

NASA Astrophysics Data System (ADS)

Schlei, Wayne R.

Space exploration efforts are shifting towards inexpensive and more agile vehicles. Versatility regarding spacecraft trajectories refers to the agility to correct deviations from an intended path or even the ability to adapt the future path to a new destination--all with limited spaceflight resources (i.e., small DeltaV budgets). Trajectory design methods for such nimble vehicles incorporate equally versatile procedures that allow for rapid and interactive decision making while attempting to reduce Delta V budgets, leading to a versatile trajectory design platform. A versatile design paradigm requires the exploitation of Poincare map topology , or the interconnected web of dynamical structures, existing within the chaotic dynamics of multi-body gravitational models to outline low-Delta V transfer options residing nearby to a current path. This investigation details an autonomous procedure to extract the periodic orbits (topology nodes) and correlated asymptotic flow structures (or the invariant manifolds representing topology links). The autonomous process summarized in this investigation (termed PMATE) overcomes discontinuities on the Poincare section that arise in the applied multi-body model (the planar circular restricted three-body problem) and detects a wide variety of novel periodic orbits. New interactive capabilities deliver a visual analytics foundation for versatile spaceflight design, especially for initial guess generation and manipulation. Such interactive strategies include the selection of states and arcs from Poincare section visualizations and the capabilities to draw and drag trajectories to remove dependency on initial state input. Furthermore, immersive selection is expanded to cull invariant manifold structures, yielding low-DeltaV or even DeltaV-free transfers between periodic orbits. The application of interactive design strategies featuring a dense extraction of Poincare map topology is demonstrated for agile spaceflight with a simple spacecraft rerouting scenario incorporating a very limited Delta V budget. In the Earth-Moon system, a low-DeltaV transfer from low Earth orbit (LEO) to the distant retrograde orbit (DRO) vicinity is derived with interactive topology-based design tactics. Finally, Poincare map topology is exploited in the Saturn-Enceladus system to explore a possible ballistic capture scenario around Enceladus.

Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output.

PubMed

Nochomovitz, Yigal D; Li, Hao

2006-03-14

Deciphering the design principles for regulatory networks is fundamental to an understanding of biological systems. We have explored the mapping from the space of network topologies to the space of dynamical phenotypes for small networks. Using exhaustive enumeration of a simple model of three- and four-node networks, we demonstrate that certain dynamical phenotypes can be generated by an atypically broad spectrum of network topologies. Such dynamical outputs are highly designable, much like certain protein structures can be designed by an unusually broad spectrum of sequences. The network topologies that encode a highly designable dynamical phenotype possess two classes of connections: a fully conserved core of dedicated connections that encodes the stable dynamical phenotype and a partially conserved set of variable connections that controls the transient dynamical flow. By comparing the topologies and dynamics of the three- and four-node network ensembles, we observe a large number of instances of the phenomenon of "mutational buffering," whereby addition of a fourth node suppresses phenotypic variation amongst a set of three-node networks.

Persistent homology and non-Gaussianity

NASA Astrophysics Data System (ADS)

Cole, Alex; Shiu, Gary

2018-03-01

In this paper, we introduce the topological persistence diagram as a statistic for Cosmic Microwave Background (CMB) temperature anisotropy maps. A central concept in 'Topological Data Analysis' (TDA), the idea of persistence is to represent a data set by a family of topological spaces. One then examines how long topological features 'persist' as the family of spaces is traversed. We compute persistence diagrams for simulated CMB temperature anisotropy maps featuring various levels of primordial non-Gaussianity of local type. Postponing the analysis of observational effects, we show that persistence diagrams are more sensitive to local non-Gaussianity than previous topological statistics including the genus and Betti number curves, and can constrain Δ fNLloc= 35.8 at the 68% confidence level on the simulation set, compared to Δ fNLloc= 60.6 for the Betti number curves. Given the resolution of our simulations, we expect applying persistence diagrams to observational data will give constraints competitive with those of the Minkowski Functionals. This is the first in a series of papers where we plan to apply TDA to different shapes of non-Gaussianity in the CMB and Large Scale Structure.

Morphological self-organizing feature map neural network with applications to automatic target recognition

NASA Astrophysics Data System (ADS)

Zhang, Shijun; Jing, Zhongliang; Li, Jianxun

2005-01-01

The rotation invariant feature of the target is obtained using the multi-direction feature extraction property of the steerable filter. Combining the morphological operation top-hat transform with the self-organizing feature map neural network, the adaptive topological region is selected. Using the erosion operation, the topological region shrinkage is achieved. The steerable filter based morphological self-organizing feature map neural network is applied to automatic target recognition of binary standard patterns and real-world infrared sequence images. Compared with Hamming network and morphological shared-weight networks respectively, the higher recognition correct rate, robust adaptability, quick training, and better generalization of the proposed method are achieved.

Mapping with Young Children.

ERIC Educational Resources Information Center

Sunal, Cynthia Szymanski; Warash, Bobbi Gibson

Techniques for encouraging young children to discover the purpose and use of maps are discussed. Motor activity and topological studies form a base from which the teacher and children can build a mapping program of progressive sophistication. Concepts important to mapping include boundaries, regions, exteriors, interiors, holes, order, point of…

From Majorana fermions to topological order.

PubMed

Terhal, Barbara M; Hassler, Fabian; DiVincenzo, David P

2012-06-29

We consider a system consisting of a 2D network of links between Majorana fermions on superconducting islands. We show that the fermionic Hamiltonian modeling this system is topologically ordered in a region of parameter space: we show that Kitaev's toric code emerges in fourth-order perturbation theory. By using a Jordan-Wigner transformation we can map the model onto a family of signed 2D Ising models in a transverse field where the signs, ferromagnetic or antiferromagnetic, are determined by additional gauge bits. Our mapping allows an understanding of the nonperturbative regime and the phase transition to a nontopological phase. We discuss the physics behind a possible implementation of this model and argue how it can be used for topological quantum computation by adiabatic changes in the Hamiltonian.

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

PubMed Central

Stadler, Michael R; Haines, Jenna E

2017-01-01

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains. PMID:29148971

Machine Learning Prediction of the Energy Gap of Graphene Nanoflakes Using Topological Autocorrelation Vectors.

PubMed

Fernandez, Michael; Abreu, Jose I; Shi, Hongqing; Barnard, Amanda S

2016-11-14

The possibility of band gap engineering in graphene opens countless new opportunities for application in nanoelectronics. In this work, the energy gaps of 622 computationally optimized graphene nanoflakes were mapped to topological autocorrelation vectors using machine learning techniques. Machine learning modeling revealed that the most relevant correlations appear at topological distances in the range of 1 to 42 with prediction accuracy higher than 80%. The data-driven model can statistically discriminate between graphene nanoflakes with different energy gaps on the basis of their molecular topology.

Topological Maxwell Metal Bands in a Superconducting Qutrit

NASA Astrophysics Data System (ADS)

Tan, Xinsheng; Zhang, Dan-Wei; Liu, Qiang; Xue, Guangming; Yu, Hai-Feng; Zhu, Yan-Qing; Yan, Hui; Zhu, Shi-Liang; Yu, Yang

2018-03-01

We experimentally explore the topological Maxwell metal bands by mapping the momentum space of condensed-matter models to the tunable parameter space of superconducting quantum circuits. An exotic band structure that is effectively described by the spin-1 Maxwell equations is imaged. Threefold degenerate points dubbed Maxwell points are observed in the Maxwell metal bands. Moreover, we engineer and observe the topological phase transition from the topological Maxwell metal to a trivial insulator, and report the first experiment to measure the Chern numbers that are higher than one.

Cloud GIS Based Watershed Management

NASA Astrophysics Data System (ADS)

Bediroğlu, G.; Colak, H. E.

2017-11-01

In this study, we generated a Cloud GIS based watershed management system with using Cloud Computing architecture. Cloud GIS is used as SAAS (Software as a Service) and DAAS (Data as a Service). We applied GIS analysis on cloud in terms of testing SAAS and deployed GIS datasets on cloud in terms of DAAS. We used Hybrid cloud computing model in manner of using ready web based mapping services hosted on cloud (World Topology, Satellite Imageries). We uploaded to system after creating geodatabases including Hydrology (Rivers, Lakes), Soil Maps, Climate Maps, Rain Maps, Geology and Land Use. Watershed of study area has been determined on cloud using ready-hosted topology maps. After uploading all the datasets to systems, we have applied various GIS analysis and queries. Results shown that Cloud GIS technology brings velocity and efficiency for watershed management studies. Besides this, system can be easily implemented for similar land analysis and management studies.

Topological phase transitions and chiral inelastic transport induced by the squeezing of light

PubMed Central

Peano, Vittorio; Houde, Martin; Brendel, Christian; Marquardt, Florian; Clerk, Aashish A.

2016-01-01

There is enormous interest in engineering topological photonic systems. Despite intense activity, most works on topological photonic states (and more generally bosonic states) amount in the end to replicating a well-known fermionic single-particle Hamiltonian. Here we show how the squeezing of light can lead to the formation of qualitatively new kinds of topological states. Such states are characterized by non-trivial Chern numbers, and exhibit protected edge modes, which give rise to chiral elastic and inelastic photon transport. These topological bosonic states are not equivalent to their fermionic (topological superconductor) counterparts and, in addition, cannot be mapped by a local transformation onto topological states found in particle-conserving models. They thus represent a new type of topological system. We study this physics in detail in the case of a kagome lattice model, and discuss possible realizations using nonlinear photonic crystals or superconducting circuits. PMID:26931620

Topological phase transitions and chiral inelastic transport induced by the squeezing of light

NASA Astrophysics Data System (ADS)

Peano, Vittorio; Houde, Martin; Brendel, Christian; Marquardt, Florian; Clerk, Aashish A.

2016-03-01

There is enormous interest in engineering topological photonic systems. Despite intense activity, most works on topological photonic states (and more generally bosonic states) amount in the end to replicating a well-known fermionic single-particle Hamiltonian. Here we show how the squeezing of light can lead to the formation of qualitatively new kinds of topological states. Such states are characterized by non-trivial Chern numbers, and exhibit protected edge modes, which give rise to chiral elastic and inelastic photon transport. These topological bosonic states are not equivalent to their fermionic (topological superconductor) counterparts and, in addition, cannot be mapped by a local transformation onto topological states found in particle-conserving models. They thus represent a new type of topological system. We study this physics in detail in the case of a kagome lattice model, and discuss possible realizations using nonlinear photonic crystals or superconducting circuits.

On the Topological Changes of Local Hurst Exponent in Polar Regions

NASA Astrophysics Data System (ADS)

Consolini, G.; De Michelis, P.

2014-12-01

Geomagnetic activity during magnetic substorms and storms is related to the dinamical and topological changes of the current systems flowing in the Earth's magnetosphere-ionosphere. This is particularly true in the case of polar regions where the enhancement of auroral electrojet current system is responsible for the observed geomagnetic perturbations. Here, using the DMA-technique we evaluate the local Hurst exponent (H"older exponent) for a set of 46 geomagnetic observatories, widely distributed in the northern hemisphere, during one of the most famous and strong geomagnetic storm, the Bastille event, and reconstruct a sequence of polar maps showing the dinamical changes of the topology of the local Hurst exponent with the geomagnetic activity level. The topological evolution of local Hurst exponent maps is discussed in relation to the dinamical changes of the current systems flowing in the polar ionosphere. G. Consolini has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant agreement no. 313038/STORM for this research.

Extended Maptree: a Representation of Fine-Grained Topology and Spatial Hierarchy of Bim

NASA Astrophysics Data System (ADS)

Wu, Y.; Shang, J.; Hu, X.; Zhou, Z.

2017-09-01

Spatial queries play significant roles in exchanging Building Information Modeling (BIM) data and integrating BIM with indoor spatial information. However, topological operators implemented for BIM spatial queries are limited to qualitative relations (e.g. touching, intersecting). To overcome this limitation, we propose an extended maptree model to represent the fine-grained topology and spatial hierarchy of indoor spaces. The model is based on a maptree which consists of combinatorial maps and an adjacency tree. Topological relations (e.g., adjacency, incidence, and covering) derived from BIM are represented explicitly and formally by extended maptrees, which can facilitate the spatial queries of BIM. To construct an extended maptree, we first use a solid model represented by vertical extrusion and boundary representation to generate the isolated 3-cells of combinatorial maps. Then, the spatial relationships defined in IFC are used to sew them together. Furthermore, the incremental edges of extended maptrees are labeled as removed 2-cells. Based on this, we can merge adjacent 3-cells according to the spatial hierarchy of IFC.

Formation of current singularity in a topologically constrained plasma

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

Zhou, Yao; Huang, Yi-Min; Qin, Hong

2016-02-01

Recently a variational integrator for ideal magnetohydrodynamics in Lagrangian labeling has been developed. Its built-in frozen-in equation makes it optimal for studying current sheet formation. We use this scheme to study the Hahm-Kulsrud-Taylor problem, which considers the response of a 2D plasma magnetized by a sheared field under sinusoidal boundary forcing. We obtain an equilibrium solution that preserves the magnetic topology of the initial field exactly, with a fluid mapping that is non-differentiable. Unlike previous studies that examine the current density output, we identify a singular current sheet from the fluid mapping. These results are benchmarked with a constrained Grad-Shafranovmore » solver. The same signature of current singularity can be found in other cases with more complex magnetic topologies.« less

Robust manipulation of light using topologically protected plasmonic modes.

PubMed

Liu, Chenxu; Gurudev Dutt, M V; Pekker, David

2018-02-05

We propose using a topological plasmonic crystal structure composed of an array of nearly parallel nanowires with unequal spacing for manipulating light. In the paraxial approximation, the Helmholtz equation that describes the propagation of light along the nanowires maps onto the Schrödinger equation of the Su-Schrieffer-Heeger (SSH) model. Using a full three-dimensional finite difference time domain solution of the Maxwell equations, we verify the existence of topological defect modes, with sub-wavelength localization, bound to domain walls of the plasmonic crystal. We show that by manipulating domain walls we can construct spatial mode filters that couple bulk modes to topological defect modes, and topological beam-splitters that couple two topological defect modes. Finally, we show that the structures are tolerant to fabrication errors with an inverse length-scale smaller than the topological band gap.

Spacetime representation of topological phononics

NASA Astrophysics Data System (ADS)

Deymier, Pierre A.; Runge, Keith; Lucas, Pierre; Vasseur, Jérôme O.

2018-05-01

Non-conventional topology of elastic waves arises from breaking symmetry of phononic structures either intrinsically through internal resonances or extrinsically via application of external stimuli. We develop a spacetime representation based on twistor theory of an intrinsic topological elastic structure composed of a harmonic chain attached to a rigid substrate. Elastic waves in this structure obey the Klein–Gordon and Dirac equations and possesses spinorial character. We demonstrate the mapping between straight line trajectories of these elastic waves in spacetime and the twistor complex space. The twistor representation of these Dirac phonons is related to their topological and fermion-like properties. The second topological phononic structure is an extrinsic structure composed of a one-dimensional elastic medium subjected to a moving superlattice. We report an analogy between the elastic behavior of this time-dependent superlattice, the scalar quantum field theory and general relativity of two types of exotic particle excitations, namely temporal Dirac phonons and temporal ghost (tachyonic) phonons. These phonons live on separate sides of a two-dimensional frequency space and are delimited by ghost lines reminiscent of the conventional light cone. Both phonon types exhibit spinorial amplitudes that can be measured by mapping the particle behavior to the band structure of elastic waves.

t-topology on the n-dimensional Minkowski space

NASA Astrophysics Data System (ADS)

Agrawal, Gunjan; Shrivastava, Sampada

2009-05-01

In this paper, a topological study of the n-dimensional Minkowski space, n >1, with t-topology, denoted by Mt, has been carried out. This topology, unlike the usual Euclidean one, is more physically appealing being defined by means of the Lorentzian metric. It shares many topological properties with similar candidate topologies and it has the advantage of being first countable. Compact sets of Mt and continuous maps into Mt are studied using the notion of Zeno sequences besides characterizing those sets that have the same subspace topologies induced from the Euclidean and t-topologies on n-dimensional Minkowski space. A necessary and sufficient condition for a compact set in the Euclidean n-space to be compact in Mt is obtained, thereby proving that the n-cube, n >1, as a subspace of Mt, is not compact, while a segment on a timelike line is compact in Mt. This study leads to the nonsimply connectedness of Mt, for n =2. Further, Minkowski space with s-topology has also been dealt with.

Comparison of Point Matching Techniques for Road Network Matching

NASA Astrophysics Data System (ADS)

Hackeloeer, A.; Klasing, K.; Krisp, J. M.; Meng, L.

2013-05-01

Map conflation investigates the unique identification of geographical entities across different maps depicting the same geographic region. It involves a matching process which aims to find commonalities between geographic features. A specific subdomain of conflation called Road Network Matching establishes correspondences between road networks of different maps on multiple layers of abstraction, ranging from elementary point locations to high-level structures such as road segments or even subgraphs derived from the induced graph of a road network. The process of identifying points located on different maps by means of geometrical, topological and semantical information is called point matching. This paper provides an overview of various techniques for point matching, which is a fundamental requirement for subsequent matching steps focusing on complex high-level entities in geospatial networks. Common point matching approaches as well as certain combinations of these are described, classified and evaluated. Furthermore, a novel similarity metric called the Exact Angular Index is introduced, which considers both topological and geometrical aspects. The results offer a basis for further research on a bottom-up matching process for complex map features, which must rely upon findings derived from suitable point matching algorithms. In the context of Road Network Matching, reliable point matches provide an immediate starting point for finding matches between line segments describing the geometry and topology of road networks, which may in turn be used for performing a structural high-level matching on the network level.

Asymmetric neighborhood functions accelerate ordering process of self-organizing maps

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

Ota, Kaiichiro; Aoki, Takaaki; Kurata, Koji

2011-02-15

A self-organizing map (SOM) algorithm can generate a topographic map from a high-dimensional stimulus space to a low-dimensional array of units. Because a topographic map preserves neighborhood relationships between the stimuli, the SOM can be applied to certain types of information processing such as data visualization. During the learning process, however, topological defects frequently emerge in the map. The presence of defects tends to drastically slow down the formation of a globally ordered topographic map. To remove such topological defects, it has been reported that an asymmetric neighborhood function is effective, but only in the simple case of mapping one-dimensionalmore » stimuli to a chain of units. In this paper, we demonstrate that even when high-dimensional stimuli are used, the asymmetric neighborhood function is effective for both artificial and real-world data. Our results suggest that applying the asymmetric neighborhood function to the SOM algorithm improves the reliability of the algorithm. In addition, it enables processing of complicated, high-dimensional data by using this algorithm.« less

Characterization of emergent synaptic topologies in noisy neural networks

NASA Astrophysics Data System (ADS)

Miller, Aaron James

Learned behaviors are one of the key contributors to an animal's ultimate survival. It is widely believed that the brain's microcircuitry undergoes structural changes when a new behavior is learned. In particular, motor learning, during which an animal learns a sequence of muscular movements, often requires precisely-timed coordination between muscles and becomes very natural once ingrained. Experiments show that neurons in the motor cortex exhibit precisely-timed spike activity when performing a learned motor behavior, and constituent stereotypical elements of the behavior can last several hundred milliseconds. The subject of this manuscript concerns how organized synaptic structures that produce stereotypical spike sequences emerge from random, dynamical networks. After a brief introduction in Chapter 1, we begin Chapter 2 by introducing a spike-timing-dependent plasticity (STDP) rule that defines how the activity of the network drives changes in network topology. The rule is then applied to idealized networks of leaky integrate-and-fire neurons (LIF). These neurons are not subjected to the variability that typically characterize neurons in vivo. In noiseless networks, synapses develop closed loops of strong connectivity that reproduce stereotypical, precisely-timed spike patterns from an initially random network. We demonstrate the characteristics of the asymptotic synaptic configuration are dependent on the statistics of the initial random network. The spike timings of the neurons simulated in Chapter 2 are generated exactly by a computationally economical, nonlinear mapping which is extended to LIF neurons injected with fluctuating current in Chapter 3. Development of an economical mapping that incorporates noise provides a practical solution to the long simulation times required to produce asymptotic synaptic topologies in networks with STDP in the presence of realistic neuronal variability. The mapping relies on generating numerical solutions to the dynamics of a LIF neuron subjected to Gaussian white noise (GWN). The system reduces to the Ornstein-Uhlenbeck first passage time problem, the solution of which we build into the mapping method of Chapter 2. We demonstrate that simulations using the stochastic mapping have reduced computation time compared to traditional Runge-Kutta methods by more than a factor of 150. In Chapter 4, we use the stochastic mapping to study the dynamics of emerging synaptic topologies in noisy networks. With the addition of membrane noise, networks with dynamical synapses can admit states in which the distribution of the synaptic weights is static under spontaneous activity, but the random connectivity between neurons is dynamical. The widely cited problem of instabilities in networks with STDP is avoided with the implementation of a synaptic decay and an activation threshold on each synapse. When such networks are presented with stimulus modeled by a focused excitatory current, chain-like networks can emerge with the addition of an axon-remodeling plasticity rule, a topological constraint on the connectivity modeling the finite resources available to each neuron. The emergent topologies are the result of an iterative stochastic process. The dynamics of the growth process suggest a strong interplay between the network topology and the spike sequences they produce during development. Namely, the existence of an embedded spike sequence alters the distribution of synaptic weights through the entire network. The roles of model parameters that affect the interplay between network structure and activity are elucidated. Finally, we propose two mathematical growth models, which are complementary, that capture the essence of the growth dynamics observed in simulations. In Chapter 5, we present an extension of the stochastic mapping that allows the possibility of neuronal cooperation. We demonstrate that synaptic topologies admitting stereotypical sequences can emerge in yet higher, biologically realistic levels of membrane potential variability when neurons cooperate to innervate shared targets. The structure that is most robust to the variability is that of a synfire chain. The principles of growth dynamics detailed in Chapter 4 are the same that sculpt the emergent synfire topologies. We conclude by discussing avenues for extensions of these results.

Spin-polarized surface resonances accompanying topological surface state formation

PubMed Central

Jozwiak, Chris; Sobota, Jonathan A.; Gotlieb, Kenneth; Kemper, Alexander F.; Rotundu, Costel R.; Birgeneau, Robert J.; Hussain, Zahid; Lee, Dung-Hai; Shen, Zhi-Xun; Lanzara, Alessandra

2016-01-01

Topological insulators host spin-polarized surface states born out of the energetic inversion of bulk bands driven by the spin-orbit interaction. Here we discover previously unidentified consequences of band-inversion on the surface electronic structure of the topological insulator Bi2Se3. By performing simultaneous spin, time, and angle-resolved photoemission spectroscopy, we map the spin-polarized unoccupied electronic structure and identify a surface resonance which is distinct from the topological surface state, yet shares a similar spin-orbital texture with opposite orientation. Its momentum dependence and spin texture imply an intimate connection with the topological surface state. Calculations show these two distinct states can emerge from trivial Rashba-like states that change topology through the spin-orbit-induced band inversion. This work thus provides a compelling view of the coevolution of surface states through a topological phase transition, enabled by the unique capability of directly measuring the spin-polarized unoccupied band structure. PMID:27739428

Interferometric measurement method for Z2 invariants of time-reversal invariant topological insulators

NASA Astrophysics Data System (ADS)

Grusdt, Fabian; Abanin, Dmitry; Demler, Eugene

2013-05-01

Recently experiments with ultracold atoms started to explore topological phases in 1D optical lattices. While transport measurements are challenging in these systems, ways to directly measure topological quantum numbers using a combination of Bloch oscillations and Ramsey interferometry have been explored (Atala et al., arXiv:1212.0572). In this talk I will present ways to measure the Z2 topological quantum numbers of two and three dimensional time-reversal invariant (TR) topological insulators. In this case non-Abelian Bloch oscillations can be combined with Ramsey interferometry to map out the topological properties of a given band-structure. Our method is very general and works even in the presence of accidental degeneracies. The applicability of the scheme is discussed for different theoretically proposed implementations of TR topological insulators using ultracold atoms. F. G. is grateful to Harvard University for hospitality and acknowledges financial support from Graduate School Materials Science in Mainz (MAINZ).

Topology in Synthetic Column Density Maps for Interstellar Turbulence

NASA Astrophysics Data System (ADS)

Putko, Joseph; Burkhart, B. K.; Lazarian, A.

2013-01-01

We show how the topology tool known as the genus statistic can be utilized to characterize magnetohydrodyanmic (MHD) turbulence in the ISM. The genus is measured with respect to a given density threshold and varying the threshold produces a genus curve, which can suggest an overall ‘‘meatball,’’ neutral, or ‘‘Swiss cheese’’ topology through its integral. We use synthetic column density maps made from three-dimensional 5123 compressible MHD isothermal simulations performed for different sonic and Alfvénic Mach numbers (Ms and MA respectively). We study eight different Ms values each with one sub- and one super-Alfvénic counterpart. We consider sight-lines both parallel (x) and perpendicular (y and z) to the mean magnetic field. We find that the genus integral shows a dependence on both Mach numbers, and this is still the case even after adding beam smoothing and Gaussian noise to the maps to mimic observational data. The genus integral increases with higher Ms values (but saturates after about Ms = 4) for all lines of sight. This is consistent with greater values of Ms resulting in stronger shocks, which results in a clumpier topology. We observe a larger genus integral for the sub-Alfvénic cases along the perpendicular lines of sight due to increased compression from the field lines and enhanced anisotropy. Application of the genus integral to column density maps should allow astronomers to infer the Mach numbers and thus learn about the environments of interstellar turbulence. This work was supported by the National Science Foundation’s REU program through NSF Award AST-1004881.

High-order computer-assisted estimates of topological entropy

NASA Astrophysics Data System (ADS)

Grote, Johannes

The concept of Taylor Models is introduced, which offers highly accurate C0-estimates for the enclosures of functional dependencies, combining high-order Taylor polynomial approximation of functions and rigorous estimates of the truncation error, performed using verified interval arithmetic. The focus of this work is on the application of Taylor Models in algorithms for strongly nonlinear dynamical systems. A method to obtain sharp rigorous enclosures of Poincare maps for certain types of flows and surfaces is developed and numerical examples are presented. Differential algebraic techniques allow the efficient and accurate computation of polynomial approximations for invariant curves of certain planar maps around hyperbolic fixed points. Subsequently we introduce a procedure to extend these polynomial curves to verified Taylor Model enclosures of local invariant manifolds with C0-errors of size 10-10--10 -14, and proceed to generate the global invariant manifold tangle up to comparable accuracy through iteration in Taylor Model arithmetic. Knowledge of the global manifold structure up to finite iterations of the local manifold pieces enables us to find all homoclinic and heteroclinic intersections in the generated manifold tangle. Combined with the mapping properties of the homoclinic points and their ordering we are able to construct a subshift of finite type as a topological factor of the original planar system to obtain rigorous lower bounds for its topological entropy. This construction is fully automatic and yields homoclinic tangles with several hundred homoclinic points. As an example rigorous lower bounds for the topological entropy of the Henon map are computed, which to the best knowledge of the authors yield the largest such estimates published so far.

Dynamic Mapping of Prominence Activity

NASA Astrophysics Data System (ADS)

Thompson, Barbara J.; Gilbert, Holly R.; Kirk, Michael S.; Mays, M. Leila.; Ofman, Leon; Uritsky, Vadim; Wyper, Peter; Hovis-Afflerbach, Beryl

2016-10-01

We present the results of a prominence mapping effort designed to extract the dynamics of erupting prominences. The material from partially erupting prominences can fall back to the sun, tracing out the topology of the mid- and post-eruptive corona. One question involving the range of observed behavior is the role of magnetic field topology and evolution in determining the motion of the erupting prominence material. A variable-g ballistic approximation is applied to study the motion of the material, using the deviations from constant angular momentum as a means of quantifying the local Lorentz (and other) forces on each piece of material. Variations in dynamic behavior can be traced back to changes in the local magnetic field and the formation of instabilities such as Rayleigh-Taylor. We discuss the use of the prominence trajectories as a means of diagnosing eruptive topologies.

D Topological Indoor Building Modeling Integrated with Open Street Map

NASA Astrophysics Data System (ADS)

Jamali, A.; Rahman, A. Abdul; Boguslawski, P.

2016-09-01

Considering various fields of applications for building surveying and various demands, geometry representation of a building is the most crucial aspect of a building survey. The interiors of the buildings need to be described along with the relative locations of the rooms, corridors, doors and exits in many kinds of emergency response, such as fire, bombs, smoke, and pollution. Topological representation is a challenging task within the Geography Information Science (GIS) environment, as the data structures required to express these relationships are particularly difficult to develop. Even within the Computer Aided Design (CAD) community, the structures for expressing the relationships between adjacent building parts are complex and often incomplete. In this paper, an integration of 3D topological indoor building modeling in Dual Half Edge (DHE) data structure and outdoor navigation network from Open Street Map (OSM) is presented.

Synaptic connectivity and spatial memory: a topological approach

NASA Astrophysics Data System (ADS)

Milton, Russell; Babichev, Andrey; Dabaghian, Yuri

2015-03-01

In the hippocampus, a network of place cells generates a cognitive map of space, in which each cell is responsive to a particular area of the environment - its place field. The peak response of each cell and the size of each place field have considerable variability. Experimental evidence suggests that place cells encode a topological map of space that serves as a basis of spatial memory and spatial awareness. Using a computational model based on Persistent Homology Theory we demonstrate that if the parameters of the place cells spiking activity fall inside of the physiological range, the network correctly encodes the topological features of the environment. We next introduce parameters of synaptic connectivity into the model and demonstrate that failures in synapses that detect coincident neuronal activity lead to spatial learning deficiencies similar to the ones that are observed in rodent models of neurodegenerative diseases. Moreover, we show that these learning deficiencies may be mitigated by increasing the number of active cells and/or by increasing their firing rate, suggesting the existence of a compensatory mechanism inherent to the cognitive map.

X-ray fluorescence microscopy artefacts in elemental maps of topologically complex samples: Analytical observations, simulation and a map correction method

NASA Astrophysics Data System (ADS)

Billè, Fulvio; Kourousias, George; Luchinat, Enrico; Kiskinova, Maya; Gianoncelli, Alessandra

2016-08-01

XRF spectroscopy is among the most widely used non-destructive techniques for elemental analysis. Despite the known angular dependence of X-ray fluorescence (XRF), topological artefacts remain an unresolved issue when using X-ray micro- or nano-probes. In this work we investigate the origin of the artefacts in XRF imaging of topologically complex samples, which are unresolved problems in studies of organic matter due to the limited travel distances of low energy XRF emission from the light elements. In particular we mapped Human Embryonic Kidney (HEK293T) cells. The exemplary results with biological samples, obtained with a soft X-ray scanning microscope installed at a synchrotron facility were used for testing a mathematical model based on detector response simulations, and for proposing an artefact correction method based on directional derivatives. Despite the peculiar and specific application, the methodology can be easily extended to hard X-rays and to set-ups with multi-array detector systems when the dimensions of surface reliefs are in the order of the probing beam size.

Recognition of abstract objects via neural oscillators: interaction among topological organization, associative memory and gamma band synchronization.

PubMed

Ursino, Mauro; Magosso, Elisa; Cuppini, Cristiano

2009-02-01

Synchronization of neural activity in the gamma band is assumed to play a significant role not only in perceptual processing, but also in higher cognitive functions. Here, we propose a neural network of Wilson-Cowan oscillators to simulate recognition of abstract objects, each represented as a collection of four features. Features are ordered in topological maps of oscillators connected via excitatory lateral synapses, to implement a similarity principle. Experience on previous objects is stored in long-range synapses connecting the different topological maps, and trained via timing dependent Hebbian learning (previous knowledge principle). Finally, a downstream decision network detects the presence of a reliable object representation, when all features are oscillating in synchrony. Simulations performed giving various simultaneous objects to the network (from 1 to 4), with some missing and/or modified properties suggest that the network can reconstruct objects, and segment them from the other simultaneously present objects, even in case of deteriorated information, noise, and moderate correlation among the inputs (one common feature). The balance between sensitivity and specificity depends on the strength of the Hebbian learning. Achieving a correct reconstruction in all cases, however, requires ad hoc selection of the oscillation frequency. The model represents an attempt to investigate the interactions among topological maps, autoassociative memory, and gamma-band synchronization, for recognition of abstract objects.

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.

Topological and trivial magnetic oscillations in nodal loop semimetals

NASA Astrophysics Data System (ADS)

Oroszlány, László; Dóra, Balázs; Cserti, József; Cortijo, Alberto

2018-05-01

Nodal loop semimetals are close descendants of Weyl semimetals and possess a topologically dressed band structure. We argue by combining the conventional theory of magnetic oscillation with topological arguments that nodal loop semimetals host coexisting topological and trivial magnetic oscillations. These originate from mapping the topological properties of the extremal Fermi surface cross sections onto the physics of two dimensional semi-Dirac systems, stemming from merging two massless Dirac cones. By tuning the chemical potential and the direction of magnetic field, a sharp transition is identified from purely trivial oscillations, arising from the Landau levels of a normal two dimensional (2D) electron gas, to a phase where oscillations of topological and trivial origin coexist, originating from 2D massless Dirac and semi-Dirac points, respectively. These could in principle be directly identified in current experiments.

Methods for enhancing mapping of thermal fronts in oil recovery

DOEpatents

Lee, David O.; Montoya, Paul C.; Wayland, Jr., James R.

1987-01-01

A method for enhancing the resistivity contrasts of a thermal front in an oil recovery production field as measured by the CSAMT technique is disclosed. This method includes the steps of: (a) preparing a CSAMT-determined topological resistivity map of the production field; (b) introducing a solution of a dopant material into the production field at a concentration effective to alter the resistivity associated with the thermal front; said dopant material having a high cation exchange capacity which might be selected from the group consisting of montmorillonite, illite, and chlorite clays; said material being soluble in the connate water of the production field; (c) preparing a CSAMT-determined topological resistivity map of the production field while said dopant material is moving therethrough; and (d) mathematically comparing the maps from step (a) and step (c) to determine the location of the thermal front. This method is effective with the steam flood, fire flood and water flood techniques.

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

NASA Astrophysics Data System (ADS)

He, Pan; Zhang, Steven S.-L.; Zhu, Dapeng; Liu, Yang; Wang, Yi; Yu, Jiawei; Vignale, Giovanni; Yang, Hyunsoo

2018-05-01

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin- and angle-resolved photoemission spectroscopy. Here we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the applied electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi2Se3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.

Topological Schemas of Cognitive Maps and Spatial Learning.

PubMed

Babichev, Andrey; Cheng, Sen; Dabaghian, Yuri A

2016-01-01

Spatial navigation in mammals is based on building a mental representation of their environment-a cognitive map. However, both the nature of this cognitive map and its underpinning in neural structures and activity remains vague. A key difficulty is that these maps are collective, emergent phenomena that cannot be reduced to a simple combination of inputs provided by individual neurons. In this paper we suggest computational frameworks for integrating the spiking signals of individual cells into a spatial map, which we call schemas. We provide examples of four schemas defined by different types of topological relations that may be neurophysiologically encoded in the brain and demonstrate that each schema provides its own large-scale characteristics of the environment-the schema integrals. Moreover, we find that, in all cases, these integrals are learned at a rate which is faster than the rate of complete training of neural networks. Thus, the proposed schema framework differentiates between the cognitive aspect of spatial learning and the physiological aspect at the neural network level.

Topology of foreign exchange markets using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Naylor, Michael J.; Rose, Lawrence C.; Moyle, Brendan J.

2007-08-01

This paper uses two physics derived hierarchical techniques, a minimal spanning tree and an ultrametric hierarchical tree, to extract a topological influence map for major currencies from the ultrametric distance matrix for 1995-2001. We find that these two techniques generate a defined and robust scale free network with meaningful taxonomy. The topology is shown to be robust with respect to method, to time horizon and is stable during market crises. This topology, appropriately used, gives a useful guide to determining the underlying economic or regional causal relationships for individual currencies and to understanding the dynamics of exchange rate price determination as part of a complex network.

Crystalline metamaterials for topological properties at subwavelength scales

PubMed Central

Yves, Simon; Fleury, Romain; Berthelot, Thomas; Fink, Mathias; Lemoult, Fabrice; Lerosey, Geoffroy

2017-01-01

The exciting discovery of topological condensed matter systems has lately triggered a search for their photonic analogues, motivated by the possibility of robust backscattering-immune light transport. However, topological photonic phases have so far only been observed in photonic crystals and waveguide arrays, which are inherently physically wavelength scaled, hindering their application in compact subwavelength systems. In this letter, we tackle this problem by patterning the deep subwavelength resonant elements of metamaterials onto specific lattices, and create crystalline metamaterials that can develop complex nonlocal properties due to multiple scattering, despite their very subwavelength spatial scale that usually implies to disregard their structure. These spatially dispersive systems can support subwavelength topological phases, as we demonstrate at microwaves by direct field mapping. Our approach gives a straightforward tabletop platform for the study of photonic topological phases, and allows to envision applications benefiting the compactness of metamaterials and the amazing potential of topological insulators. PMID:28719573

Exploring photonic topological insulator states in a circuit-QED lattice

NASA Astrophysics Data System (ADS)

Li, Jing-Ling; Shan, Chuan-Jia; Zhao, Feng

2018-04-01

We propose a simple protocol to explore the topological properties of photonic integer quantum Hall states in a one-dimensional circiut-QED lattice. By periodically modulating the on-site photonic energies in such a lattice, we demonstrate that this one-dimensional lattice model can be mapped into a two-dimensional integer quantum Hall insulator model. Based on the lattice-based cavity input-output theory, we show that both the photonic topological protected edge states and topological invariants can be clearly measured from the final steady state of the resonator lattice after taking into account cavity dissipation. Interestingly, we also find that the measurement signals associated with the above topological features are quite unambitious even in five coupled dissipative resonators. Our work opens up a new prospect of exploring topological states with a small-size dissipative quantum artificial lattice, which is quite attractive to the current quantum optics community.

Crystalline metamaterials for topological properties at subwavelength scales

NASA Astrophysics Data System (ADS)

Yves, Simon; Fleury, Romain; Berthelot, Thomas; Fink, Mathias; Lemoult, Fabrice; Lerosey, Geoffroy

2017-07-01

The exciting discovery of topological condensed matter systems has lately triggered a search for their photonic analogues, motivated by the possibility of robust backscattering-immune light transport. However, topological photonic phases have so far only been observed in photonic crystals and waveguide arrays, which are inherently physically wavelength scaled, hindering their application in compact subwavelength systems. In this letter, we tackle this problem by patterning the deep subwavelength resonant elements of metamaterials onto specific lattices, and create crystalline metamaterials that can develop complex nonlocal properties due to multiple scattering, despite their very subwavelength spatial scale that usually implies to disregard their structure. These spatially dispersive systems can support subwavelength topological phases, as we demonstrate at microwaves by direct field mapping. Our approach gives a straightforward tabletop platform for the study of photonic topological phases, and allows to envision applications benefiting the compactness of metamaterials and the amazing potential of topological insulators.

Spin-polarized surface resonances accompanying topological surface state formation

DOE PAGES

Jozwiak, Chris; Sobota, Jonathan A.; Gotlieb, Kenneth; ...

2016-10-14

Topological insulators host spin-polarized surface states born out of the energetic inversion of bulk bands driven by the spin-orbit interaction. Here we discover previously unidentified consequences of band-inversion on the surface electronic structure of the topological insulator Bi 2Se 3. By performing simultaneous spin, time, and angle-resolved photoemission spectroscopy, we map the spin-polarized unoccupied electronic structure and identify a surface resonance which is distinct from the topological surface state, yet shares a similar spin-orbital texture with opposite orientation. Its momentum dependence and spin texture imply an intimate connection with the topological surface state. Calculations show these two distinct states canmore » emerge from trivial Rashba-like states that change topology through the spin-orbit-induced band inversion. As a result, this work thus provides a compelling view of the coevolution of surface states through a topological phase transition, enabled by the unique capability of directly measuring the spin-polarized unoccupied band structure.« less

Realization of space-time inversion-invariant topological semimetal-bands in superconducting quantum circuits.

NASA Astrophysics Data System (ADS)

Yu, Y.; Tan, X.; Liu, Q.; Xue, G.; Yu, H.; Zhao, Y.; Wang, Z.

Topological band theory has attracted much attention since several types of topological metals and semimetals have been explored. These robustness of nodal band structures are symmetry-protected, whose topological features have deepened and widened the understandings of condensed matter physics. Meanwhile, as artificial quantum systems superconducting circuits possess high controllability, supplying a powerful approach to investigate topological properties of condensed matter systems. We realize a Hamiltonian with space-time (PT) symmetry by mapping momentum space of nodal band structure to parameter space in a superconducting quantum circuit. By measuring energy spectrum of the system, we observe the gapless band structure of topological semimetals, shown as Dirac points in momentum space. The phase transition from topological semimetal to topological insulator can be realized by continuously tuning the parameter in Hamiltonian. We add perturbation to broken time reversal symmetry. As long as the combined PT symmetry is preserved, the Dirac points of the topological semimetal are still observable, suggesting the robustness of the topological protection of the gapless energy band. Our work open a platform to simulate the relation between the symmetry and topological stability in condensed matter systems. Supported by the NKRDP of China (2016YFA0301802) and the GRF of Hong Kong (HKU173051/14P&HKU173055/15P).

Modeling shape and topology of low-resolution density maps of biological macromolecules.

PubMed Central

De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

2002-01-01

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

Effects of low and high mode number tearing modes in divertor tokamaks

NASA Astrophysics Data System (ADS)

Punjabi, Alkesh; Ali, Halima; Boozer, Allen; Evans, Todd

2007-08-01

The topological effects of magnetic perturbations on a divertor tokamak, such as DIII-D, are studied using field-line maps that were developed by Punjabi et al. [A. Punjabi, A. Verma, and A. Boozer, Phys. Rev. Lett. 69, 3322 (1992)]. The studies consider both long-wavelength perturbations, such as those of m =1, n =1 tearing modes, and localized perturbations, which are represented as a magnetic dipole. The parameters of the dipole map are set using DIII-D data from shot 115467 in which the C-coils were activated [J. L. Luxon and L. E. Davis, Fusion Technol. 8, 441 (1985)]. The long-wavelength perturbations alter the structure of the interception of magnetic field lines with the divertor plates, but the interception is in sharp lines. The dipole perturbations cause a spreading of the interception of the field lines with the divertor plates, which alleviates problems associated with heat deposition. Magnetic field lines are the trajectories of a one-and-a-half degree of freedom Hamiltonian, which strongly constrains the topological features of the lines. Although the field line maps that we use do not accurately represent the trajectories through ordinary space of individual field lines, they do represent their topological structure.

A 125 year history of topographic mapping and GIS in the U.S. Geological Survey 1884-2009, part 2: 1980-2009

USGS Publications Warehouse

Usery, E. Lynn; Varanka, Dalia; Finn, Michael P.

2009-01-01

The United States Geological Survey (USGS) entered the mainstream of developments in computer-assisted technology for mapping during the 1970s. The introduction by USGS of digital line graphs (DLGs), digital elevation models (DEMs), and land use data analysis (LUDA) nationwide land-cover data provided a base for the rapid expansion of the use of GIS in the 1980s. Whereas USGS had developed the topologically structured DLG data and the Geographic Information Retrieval and Analysis System (GIRAS) for land-cover data, the Map Overlay Statistical System (MOSS), a nontopologically structured GIS software package developed by Autometric, Inc., under contract to the U.S. Fish and Wildlife Service, dominated the use of GIS by federal agencies in the 1970s. Thus, USGS data was used in MOSS, but the topological structure, which later became a requirement for GIS vector datasets, was not used in early GIS applications. The introduction of Esri's ARC/INFO in 1982 changed that, and by the end of the 1980s, topological structure for vector data was essential, and ARC/INFO was the dominant GIS software package used by federal agencies.

Topological bound states of a quantum walk with cold atoms

NASA Astrophysics Data System (ADS)

Mugel, Samuel; Celi, Alessio; Massignan, Pietro; Asbóth, János K.; Lewenstein, Maciej; Lobo, Carlos

2016-08-01

We suggest a method for engineering a quantum walk, with cold atoms as walkers, which presents topologically nontrivial properties. We derive the phase diagram, and show that we are able to produce a boundary between topologically distinct phases using the finite beam width of the applied lasers. A topologically protected bound state can then be observed, which is pinned to the interface and is robust to perturbations. We show that it is possible to identify this bound state by averaging over spin sensitive measures of the atom's position, based on the spin distribution that these states display. Interestingly, there exists a parameter regime in which our system maps on to the Creutz ladder.

Exploring the spatio-temporal interrelation between groundwater and surface water by using the self-organizing maps

NASA Astrophysics Data System (ADS)

Chen, I.-Ting; Chang, Li-Chiu; Chang, Fi-John

2018-01-01

In this study, we propose a soft-computing methodology to visibly explore the spatio-temporal groundwater variations of the Kuoping River basin in southern Taiwan. The self-organizing map (SOM) is implemented to investigate the interactive mechanism between surface water and groundwater over the river basin based on large high-dimensional data sets coupled with their occurrence times. We find that extracting the occurrence time from each 30-day moving average data set in the clustered neurons of the SOM is a crucial step to learn the spatio-temporal interaction between surface water and groundwater. We design 2-D Topological Bubble Map to summarize all the groundwater values of four aquifers in a neuron, which can visibly explore the major features of the groundwater in the vertical direction. The constructed SOM topological maps nicely display that: (1) the groundwater movement, in general, extends from the eastern area to the western, where groundwater in the eastern area can be easily recharged from precipitation in wet seasons and discharged into streams during dry seasons due to the high permeability in this area; (2) the water movements in the four aquifers of the study area are quite different, and the seasonal variations of groundwater in the second and third aquifers are larger than those of the others; and (3) the spatial distribution and seasonal variations of groundwater and surface water are comprehensively linked together over the constructed maps to present groundwater characteristics and the interrelation between groundwater and surface water. The proposed modeling methodology not only can classify the large complex high-dimensional data sets into visible topological maps to effectively facilitate the quantitative status of regional groundwater resources but can also provide useful elaboration for future groundwater management.

Topology and the universe

NASA Astrophysics Data System (ADS)

Gott, J. Richard, III

1998-09-01

Topology may play an important role in cosmology in several different ways. First, Einstein's field equations tell us about the local geometry of the universe but not about its topology. Therefore, the universe may be multiply connected. Inflation predicts that the fluctuations that made clusters and groups of galaxies arose from random quantum fluctuations in the early universe. These should be Gaussian random phase. This can be tested by quantitatively measuring the topology of large-scale structure in the universe using the genus statistic. If the original fluctuations were Gaussian random phase then the structure we see today should have a spongelike topology. A number of studies by our group and others have shown that this is indeed the case. Future tests using the Sloan Digital Sky Survey should be possible. Microwave background fluctuations should also exhibit a characteristic symmetric pattern of hot and cold spots. The COBE data are consistent with this pattern and the MAP and PLANCK satellites should provide a definitive test. If the original inflationary state was metastable then it should decay by making an infinite number of open inflationary bubble universes. This model makes a specific prediction for the power spectrum of fluctuations in the microwave background which can be checked by the MAP and PLANCK satellites. Finally, Gott and Li have proposed how a multiply connected cosmology with an early epoch of closed timelike curves might allow the universe to be its own mother.

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

DOE PAGES

He, Pan; Zhang, Steven S. -L.; Zhu, Dapeng; ...

2018-02-05

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin-and angle-resolved photoemission spectroscopy. Here in this paper we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the appliedmore » electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi 2Se 3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.« less

Effects of variation in solar conditions and crustal sources' orientation on the Martian magnetic field topology

NASA Astrophysics Data System (ADS)

Ulusen, D.; Luhmann, J. G.; Ma, Y.; Brain, D. A.

2013-12-01

Strong crustal magnetic sources on the surface of Mars directly interact with the solar magnetic field and plasma, resulting a very dynamic environment near the planet. Effects of the orientation of these remnant magnetic sources with respect to the sun and variation of the solar conditions on the Martian plasma interaction have been investigated in a previous paper. In this previous study, magnetic topology maps obtained from ~7 years of Mars Global Surveyor (MGS) directional electron observations (obtained by Dave Brain) were compared with the topology maps obtained from a set of BATS-R-US MHD simulations for Mars. One conclusion from this study was that although the MHD model is consistent with the data and provides insight about the global magnetic field topology variation with changing crustal field orientation and solar parameters, detailed investigation of local effects is difficult due to MGS orbital bias. Moreover, proper comparison of the observations with the model requires more careful data selection rather than using 7 years time averages. In this paper, we readdress the study to tackle the problems of our previous work by performing more detailed data analysis and present the results of the updated model-data comparison.

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

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

He, Pan; Zhang, Steven S. -L.; Zhu, Dapeng

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin-and angle-resolved photoemission spectroscopy. Here in this paper we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the appliedmore » electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi 2Se 3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.« less

Magnetic field topology of τ Scorpii. The uniqueness problem of Stokes V ZDI inversions

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Wade, G. A.

2016-02-01

Context. The early B-type star τ Sco exhibits an unusually complex, relatively weak surface magnetic field. Its topology was previously studied with the Zeeman Doppler imaging (ZDI) modelling of high-resolution circular polarisation (Stokes V) observations. Aims: Here we assess the robustness of the Stokes V ZDI reconstruction of the magnetic field geometry of τ Sco and explore the consequences of using different parameterisations of the surface magnetic maps. Methods: This analysis is based on the archival ESPaDOnS high-resolution Stokes V observations and employs an independent ZDI magnetic inversion code. Results: We succeeded in reproducing previously published magnetic field maps of τ Sco using both general harmonic expansion and a direct, pixel-based representation of the magnetic field. These maps suggest that the field topology of τ Sco is comprised of comparable contributions of the poloidal and toroidal magnetic components. At the same time, we also found that available Stokes V observations can be successfully fitted with restricted harmonic expansions, by either neglecting the toroidal field altogether, or linking the radial and horizontal components of the poloidal field as required by the widely used potential field extrapolation technique. These alternative modelling approaches lead to a stronger and topologically more complex surface field structure. The field distributions, which were recovered with different ZDI options, differ significantly and yield indistinguishable Stokes V profiles but different linear polarisation (Stokes Q and U) signatures. Conclusions: Our investigation underscores the well-known problem of non-uniqueness of the Stokes V ZDI inversions. For the magnetic stars with properties similar to τ Sco (relatively complex field, slow rotation) the outcome of magnetic reconstruction strongly depends on the adopted field parameterisation, rendering photospheric magnetic mapping and determination of the extended magnetospheric field topology ambiguous. Stokes Q and U spectropolarimetric observations represent the only way of breaking the degeneracy of surface magnetic field models. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

Methods for enhancing mapping of thermal fronts in oil recovery

DOEpatents

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

1984-03-30

A method for enhancing the resistivity contrasts of a thermal front in an oil recovery production field as measured by the controlled source audio frequency magnetotelluric (CSAMT) technique is disclosed. This method includes the steps of: (1) preparing a CSAMT-determined topological resistivity map of the production field; (2) introducing a solution of a dopant material into the production field at a concentration effective to alter the resistivity associated with the thermal front; said dopant material having a high cation exchange capacity which might be selected from the group consisting of montmorillonite, illite, and chlorite clays; said material being soluble in the conate water of the production field; (3) preparing a CSAMT-determined topological resistivity map of the production field while said dopant material is moving therethrough; and (4) mathematically comparing the maps from step (1) and step (3) to determine the location of the thermal front. This method is effective with the steam flood, fire flood and water flood techniques.

A Fixed Point Theorem in Weak Topology for Successively Recurrent System of Set-Valued Mapping Equations and Its Applications

NASA Astrophysics Data System (ADS)

Horiuchi, Kazuo

Let us introduce n (≥ 2) mappings fi(i = 1, …, n ≡ 0) defined on reflexive real Banach spaces Xi-1 and let fi : Xi-1 → Yi be completely continuous on bounded convex closed subsets X_{i-1}^{(0)} \\\\subset X_{i-1}. Moreover, let us introduce n set-valued mappings F_i : X_{i-1} \\\\times Y_i \\\\to {\\\\cal F}_c(X_i) (the family of all non-empty compact subsets of Xi), (i=1, …, n ≡ 0). Here, we have a fixed point theorem in weak topology on the successively recurrent system of set-valued mapping equations: xi ∈ Fi(xi-1, fi(xi-1)), (i=1, …, n ≡ 0). This theorem can be applied immediately to analysis of the availability of system of circular networks of channels undergone by uncertain fluctuations and to evaluation of the tolerability of behaviors of those systems.

The Voronoi spatio-temporal data structure

NASA Astrophysics Data System (ADS)

Mioc, Darka

2002-04-01

Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal information. This formal model of spatio-temporal change representation is currently applied to retroactive map updates and visualization of map evolution. It offers new possibilities in the domains of temporal GIS, transaction processing, spatio-temporal queries, spatio-temporal analysis, map animation and map visualization.

Simple Map in Action-Angle Coordinates.

NASA Astrophysics Data System (ADS)

Kerwin, Olivia; Punjabi, Alkesh; Ali, Halima

2008-04-01

The simple map is the simplest map that has the topology of a divertor tokamak. The simple map has three canonical representations: (i) the natural coordinates - toroidal magnetic flux and poloidal angle (ψ,θ), (ii) the physical coordinates - the physical variables (R,Z) or (X,Y), and (iii) the action-angle coordinates - (J,θ) or magnetic coordinates (ψ, θ). All three are canonical coordinates for field lines. The simple map in the (X,Y) representation has been studied extensively ^1, 2. Here we analytically calculate the action-angle coordinates and safety factor q for the simple map. We construct the equilibrium generating function for the simple map in action-angle coordinates. We derive the simple map in action-angle representation, and calculate the stochastic broadening of the ideal separatrix due to topological noise in action-angle representation. We also show how the geometric effects such as elongation, the height, and width of the ideal separatrix surface can be investigated using a slight modification of the simple map in action-angle representation. This work is supported by the following grants US Department of Energy - OFES DE-FG02-01ER54624 and DE-FG02-04ER54793 and National Science Foundation - HRD-0630372 and 0411394. [1] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A, 364 140-145 (2007). [2] A. Punjabi, A. Verma, and A. Boozer, Phys.Rev. Lett. 69, 3322 (1992).

Training Aids for Basic Combat Skills: Developing Map-Reading Skills

DTIC Science & Technology

2011-03-01

types of training aids were developed for determining grid coordinates. Each training aid consisted of a set of self-study flashcards . One set of... flashcards contained scaled sections of topological maps and asked the Soldiers to find map features based on grid coordinates or to provide the grid...coordinates for a given map feature. The reverse of each flashcard provided feedback (i.e., correct answers and rationale to help the Soldier

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

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

DOE PAGES

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.; ...

2017-01-26

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

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

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Superconducting pairing of topological surface states in bismuth selenide films on niobium

PubMed Central

Zhang, Can; Tsuzuki, Akihiro

2018-01-01

A topological insulator film coupled to a simple isotropic s-wave superconductor substrate can foster helical pairing of the Dirac fermions associated with the topological surface states. Experimental realization of such a system is exceedingly difficult, however using a novel “flip-chip” technique, we have prepared single-crystalline Bi2Se3 films with predetermined thicknesses in terms of quintuple layers (QLs) on top of Nb substrates fresh from in situ cleavage. Our angle-resolved photoemission spectroscopy (ARPES) measurements of the film surface disclose superconducting gaps and coherence peaks of similar magnitude for both the topological surface states and bulk states. The ARPES spectral map as a function of temperature and film thickness up to 10 QLs reveals key characteristics relevant to the mechanism of coupling between the topological surface states and the superconducting Nb substrate; the effective coupling length is found to be much larger than the decay length of the topological surface states. PMID:29719866

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Adaptive Neuron Model: An architecture for the rapid learning of nonlinear topological transformations

NASA Technical Reports Server (NTRS)

Tawel, Raoul (Inventor)

1994-01-01

A method for the rapid learning of nonlinear mappings and topological transformations using a dynamically reconfigurable artificial neural network is presented. This fully-recurrent Adaptive Neuron Model (ANM) network was applied to the highly degenerate inverse kinematics problem in robotics, and its performance evaluation is bench-marked. Once trained, the resulting neuromorphic architecture was implemented in custom analog neural network hardware and the parameters capturing the functional transformation downloaded onto the system. This neuroprocessor, capable of 10(exp 9) ops/sec, was interfaced directly to a three degree of freedom Heathkit robotic manipulator. Calculation of the hardware feed-forward pass for this mapping was benchmarked at approximately 10 microsec.

THE PHYSICS OF ELEMENTARY PARTICLES AND FIELDS: Topological aspects in a two-component Bose condensed system in a neutron star

NASA Astrophysics Data System (ADS)

Ren, Ji-Rong; Guo, Heng

2009-08-01

By making use of Duan-Ge's decomposition theory of gauge potential and the topological current theory proposed by Prof. Duan Yi-Shi, we study a two-component superfluid Bose condensed system, which is supposed to be realized in the interior of neutron stars in the form of the coexistence of a neutron superfluid and a protonic superconductor. We propose that this system possesses vortex lines. The topological charges of the vortex lines are characterized by the Hopf indices and the Brower degrees of ø-mapping.

d-Neighborhood system and generalized F-contraction in dislocated metric space.

PubMed

Kumari, P Sumati; Zoto, Kastriot; Panthi, Dinesh

2015-01-01

This paper, gives an answer for the Question 1.1 posed by Hitzler (Generalized metrics and topology in logic programming semantics, 2001) by means of "Topological aspects of d-metric space with d-neighborhood system". We have investigated the topological aspects of a d-neighborhood system obtained from dislocated metric space (simply d-metric space) which has got useful applications in the semantic analysis of logic programming. Further more we have generalized the notion of F-contraction in the view of d-metric spaces and investigated the uniqueness of fixed point and coincidence point of such mappings.

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.

Persistent topological features of dynamical systems

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

Maletić, Slobodan, E-mail: slobodan@hitsz.edu.cn; Institute of Nuclear Sciences Vinča, University of Belgrade, Belgrade; Zhao, Yi, E-mail: zhao.yi@hitsz.edu.cn

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

Annealing-Induced Bi Bilayer on Bi2Te3 Investigated via Quasi-Particle-Interference Mapping.

PubMed

Schouteden, Koen; Govaerts, Kirsten; Debehets, Jolien; Thupakula, Umamahesh; Chen, Taishi; Li, Zhe; Netsou, Asteriona; Song, Fengqi; Lamoen, Dirk; Van Haesendonck, Chris; Partoens, Bart; Park, Kyungwha

2016-09-27

Topological insulators (TIs) are renowned for their exotic topological surface states (TSSs) that reside in the top atomic layers, and hence, detailed knowledge of the surface top atomic layers is of utmost importance. Here we present the remarkable morphology changes of Bi2Te3 surfaces, which have been freshly cleaved in air, upon subsequent systematic annealing in ultrahigh vacuum and the resulting effects on the local and area-averaging electronic properties of the surface states, which are investigated by combining scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and Auger electron spectroscopy (AES) experiments with density functional theory (DFT) calculations. Our findings demonstrate that the annealing induces the formation of a Bi bilayer atop the Bi2Te3 surface. The adlayer results in n-type doping, and the atomic defects act as scattering centers of the TSS electrons. We also investigated the annealing-induced Bi bilayer surface on Bi2Te3 via voltage-dependent quasi-particle-interference (QPI) mapping of the surface local density of states and via comparison with the calculated constant-energy contours and QPI patterns. We observed closed hexagonal patterns in the Fourier transform of real-space QPI maps with secondary outer spikes. DFT calculations attribute these complex QPI patterns to the appearance of a "second" cone due to the surface charge transfer between the Bi bilayer and the Bi2Te3. Annealing in ultrahigh vacuum offers a facile route for tuning of the topological properties and may yield similar results for other topological materials.

Linear response formula for piecewise expanding unimodal maps

NASA Astrophysics Data System (ADS)

Baladi, Viviane; Smania, Daniel

2008-04-01

The average R(t)=\\int \\varphi\\,\\rmd \\mu_t of a smooth function phiv with respect to the SRB measure μt of a smooth one-parameter family ft of piecewise expanding interval maps is not always Lipschitz (Baladi 2007 Commun. Math. Phys. 275 839-59, Mazzolena 2007 Master's Thesis Rome 2, Tor Vergata). We prove that if ft is tangent to the topological class of f, and if ∂t ft|t = 0 = X circle f, then R(t) is differentiable at zero, and R'(0) coincides with the resummation proposed (Baladi 2007) of the (a priori divergent) series \\sum_{n=0}^\\infty \\int X(y) \\partial_y (\\varphi \\circ f^n)(y)\\,\\rmd \\mu_0(y) given by Ruelle's conjecture. In fact, we show that t map μt is differentiable within Radon measures. Linear response is violated if and only if ft is transversal to the topological class of f.

Crowdsourcing Physical Network Topology Mapping With Net.Tagger

DTIC Science & Technology

2016-03-01

backend server infrastructure . This in- cludes a full security audit, better web services handling, and integration with the OSM stack and dataset to...a novel approach to network infrastructure mapping that combines smartphone apps with crowdsourced collection to gather data for offline aggregation...and analysis. The project aims to build a map of physical network infrastructure such as fiber-optic cables, facilities, and access points. The

The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer

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

Slattery, S. R.; Wilson, P. P. H.; Pawlowski, R. P.

2013-07-01

The Data Transfer Kit (DTK) is a software library designed to provide parallel data transfer services for arbitrary physics components based on the concept of geometric rendezvous. The rendezvous algorithm provides a means to geometrically correlate two geometric domains that may be arbitrarily decomposed in a parallel simulation. By repartitioning both domains such that they have the same geometric domain on each parallel process, efficient and load balanced search operations and data transfer can be performed at a desirable algorithmic time complexity with low communication overhead relative to other types of mapping algorithms. With the increased development efforts in multiphysicsmore » simulation and other multiple mesh and geometry problems, generating parallel topology maps for transferring fields and other data between geometric domains is a common operation. The algorithms used to generate parallel topology maps based on the concept of geometric rendezvous as implemented in DTK are described with an example using a conjugate heat transfer calculation and thermal coupling with a neutronics code. In addition, we provide the results of initial scaling studies performed on the Jaguar Cray XK6 system at Oak Ridge National Laboratory for a worse-case-scenario problem in terms of algorithmic complexity that shows good scaling on 0(1 x 104) cores for topology map generation and excellent scaling on 0(1 x 105) cores for the data transfer operation with meshes of O(1 x 109) elements. (authors)« less

A non-linear dimension reduction methodology for generating data-driven stochastic input models

NASA Astrophysics Data System (ADS)

Ganapathysubramanian, Baskar; Zabaras, Nicholas

2008-06-01

Stochastic analysis of random heterogeneous media (polycrystalline materials, porous media, functionally graded materials) provides information of significance only if realistic input models of the topology and property variations are used. This paper proposes a framework to construct such input stochastic models for the topology and thermal diffusivity variations in heterogeneous media using a data-driven strategy. Given a set of microstructure realizations (input samples) generated from given statistical information about the medium topology, the framework constructs a reduced-order stochastic representation of the thermal diffusivity. This problem of constructing a low-dimensional stochastic representation of property variations is analogous to the problem of manifold learning and parametric fitting of hyper-surfaces encountered in image processing and psychology. Denote by M the set of microstructures that satisfy the given experimental statistics. A non-linear dimension reduction strategy is utilized to map M to a low-dimensional region, A. We first show that M is a compact manifold embedded in a high-dimensional input space Rn. An isometric mapping F from M to a low-dimensional, compact, connected set A⊂Rd(d≪n) is constructed. Given only a finite set of samples of the data, the methodology uses arguments from graph theory and differential geometry to construct the isometric transformation F:M→A. Asymptotic convergence of the representation of M by A is shown. This mapping F serves as an accurate, low-dimensional, data-driven representation of the property variations. The reduced-order model of the material topology and thermal diffusivity variations is subsequently used as an input in the solution of stochastic partial differential equations that describe the evolution of dependant variables. A sparse grid collocation strategy (Smolyak algorithm) is utilized to solve these stochastic equations efficiently. We showcase the methodology by constructing low-dimensional input stochastic models to represent thermal diffusivity in two-phase microstructures. This model is used in analyzing the effect of topological variations of two-phase microstructures on the evolution of temperature in heat conduction processes.

Duality between Time Series and Networks

PubMed Central

Campanharo, Andriana S. L. O.; Sirer, M. Irmak; Malmgren, R. Dean; Ramos, Fernando M.; Amaral, Luís A. Nunes.

2011-01-01

Studying the interaction between a system's components and the temporal evolution of the system are two common ways to uncover and characterize its internal workings. Recently, several maps from a time series to a network have been proposed with the intent of using network metrics to characterize time series. Although these maps demonstrate that different time series result in networks with distinct topological properties, it remains unclear how these topological properties relate to the original time series. Here, we propose a map from a time series to a network with an approximate inverse operation, making it possible to use network statistics to characterize time series and time series statistics to characterize networks. As a proof of concept, we generate an ensemble of time series ranging from periodic to random and confirm that application of the proposed map retains much of the information encoded in the original time series (or networks) after application of the map (or its inverse). Our results suggest that network analysis can be used to distinguish different dynamic regimes in time series and, perhaps more importantly, time series analysis can provide a powerful set of tools that augment the traditional network analysis toolkit to quantify networks in new and useful ways. PMID:21858093

Universal map for cellular automata

NASA Astrophysics Data System (ADS)

García-Morales, V.

2012-08-01

A universal map is derived for all deterministic 1D cellular automata (CAs) containing no freely adjustable parameters and valid for any alphabet size and any neighborhood range (including non-symmetrical neighborhoods). The map can be extended to an arbitrary number of dimensions and topologies and to arbitrary order in time. Specific CA maps for the famous Conway's Game of Life and Wolfram's 256 elementary CAs are given. An induction method for CAs, based in the universal map, allows mathematical expressions for the orbits of a wide variety of elementary CAs to be systematically derived.

Palinspastic reconstruction of structure maps: an automated finite element approach with heterogeneous strain

NASA Astrophysics Data System (ADS)

Dunbar, John A.; Cook, Richard W.

2003-07-01

Existing methods for the palinspastic reconstruction of structure maps do not adequately account for heterogeneous rock strain and hence cannot accurately treat features such as fault terminations and non-cylindrical folds. We propose a new finite element formulation of the map reconstruction problem that treats such features explicitly. In this approach, a model of the map surface, with internal openings that honor the topology of the fault-gap network, is constructed of triangular finite elements. Both model building and reconstruction algorithms are guided by rules relating fault-gap topology to the kinematics of fault motion and are fully automated. We represent the total strain as the sum of a prescribed component of locally homogeneous simple shear and a minimum amount of heterogeneous residual strain. The region within which a particular orientation of simple shear is treated as homogenous can be as small as an individual element or as large as the entire map. For residual strain calculations, we treat the map surface as a hyperelastic membrane. A globally optimum reconstruction is found that unfolds the map while faithfully honoring assigned strain mechanisms, closes fault gaps without overlap or gap and imparts the least possible residual strain in the restored surface. The amount and distribution of the residual strain serves as a diagnostic tool for identifying mapping errors. The method can be used to reconstruct maps offset by any number of faults that terminate, branch and offset each other in arbitrarily complex ways.

A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

2003-01-01

In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

A Bifurcation Problem for a Nonlinear Partial Differential Equation of Parabolic Type,

DTIC Science & Technology

NONLINEAR DIFFERENTIAL EQUATIONS, INTEGRATION), (*PARTIAL DIFFERENTIAL EQUATIONS, BOUNDARY VALUE PROBLEMS), BANACH SPACE , MAPPING (TRANSFORMATIONS), SET THEORY, TOPOLOGY, ITERATIONS, STABILITY, THEOREMS

Long-range Kitaev chains via planar Josephson junctions

NASA Astrophysics Data System (ADS)

Liu, Dillon T.; Shabani, Javad; Mitra, Aditi

2018-06-01

We show how a recently proposed solid-state Majorana platform comprising a planar Josephson junction proximitized to a 2D electron gas (2DEG) with Rashba spin-orbit coupling and Zeeman field can be viewed as an effectively one-dimensional (1D) Kitaev chain with long-range pairing and hopping terms. We highlight how the couplings of the 1D system may be tuned by changing experimentally realistic parameters. We also show that the mapping is robust to disorder by computing the Clifford pseudospectrum index in real space for the long-range Kitaev chain across several topological phases. This mapping opens up the possibility of using current experimental setups to explore 1D topological superconductors with nonstandard and tunable couplings.

Number magnitude to finger mapping is disembodied and topological.

PubMed

Plaisier, Myrthe A; Smeets, Jeroen B J

2011-03-01

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

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.

Nanoscale β-nuclear magnetic resonance depth imaging of topological insulators

PubMed Central

Koumoulis, Dimitrios; Morris, Gerald D.; He, Liang; Kou, Xufeng; King, Danny; Wang, Dong; Hossain, Masrur D.; Wang, Kang L.; Fiete, Gregory A.; Kanatzidis, Mercouri G.; Bouchard, Louis-S.

2015-01-01

Considerable evidence suggests that variations in the properties of topological insulators (TIs) at the nanoscale and at interfaces can strongly affect the physics of topological materials. Therefore, a detailed understanding of surface states and interface coupling is crucial to the search for and applications of new topological phases of matter. Currently, no methods can provide depth profiling near surfaces or at interfaces of topologically inequivalent materials. Such a method could advance the study of interactions. Herein, we present a noninvasive depth-profiling technique based on β-detected NMR (β-NMR) spectroscopy of radioactive 8Li+ ions that can provide “one-dimensional imaging” in films of fixed thickness and generates nanoscale views of the electronic wavefunctions and magnetic order at topological surfaces and interfaces. By mapping the 8Li nuclear resonance near the surface and 10-nm deep into the bulk of pure and Cr-doped bismuth antimony telluride films, we provide signatures related to the TI properties and their topological nontrivial characteristics that affect the electron–nuclear hyperfine field, the metallic shift, and magnetic order. These nanoscale variations in β-NMR parameters reflect the unconventional properties of the topological materials under study, and understanding the role of heterogeneities is expected to lead to the discovery of novel phenomena involving quantum materials. PMID:26124141

The phase topology of a special case of Goryachev integrability in rigid body dynamics

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

Ryabov, P. E., E-mail: orelryabov@mail.ru

2014-07-31

The phase topology of a special case of Goryachev integrability in the problem of motion of a rigid body in a fluid is investigated using the method of Boolean functions, which was developed by Kharlamov for algebraically separated systems. The bifurcation diagram of the moment map is found and the Fomenko invariant, which classifies the systems up to rough Liouville equivalence, is specified. Bibliography: 15 titles. (paper)

Electronic-projecting Moire method applying CBR-technology

NASA Astrophysics Data System (ADS)

Kuzyakov, O. N.; Lapteva, U. V.; Andreeva, M. A.

2018-01-01

Electronic-projecting method based on Moire effect for examining surface topology is suggested. Conditions of forming Moire fringes and their parameters’ dependence on reference parameters of object and virtual grids are analyzed. Control system structure and decision-making subsystem are elaborated. Subsystem execution includes CBR-technology, based on applying case base. The approach related to analysing and forming decision for each separate local area with consequent formation of common topology map is applied.

Unconventional topological Hall effect in skyrmion crystals caused by the topology of the lattice

NASA Astrophysics Data System (ADS)

Göbel, Börge; Mook, Alexander; Henk, Jürgen; Mertig, Ingrid

2017-03-01

The hallmark of a skyrmion crystal (SkX) is the topological Hall effect (THE). In this article we predict and explain an unconventional behavior of the topological Hall conductivity in SkXs. In simple terms, the spin texture of the skyrmions causes an inhomogeneous emergent magnetic field whose associated Lorentz force acts on the electrons. By making the emergent field homogeneous, the THE is mapped onto the quantum Hall effect (QHE). Consequently, each electronic band of the SkX is assigned to a Landau level. This correspondence of THE and QHE allows us to explain the unconventional behavior of the THE of electrons in SkXs. For example, a skyrmion crystal on a triangular lattice exhibits a quantized topological Hall conductivity with steps of 2 .e2/h below and with steps of 1 .e2/h above the van Hove singularity. On top of this, the conductivity shows a prominent sign change at the van Hove singularity. These unconventional features are deeply connected to the topology of the structural lattice.

Scaling of Topologically Similar Functional Modules Defines Mouse Primary Auditory and Somatosensory Microcircuitry

PubMed Central

Sadovsky, Alexander J.

2013-01-01

Mapping the flow of activity through neocortical microcircuits provides key insights into the underlying circuit architecture. Using a comparative analysis we determined the extent to which the dynamics of microcircuits in mouse primary somatosensory barrel field (S1BF) and auditory (A1) neocortex generalize. We imaged the simultaneous dynamics of up to 1126 neurons spanning multiple columns and layers using high-speed multiphoton imaging. The temporal progression and reliability of reactivation of circuit events in both regions suggested common underlying cortical design features. We used circuit activity flow to generate functional connectivity maps, or graphs, to test the microcircuit hypothesis within a functional framework. S1BF and A1 present a useful test of the postulate as both regions map sensory input anatomically, but each area appears organized according to different design principles. We projected the functional topologies into anatomical space and found benchmarks of organization that had been previously described using physiology and anatomical methods, consistent with a close mapping between anatomy and functional dynamics. By comparing graphs representing activity flow we found that each region is similarly organized as highlighted by hallmarks of small world, scale free, and hierarchical modular topologies. Models of prototypical functional circuits from each area of cortex were sufficient to recapitulate experimentally observed circuit activity. Convergence to common behavior by these models was accomplished using preferential attachment to scale from an auditory up to a somatosensory circuit. These functional data imply that the microcircuit hypothesis be framed as scalable principles of neocortical circuit design. PMID:23986241

Independent psychophysical measurement of experimental modulations in the somatotopy of cutaneous heat-pain stimuli.

PubMed

Trojan, Jörg; Kleinböhl, Dieter; Stolle, Annette M; Andersen, Ole K; Hölzl, Rupert; Arendt-Nielsen, Lars

2009-03-01

Distortions of the body image have been repeatedly reported for various clinical conditions, but direct experimental analyses of the perceptual changes involved are still scarce. In addition, most experimental studies rely on cerebral activation patterns to assess neuroplastic changes in central representation, although the relationship between cerebral topography and the topology of the perceptual space is not clear. This study examines whether the direct psychophysical mapping approach we introduced recently (Trojan et al., Brain Res 2006;1120:106-113) is capable of tracking perceptual distortions in the somatotopic representation of heat-pain stimuli. Eleven healthy participants indicated the perceived positions of CO(2) laser stimuli, repetitively presented to the dorsal forearm, with a 3D tracking system in two consecutive sessions, separated by the topical application of capsaicin cream. In line with earlier reports, we expected that the resulting individual perceptual maps (i.e., one-dimensional projections of the perceived positions onto the forearm surface) would be subject to modulation through the altered sensory input, to be measured in terms of altered topological parameters. We found that the topology and metrics of the somatotopic representation were well preserved in the second session, but that the perceptual map was compressed to a smaller range in 9 out of 11 participants. By providing dimensional measures of perceptual representations, perceptual maps constitute an independent, genuinely psychological complement to the topography of cortical activations measured with neuroimaging methods. In addition, we expect them to be useful in diagnosing pathological changes in body perception accompanying chronic pain and other disorders.

ICD-10 procedure codes produce transition challenges.

PubMed

Boyd, Andrew D; Li, Jianrong 'John'; Kenost, Colleen; Zaim, Samir Rachid; Krive, Jacob; Mittal, Manish; Satava, Richard A; Burton, Michael; Smith, Jacob; Lussier, Yves A

2018-01-01

The transition of procedure coding from ICD-9-CM-Vol-3 to ICD-10-PCS has generated problems for the medical community at large resulting from the lack of clarity required to integrate two non-congruent coding systems. We hypothesized that quantifying these issues with network topology analyses offers a better understanding of the issues, and therefore we developed solutions (online tools) to empower hospital administrators and researchers to address these challenges. Five topologies were identified: "identity"(I), "class-to-subclass"(C2S), "subclass-toclass"(S2C), "convoluted(C)", and "no mapping"(NM). The procedure codes in the 2010 Illinois Medicaid dataset (3,290 patients, 116 institutions) were categorized as C=55%, C2S=40%, I=3%, NM=2%, and S2C=1%. Majority of the problematic and ambiguous mappings (convoluted) pertained to operations in ophthalmology cardiology, urology, gyneco-obstetrics, and dermatology. Finally, the algorithms were expanded into a user-friendly tool to identify problematic topologies and specify lists of procedural codes utilized by medical professionals and researchers for mitigating error-prone translations, simplifying research, and improving quality.http://www.lussiergroup.org/transition-to-ICD10PCS.

The influence of Mars' magnetic topology on atmospheric escape

NASA Astrophysics Data System (ADS)

Curry, S.; Luhmann, J. G.; DiBraccio, G. A.; Dong, C.; Xu, S.; Mitchell, D.; Gruesbeck, J.; Espley, J. R.; Connerney, J. E. P.; McFadden, J. P.; Ma, Y. J.; Brain, D.

2017-12-01

At weakly magnetized planets such as Mars and Venus, the solar wind directly interacts with the upper atmosphere where ions can be picked up and swept away by the background convection electric field. These pick-up ions have a gyroradius on the planetary scale that is largely dominated by the interplanetary magnetic field (IMF). But at Mars, their trajectory is also influenced by the existence of remanent crustal magnetic fields, which are thought to create a shielding effect for escaping planetary ions when they are on the dayside. Consequently, the magnetic topology changes at Mars as magnetic reconnection occurs between the draped (IMF) and the crustal magnetic fields (closed). The resulting topology includes open field lines in the solar wind with one footprint attached to the planet. Using magnetohydrodynamic (MHD) and test particle simulations, we will explore the influence of the magnetic topology on ion escape. We will present escape rates for planetary ions for different crustal field positions during different IMF configurations, with +/-BY and +/-BZ components in the Mars Sun Orbit (MSO) coordinate system. We will also compare global maps of ion outflow and escape with open / closed magnetic field line maps and compare our results with ion fluxes and magnetic field data from the Mars Atmospheric and Volatile EvolutioN (MAVEN) mission. Our results relating the dynamic magnetic field topology at Mars and planetary ion escape are an important aspect of magnetospheric physics and planetary evolution, both of which have applications to our own solar system and the increasing number of exoplanets discovered every year.

Topological color codes on Union Jack lattices: a stable implementation of the whole Clifford group

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

Katzgraber, Helmut G.; Theoretische Physik, ETH Zurich, CH-8093 Zurich; Bombin, H.

We study the error threshold of topological color codes on Union Jack lattices that allow for the full implementation of the whole Clifford group of quantum gates. After mapping the error-correction process onto a statistical mechanical random three-body Ising model on a Union Jack lattice, we compute its phase diagram in the temperature-disorder plane using Monte Carlo simulations. Surprisingly, topological color codes on Union Jack lattices have a similar error stability to color codes on triangular lattices, as well as to the Kitaev toric code. The enhanced computational capabilities of the topological color codes on Union Jack lattices with respectmore » to triangular lattices and the toric code combined with the inherent robustness of this implementation show good prospects for future stable quantum computer implementations.« less

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.

Topological semimetals with Riemann surface states

NASA Astrophysics Data System (ADS)

Fang, Chen; Lu, Ling; Liu, Junwei; Fu, Liang

Topological semimetals have robust bulk band crossings between the conduction and the valence bands. Among them, Weyl semimetals are so far the only class having topologically protected signatures on the surface known as the ``Fermi arcs''. Here we theoretically find new classes of topological semimetals protected by nonsymmorphic glide reflection symmetries. On a symmetric surface, there are multiple Fermi arcs protected by nontrivial Z2 spectral flows between two high-symmetry lines (or two segments of one line) in the surface Brillouin zone. We observe that so far topological semimetals with protected Fermi arcs have surface dispersions that can be mapped to noncompact Riemann surfaces representing simple holomorphic functions. We propose perovskite superlattice [(SrIrO3)2m, (CaIrO3)2n] as a nonsymmorphic Dirac semimetal. C.F. and L.F. were supported by the S3TEC Solid State Solar Thermal Energy Conversion Center, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES), under Award No. DE-SC0001299/DE.

Topologies on quantum topoi induced by quantization

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

Nakayama, Kunji

2013-07-15

In the present paper, we consider effects of quantization in a topos approach of quantum theory. A quantum system is assumed to be coded in a quantum topos, by which we mean the topos of presheaves on the context category of commutative subalgebras of a von Neumann algebra of bounded operators on a Hilbert space. A classical system is modeled by a Lie algebra of classical observables. It is shown that a quantization map from the classical observables to self-adjoint operators on the Hilbert space naturally induces geometric morphisms from presheaf topoi related to the classical system to the quantummore » topos. By means of the geometric morphisms, we give Lawvere-Tierney topologies on the quantum topos (and their equivalent Grothendieck topologies on the context category). We show that, among them, there exists a canonical one which we call a quantization topology. We furthermore give an explicit expression of a sheafification functor associated with the quantization topology.« less

Imaging electronic states on topological semimetals using scanning tunneling microscopy

DOE PAGES

Gyenis, András; Inoue, Hiroyuki; Jeon, Sangjun; ...

2016-10-18

Following the intense studies on topological insulators, significant efforts have recently been devoted to the search for gapless topological systems. These materials not only broaden the topological classification of matter but also provide a condensed matter realization of various relativistic particles and phenomena previously discussed mainly in high energy physics. Weyl semimetals host massless, chiral, low-energy excitations in the bulk electronic band structure, whereas a symmetry protected pair of Weyl fermions gives rise to massless Dirac fermions.Weemployed scanning tunneling microscopy/spectroscopy to explore the behavior of electronic states both on the surface and in the bulk of topological semimetal phases. Bymore » mapping the quasiparticle interference (QPI) and emerging Landau levels at high magnetic field in Dirac semimetals Cd 3As 2 and Na 3Bi, we observed extended Dirac-like bulk electronic bands. QPI imaged on Weyl semimetal TaAs demonstrated the predicted momentum dependent delocalization of Fermi arc surface states in the vicinity of the surface projected Weyl nodes.« less

Navigation and Self-Semantic Location of Drones in Indoor Environments by Combining the Visual Bug Algorithm and Entropy-Based Vision.

PubMed

Maravall, Darío; de Lope, Javier; Fuentes, Juan P

2017-01-01

We introduce a hybrid algorithm for the self-semantic location and autonomous navigation of robots using entropy-based vision and visual topological maps. In visual topological maps the visual landmarks are considered as leave points for guiding the robot to reach a target point (robot homing) in indoor environments. These visual landmarks are defined from images of relevant objects or characteristic scenes in the environment. The entropy of an image is directly related to the presence of a unique object or the presence of several different objects inside it: the lower the entropy the higher the probability of containing a single object inside it and, conversely, the higher the entropy the higher the probability of containing several objects inside it. Consequently, we propose the use of the entropy of images captured by the robot not only for the landmark searching and detection but also for obstacle avoidance. If the detected object corresponds to a landmark, the robot uses the suggestions stored in the visual topological map to reach the next landmark or to finish the mission. Otherwise, the robot considers the object as an obstacle and starts a collision avoidance maneuver. In order to validate the proposal we have defined an experimental framework in which the visual bug algorithm is used by an Unmanned Aerial Vehicle (UAV) in typical indoor navigation tasks.

Navigation and Self-Semantic Location of Drones in Indoor Environments by Combining the Visual Bug Algorithm and Entropy-Based Vision

PubMed Central

Maravall, Darío; de Lope, Javier; Fuentes, Juan P.

2017-01-01

We introduce a hybrid algorithm for the self-semantic location and autonomous navigation of robots using entropy-based vision and visual topological maps. In visual topological maps the visual landmarks are considered as leave points for guiding the robot to reach a target point (robot homing) in indoor environments. These visual landmarks are defined from images of relevant objects or characteristic scenes in the environment. The entropy of an image is directly related to the presence of a unique object or the presence of several different objects inside it: the lower the entropy the higher the probability of containing a single object inside it and, conversely, the higher the entropy the higher the probability of containing several objects inside it. Consequently, we propose the use of the entropy of images captured by the robot not only for the landmark searching and detection but also for obstacle avoidance. If the detected object corresponds to a landmark, the robot uses the suggestions stored in the visual topological map to reach the next landmark or to finish the mission. Otherwise, the robot considers the object as an obstacle and starts a collision avoidance maneuver. In order to validate the proposal we have defined an experimental framework in which the visual bug algorithm is used by an Unmanned Aerial Vehicle (UAV) in typical indoor navigation tasks. PMID:28900394

The Map Is the Territory: Educational Evaluation and the Topology of Power

ERIC Educational Resources Information Center

Saari, Antti

2012-01-01

In recent years there has been a global call for more scientific knowledge about education as a basis of governance. This means that exact descriptions of the reality of schooling should inform decisions about what works in education. In this article, evaluation and testing are analysed as cartography, the art of mapping educational spaces, which…

Ranking the Difficulty Level of the Knowledge Units Based on Learning Dependency

ERIC Educational Resources Information Center

Liu, Jun; Sha, Sha; Zheng, Qinghua; Zhang, Wei

2012-01-01

Assigning difficulty level indicators to the knowledge units helps the learners plan their learning activities more efficiently. This paper focuses on how to use the topology of a knowledge map to compute and rank the difficulty levels of knowledge units. Firstly, the authors present the hierarchical structure and properties of the knowledge map.…

A volumetric conformal mapping approach for clustering white matter fibers in the brain

PubMed Central

Gupta, Vikash; Prasad, Gautam; Thompson, Paul

2017-01-01

The human brain may be considered as a genus-0 shape, topologically equivalent to a sphere. Various methods have been used in the past to transform the brain surface to that of a sphere using harmonic energy minimization methods used for cortical surface matching. However, very few methods have studied volumetric parameterization of the brain using a spherical embedding. Volumetric parameterization is typically used for complicated geometric problems like shape matching, morphing and isogeometric analysis. Using conformal mapping techniques, we can establish a bijective mapping between the brain and the topologically equivalent sphere. Our hypothesis is that shape analysis problems are simplified when the shape is defined in an intrinsic coordinate system. Our goal is to establish such a coordinate system for the brain. The efficacy of the method is demonstrated with a white matter clustering problem. Initial results show promise for future investigation in these parameterization technique and its application to other problems related to computational anatomy like registration and segmentation. PMID:29177252

Simple Map with Low MN Perturbation for a Single-Null Divertor Tokamak with Constant Width of Stochastic Layer

NASA Astrophysics Data System (ADS)

Verma, Arun; Smith, Terry; Punjabi, Alkesh; Boozer, Allen

1996-11-01

In this work, we investigate the effects of low MN perturbations in a single-null divertor tokamak with stochastic scrape-off layer. The unperturbed magnetic topology of a single-null divertor tokamak is represented by Simple Map (Punjabi A, Verma A and Boozer A, Phys Rev Lett), 69, 3322 (1992) and J Plasma Phys, 52, 91 (1994). We choose the combinations of the map parameter k, and the strength of the low MN perturbation such that the width of stochastic layer remains unchanged. We give detailed results on the effects of low MN perturbation on the magnetic topology of the stochastic layer and on the footprint of field lines on the divertor plate given the constraint of constant width of the stochastic layer. The low MN perturbations occur naturally and therefore their effects are of considerable importance in tokamak divertor physics. This work is supported by US DOE OFES. Use of CRAY at HU and at NERSC is gratefully acknowledged.

Transport, shot noise, and topology in AC-driven dimer arrays

NASA Astrophysics Data System (ADS)

Niklas, Michael; Benito, Mónica; Kohler, Sigmund; Platero, Gloria

2016-11-01

We analyze an AC-driven dimer chain connected to a strongly biased electron source and drain. It turns out that the resulting transport exhibits fingerprints of topology. They are particularly visible in the driving-induced current suppression and the Fano factor. Thus, shot noise measurements provide a topological phase diagram as a function of the driving parameters. The observed phenomena can be explained physically by a mapping to an effective time-independent Hamiltonian and the emergence of edge states. Moreover, by considering quantum dissipation, we determine the requirements for the coherence properties in a possible experimental realization. For the computation of the zero-frequency noise, we develop an efficient method based on matrix-continued fractions.

Rapid geodesic mapping of brain functional connectivity: implementation of a dedicated co-processor in a field-programmable gate array (FPGA) and application to resting state functional MRI.

PubMed

Minati, Ludovico; Cercignani, Mara; Chan, Dennis

2013-10-01

Graph theory-based analyses of brain network topology can be used to model the spatiotemporal correlations in neural activity detected through fMRI, and such approaches have wide-ranging potential, from detection of alterations in preclinical Alzheimer's disease through to command identification in brain-machine interfaces. However, due to prohibitive computational costs, graph-based analyses to date have principally focused on measuring connection density rather than mapping the topological architecture in full by exhaustive shortest-path determination. This paper outlines a solution to this problem through parallel implementation of Dijkstra's algorithm in programmable logic. The processor design is optimized for large, sparse graphs and provided in full as synthesizable VHDL code. An acceleration factor between 15 and 18 is obtained on a representative resting-state fMRI dataset, and maps of Euclidean path length reveal the anticipated heterogeneous cortical involvement in long-range integrative processing. These results enable high-resolution geodesic connectivity mapping for resting-state fMRI in patient populations and real-time geodesic mapping to support identification of imagined actions for fMRI-based brain-machine interfaces. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

A highly efficient approach to protein interactome mapping based on collaborative filtering framework.

PubMed

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-09

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.

A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

PubMed Central

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-01

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly. PMID:25572661

A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

NASA Astrophysics Data System (ADS)

Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

2015-01-01

The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the problem of binary interactome mapping. Network topology-based approaches prove to be highly efficient in addressing this problem; however, their performance deteriorates significantly on sparse putative PPI networks. Motivated by the success of collaborative filtering (CF)-based approaches to the problem of personalized-recommendation on large, sparse rating matrices, this work aims at implementing a highly efficient CF-based approach to binary interactome mapping. To achieve this, we first propose a CF framework for it. Under this framework, we model the given data into an interactome weight matrix, where the feature-vectors of involved proteins are extracted. With them, we design the rescaled cosine coefficient to model the inter-neighborhood similarity among involved proteins, for taking the mapping process. Experimental results on three large, sparse datasets demonstrate that the proposed approach outperforms several sophisticated topology-based approaches significantly.

Symmetric Simple Map with Dipole Map for a Single-Null Divertor Tokamak

NASA Astrophysics Data System (ADS)

Ali, Halima; Watson, Michael; Punjabi, Alkesh; Boozer, Allen

1996-11-01

This investigation focuses on the effects of an externally placed dipole coil on the magnetic topology of a single-null divertor tokamak with a stochastic scrape-off layer using the Method of Maps (Punjabi A, Verma A and Boozer A, Phys Rev Lett), 69, 3322 (1992) and J Plasma Phys, 52, 91 (1994). The unperturbed magnetic topology is represented by the Symmetric Simple Map (Ali H, Watson M, Mayer C, Punjabi A and Boozer A, Bull Am Phys Soc), 40, 1855 (1995). The effect of dipole perturbation is repesented by the Dipole Map (Ali H, Watson M, Punjabi A and Boozer A, Sherwood Mtg), paper 1C20 (1996). A single dipole coil is placed across from the X-point below the last good surface. The strength of the dipole perturbation and the distance of the coil from the last good surface are varied. We observe that the dipole perturbation causes spatially intermittent chaos. This has significant implications for radiative divertor concepts as well for impurity control. We also present the detailed results on the effects of the dipole coil on the properties of the stochastic layer and the footprint of the field lines on the divertor plate. This work is supported by the US DOE OFES.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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

PubMed

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

2018-01-03

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

A non-linear dimension reduction methodology for generating data-driven stochastic input models

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

Ganapathysubramanian, Baskar; Zabaras, Nicholas

Stochastic analysis of random heterogeneous media (polycrystalline materials, porous media, functionally graded materials) provides information of significance only if realistic input models of the topology and property variations are used. This paper proposes a framework to construct such input stochastic models for the topology and thermal diffusivity variations in heterogeneous media using a data-driven strategy. Given a set of microstructure realizations (input samples) generated from given statistical information about the medium topology, the framework constructs a reduced-order stochastic representation of the thermal diffusivity. This problem of constructing a low-dimensional stochastic representation of property variations is analogous to the problem ofmore » manifold learning and parametric fitting of hyper-surfaces encountered in image processing and psychology. Denote by M the set of microstructures that satisfy the given experimental statistics. A non-linear dimension reduction strategy is utilized to map M to a low-dimensional region, A. We first show that M is a compact manifold embedded in a high-dimensional input space R{sup n}. An isometric mapping F from M to a low-dimensional, compact, connected set A is contained in R{sup d}(d<

A symplectic map for trajectories of magnetic field lines in double-null divertor tokamaks

NASA Astrophysics Data System (ADS)

Crank, Willie; Ali, Halima; Punjabi, Alkesh

2009-11-01

The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in tokamaks can be any coordinates for which a transformation to (ψ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct a map that represents the magnetic topology of double-null divertor tokamaks. For this purpose, the generating function of the simple map [A. Punjabi, A. Verma, and A. Boozer, Phys. Rev. Lett. 69, 3322 (1992)] is slightly modified. The resulting map equations for the double-null divertor tokamaks are: x1=x0-ky0(1-y0^2 ), y1=y0+kx1. k is the map parameter. It represents the generic topological effects of toroidal asymmetries. The O-point is at (0.0). The X-points are at (0,±1). The equilibrium magnetic surfaces are calculated. These surfaces are symmetric about the x- and y- axes. The widths of stochastic layer near the X-points in the principal plane, and the fractal dimensions of the magnetic footprints on the inboard and outboard side of upper and lower X-points are calculated from the map. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

Optimal Mass Transport for Shape Matching and Comparison

PubMed Central

Su, Zhengyu; Wang, Yalin; Shi, Rui; Zeng, Wei; Sun, Jian; Luo, Feng; Gu, Xianfeng

2015-01-01

Surface based 3D shape analysis plays a fundamental role in computer vision and medical imaging. This work proposes to use optimal mass transport map for shape matching and comparison, focusing on two important applications including surface registration and shape space. The computation of the optimal mass transport map is based on Monge-Brenier theory, in comparison to the conventional method based on Monge-Kantorovich theory, this method significantly improves the efficiency by reducing computational complexity from O(n2) to O(n). For surface registration problem, one commonly used approach is to use conformal map to convert the shapes into some canonical space. Although conformal mappings have small angle distortions, they may introduce large area distortions which are likely to cause numerical instability thus resulting failures of shape analysis. This work proposes to compose the conformal map with the optimal mass transport map to get the unique area-preserving map, which is intrinsic to the Riemannian metric, unique, and diffeomorphic. For shape space study, this work introduces a novel Riemannian framework, Conformal Wasserstein Shape Space, by combing conformal geometry and optimal mass transport theory. In our work, all metric surfaces with the disk topology are mapped to the unit planar disk by a conformal mapping, which pushes the area element on the surface to a probability measure on the disk. The optimal mass transport provides a map from the shape space of all topological disks with metrics to the Wasserstein space of the disk and the pullback Wasserstein metric equips the shape space with a Riemannian metric. We validate our work by numerous experiments and comparisons with prior approaches and the experimental results demonstrate the efficiency and efficacy of our proposed approach. PMID:26440265

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

Gyenis, András; Inoue, Hiroyuki; Jeon, Sangjun

Following the intense studies on topological insulators, significant efforts have recently been devoted to the search for gapless topological systems. These materials not only broaden the topological classification of matter but also provide a condensed matter realization of various relativistic particles and phenomena previously discussed mainly in high energy physics. Weyl semimetals host massless, chiral, low-energy excitations in the bulk electronic band structure, whereas a symmetry protected pair of Weyl fermions gives rise to massless Dirac fermions.Weemployed scanning tunneling microscopy/spectroscopy to explore the behavior of electronic states both on the surface and in the bulk of topological semimetal phases. Bymore » mapping the quasiparticle interference (QPI) and emerging Landau levels at high magnetic field in Dirac semimetals Cd 3As 2 and Na 3Bi, we observed extended Dirac-like bulk electronic bands. QPI imaged on Weyl semimetal TaAs demonstrated the predicted momentum dependent delocalization of Fermi arc surface states in the vicinity of the surface projected Weyl nodes.« less

Experiments with arbitrary networks in time-multiplexed delay systems

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Schmadel, Don C.; Murphy, Thomas E.; Roy, Rajarshi

2017-12-01

We report a new experimental approach using an optoelectronic feedback loop to investigate the dynamics of oscillators coupled on large complex networks with arbitrary topology. Our implementation is based on a single optoelectronic feedback loop with time delays. We use the space-time interpretation of systems with time delay to create large networks of coupled maps. Others have performed similar experiments using high-pass filters to implement the coupling; this restricts the network topology to the coupling of only a few nearest neighbors. In our experiment, the time delays and coupling are implemented on a field-programmable gate array, allowing the creation of networks with arbitrary coupling topology. This system has many advantages: the network nodes are truly identical, the network is easily reconfigurable, and the network dynamics occur at high speeds. We use this system to study cluster synchronization and chimera states in both small and large networks of different topologies.

Differential Models for B-Type Open-Closed Topological Landau-Ginzburg Theories

NASA Astrophysics Data System (ADS)

Babalic, Elena Mirela; Doryn, Dmitry; Lazaroiu, Calin Iuliu; Tavakol, Mehdi

2018-05-01

We propose a family of differential models for B-type open-closed topological Landau-Ginzburg theories defined by a pair (X,W), where X is any non-compact Calabi-Yau manifold and W is any holomorphic complex-valued function defined on X whose critical set is compact. The models are constructed at cochain level using smooth data, including the twisted Dolbeault algebra of polyvector-valued forms and a twisted Dolbeault category of holomorphic factorizations of W. We give explicit proposals for cochain level versions of the bulk and boundary traces and for the bulk-boundary and boundary-bulk maps of the Landau-Ginzburg theory. We prove that most of the axioms of an open-closed TFT (topological field theory) are satisfied on cohomology and conjecture that the remaining two axioms (namely non-degeneracy of bulk and boundary traces and the topological Cardy constraint) are also satisfied.

Alloy Engineering of Topological Semimetal Phase Transition in MgTa2 -xNbxN3

NASA Astrophysics Data System (ADS)

Huang, Huaqing; Jin, Kyung-Hwan; Liu, Feng

2018-03-01

Dirac, triple-point, and Weyl fermions represent three topological semimetal phases, characterized with a descending degree of band degeneracy, which have been realized separately in specific crystalline materials with different lattice symmetries. Here we demonstrate an alloy engineering approach to realize all three types of fermions in one single material system of MgTa2 -xNbx N3 . Based on symmetry analysis and first-principles calculations, we map out a phase diagram of topological order in the parameter space of alloy concentration and crystalline symmetry, where the intrinsic MgTa2 N3 with the highest symmetry hosts the Dirac semimetal phase, which transforms into the triple-point and then the Weyl semimetal phases with increasing Nb concentration that lowers the crystalline symmetries. Therefore, alloy engineering affords a unique approach for the experimental investigation of topological transitions of semimetallic phases manifesting different fermionic behaviors.

Magnetic field topology of the unique chemically peculiar star CU Virginis

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Lüftinger, T.; Neiner, C.; Alecian, E.; MiMeS Collaboration

2014-05-01

Context. The late-B, magnetic, chemically peculiar star CU Vir is one of the fastest rotators among the intermediate-mass stars with strong fossil magnetic fields. It shows a prominent rotational modulation of the spectral energy distribution and absorption line profiles due to chemical spots and exhibits a unique, strongly beamed variable radio emission. Aims: Little is known about the magnetic field topology of CU Vir. In this study, we aim to derive detailed maps of the magnetic field distribution over the surface of this star for the first time. Methods: We use high-resolution spectropolarimetric observations covering the entire rotational period. These data are interpreted using a multi-line technique of least-squares deconvolution (LSD) and a new Zeeman Doppler imaging code, which is based on detailed polarised radiative transfer modelling of the Stokes I and V LSD profiles. This new magnetic inversion approach relies on the spectrum synthesis calculations over the full wavelength range that is covered by observations and does not assume that the LSD profiles behave as a single spectral line with mean parameters. Results: We present magnetic and chemical abundance maps derived from the Si and Fe lines. Mean polarisation profiles of both elements reveal a significant departure of CU Vir's magnetic field topology from the commonly assumed axisymmetric dipolar configuration. The field of CU Vir is dipolar-like but clearly non-axisymmetric, showing a large difference in the field strength between the regions of opposite polarity. The main relative abundance depletion features in both Si and Fe maps coincide with the weak-field region in the magnetic map. Conclusions: The detailed information on the distorted dipolar magnetic field topology of CU Vir provided by our study is essential for understanding chemical spot formation, radio emission, and rotational period variation of this star. Based on observations obtained at the Bernard Lyot Telescope (USR5026) operated by the Observatoire Midi-Pyrénées, Université de Toulouse (Paul Sabatier), Centre National de la Recherche Scientifique of France.

Model-free learning on robot kinematic chains using a nested multi-agent topology

NASA Astrophysics Data System (ADS)

Karigiannis, John N.; Tzafestas, Costas S.

2016-11-01

This paper proposes a model-free learning scheme for the developmental acquisition of robot kinematic control and dexterous manipulation skills. The approach is based on a nested-hierarchical multi-agent architecture that intuitively encapsulates the topology of robot kinematic chains, where the activity of each independent degree-of-freedom (DOF) is finally mapped onto a distinct agent. Each one of those agents progressively evolves a local kinematic control strategy in a game-theoretic sense, that is, based on a partial (local) view of the whole system topology, which is incrementally updated through a recursive communication process according to the nested-hierarchical topology. Learning is thus approached not through demonstration and training but through an autonomous self-exploration process. A fuzzy reinforcement learning scheme is employed within each agent to enable efficient exploration in a continuous state-action domain. This paper constitutes in fact a proof of concept, demonstrating that global dexterous manipulation skills can indeed evolve through such a distributed iterative learning of local agent sensorimotor mappings. The main motivation behind the development of such an incremental multi-agent topology is to enhance system modularity, to facilitate extensibility to more complex problem domains and to improve robustness with respect to structural variations including unpredictable internal failures. These attributes of the proposed system are assessed in this paper through numerical experiments in different robot manipulation task scenarios, involving both single and multi-robot kinematic chains. The generalisation capacity of the learning scheme is experimentally assessed and robustness properties of the multi-agent system are also evaluated with respect to unpredictable variations in the kinematic topology. Furthermore, these numerical experiments demonstrate the scalability properties of the proposed nested-hierarchical architecture, where new agents can be recursively added in the hierarchy to encapsulate individual active DOFs. The results presented in this paper demonstrate the feasibility of such a distributed multi-agent control framework, showing that the solutions which emerge are plausible and near-optimal. Numerical efficiency and computational cost issues are also discussed.

Multipartite entanglement via the Mayer-Vietoris theorem

NASA Astrophysics Data System (ADS)

Patrascu, Andrei T.

2017-10-01

The connection between entanglement and topology manifests itself in the form of the ER-EPR duality. This statement however refers to the maximally entangled states only. In this article I study the multipartite entanglement and the way in which it relates to the topological interpretation of the ER-EPR duality. The 2 dimensional genus 1 torus will be generalised to a n-dimensional general torus, where the information about the multipartite entanglement will be encoded in the higher inclusion maps of the Mayer-Vietorist sequence.

Nodal Topological Phases in s-wave Superfluid of Ultracold Fermionic Gases

NASA Astrophysics Data System (ADS)

Huang, Bei-Bing; Yang, Xiao-Sen

2018-02-01

The gapless Weyl superfluid has been widely studied in the three-dimensional ultracold fermionic superfluid. In contrast to Weyl superfluid, there exists another kind of gapless superfluid with topologically protected nodal lines, which can be regarded as the superfluid counterpart of nodal line semimetal in the condensed matter physics, just as Weyl superfluid with Weyl semimetal. In this paper we study the ground states of the cold fermionic gases in cubic optical lattices with one-dimensional spin-orbit coupling and transverse Zeeman field and map out the topological phase diagram of the system. We demonstrate that in addition to a fully gapped topologically trivial phase, some different nodal line superfluid phases appear when the Zeeman field is adjusted. The presence of topologically stable nodal lines implies the dispersionless zero-energy flat band in a finite region of the surface Brillouin zone. Experimentally these nodal line superfluid states can be detected via the momentum-resolved radio-frequency spectroscopy. The nodal line topological superfluid provide fertile grounds for exploring exotic quantum matters in the context of ultracold atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11547047 and 11504143

Feynman diagrams and rooted maps

NASA Astrophysics Data System (ADS)

Prunotto, Andrea; Alberico, Wanda Maria; Czerski, Piotr

2018-04-01

The rooted maps theory, a branch of the theory of homology, is shown to be a powerful tool for investigating the topological properties of Feynman diagrams, related to the single particle propagator in the quantum many-body systems. The numerical correspondence between the number of this class of Feynman diagrams as a function of perturbative order and the number of rooted maps as a function of the number of edges is studied. A graphical procedure to associate Feynman diagrams and rooted maps is then stated. Finally, starting from rooted maps principles, an original definition of the genus of a Feynman diagram, which totally differs from the usual one, is given.

H I Structure and Topology of the Galaxy Revealed by the I-GALFA H I 21-cm Line Survey

NASA Astrophysics Data System (ADS)

Koo, Bon-Chul; Park, G.; Cho, W.; Gibson, S. J.; Kang, J.; Douglas, K. A.; Peek, J. E. G.; Korpela, E. J.; Heiles, C. E.

2011-05-01

The I-GALFA survey mapping all the H I in the inner Galactic disk visible to the Arecibo 305m telescope within 10 degrees of the Galactic plane (longitudes of 32 to 77 degrees at b = 0) completed observations in 2009 September and will soon be made publicly available. The high (3.4 arcmin) resolution and tremendous sensitivity of the survey offer a great opportunity to observe the fine details of H I both in the inner and in the far outer Galaxy. The reduced HI column density maps show that the HI structure is highly filamentary and clumpy, pervaded by shell-like structures, vertical filaments, and small clumps. By inspecting individual maps, we have found 36 shell candidates of angular sizes ranging from 0.4 to 12 degrees, half of which appear to be expanding. In order to characterize the filamentary/clumpy morphology of the HI structure, we have carried out statistical analyses of selected areas representing the spiral arms in the inner and outer Galaxy. Genus statistics that can distinguish the ``meatball'' and ``swiss-cheese'' topologies show that the HI topology is clump-like in most regions. The two-dimensional Fourier analysis further shows the HI structures are filamentary and mainly parallel to the plane in the outer Galaxy. We also examine the level-crossing statistics, the results of which are described in detail in an accompanying poster by Park et al.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

PubMed

O'Reilly, Joseph E; Donoghue, Philip C J

2018-03-01

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

PubMed Central

O’Reilly, Joseph E; Donoghue, Philip C J

2018-01-01

Abstract Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data. PMID:29106675

Explore the interrelationships of the WFE Nexus by relational topological mapping techniques - a case in northern Taiwan

NASA Astrophysics Data System (ADS)

Liao, Y. Y.; Tsai, W. P.; Chang, F. J.

2016-12-01

In recent years, Water-Food-Energy Nexus (WFE Nexus) has become a global issue due to the scarcity of natural resources. Besides, the resource management of water, energy and food at spatial and temporal scales raises multiple interwoven concerns ranging from co-opetitive relationship to resource accessibility. Over the past few decades, the socio-economic development of Taiwan has experienced drastic transformation because of population growth, urbanization and excessive consumption of natural resources. Therefore, our research intends to explore the interrelationships of the WFE Nexus by means of data mining techniques, such as artificial intelligence (AI). Our study area is the Tamsui River watershed in northern Taiwan. At first, we collect and analyze long-term WFE-related multidimensional heterogeneous observational data, such as water demand, food consumption and energy requirements. Then in order to explore the interrelationships and interactions of the WFE Nexus, the self-organizing map (SOM) is used to classify multidimensional heterogeneous data for building two-dimensional topological maps for clustering purpose. Consequently, we aim to establish the interrelationships in the WFE Nexus based on the obtained SOM topologies. This research will also explore the collaborative synergies of resource allocation and utilization that may influence the development of urbanization in the future. Ultimately, based on our proposed methodology and findings, the considerable impacts of the WFE Nexus on resource supply and demand and how the potential collaborative synergies would promote sustainable socio-economic development will be illuminated.

On the dual equivalence of the self-dual and topologically massive /B∧F models coupled to dynamical fermionic matter

NASA Astrophysics Data System (ADS)

Menezes, R.; Nascimento, J. R. S.; Ribeiro, R. F.; Wotzasek, C.

2002-06-01

We study the equivalence between the /B∧F self-dual (SDB∧F) and the /B∧F topologically massive (TMB∧F) models including the coupling to dynamical, U(1) charged fermionic matter. This is done through an iterative procedure of gauge embedding that produces the dual mapping. In the interactive cases, the minimal coupling adopted for both vector and tensor fields in the self-dual representation is transformed into a non-minimal magnetic like coupling in the topologically massive representation but with the currents swapped. It is known that to establish this equivalence a current-current interaction term is needed to render the matter sector unchanged. We show that both terms arise naturally from the embedding procedure.

Interplay between bulk and edge-bound topological defects in a square micromagnet

DOE PAGES

Sloetjes, Sam D.; Digernes, Einar; Olsen, Fredrik K.; ...

2018-01-22

A field-driven transformation of a domain pattern in a square micromagnet, defined in a thin film of La 0.7Sr 0.3MnO 3, is discussed in terms of creation and annihilation of bulk vortices and edge-bound topological defects with half-integer winding numbers. The evolution of the domain pattern was mapped with soft x-ray photoemission electron microscopy and magnetic force microscopy. Micromagnetic modeling, permitting detailed analysis of the spin texture, accurately reproduces the measured domain state transformation. The simulations also helped stipulate the energy barriers associated with the creation and annihilation of the topological charges and thus to assess the stability of themore » domain states in this magnetic microstructure.« less

Interplay between bulk and edge-bound topological defects in a square micromagnet

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

Sloetjes, Sam D.; Digernes, Einar; Olsen, Fredrik K.

A field-driven transformation of a domain pattern in a square micromagnet, defined in a thin film of La 0.7Sr 0.3MnO 3, is discussed in terms of creation and annihilation of bulk vortices and edge-bound topological defects with half-integer winding numbers. The evolution of the domain pattern was mapped with soft x-ray photoemission electron microscopy and magnetic force microscopy. Micromagnetic modeling, permitting detailed analysis of the spin texture, accurately reproduces the measured domain state transformation. The simulations also helped stipulate the energy barriers associated with the creation and annihilation of the topological charges and thus to assess the stability of themore » domain states in this magnetic microstructure.« less

A Study of the Crystal Structure of Co40Fe40B20 Epitaxial Films on a Bi2Te3 Topological Insulator

NASA Astrophysics Data System (ADS)

Kaveev, A. K.; Suturin, S. M.; Sokolov, N. S.; Kokh, K. A.; Tereshchenko, O. E.

2018-03-01

Laser molecular-beam epitaxy has been used to form Co40Fe40B20 layers on Bi2Te3 topological insulator substrates, and their growth conditions have been studied. The possibility of growing epitaxial ferromagnetic layers on the surface of a topological insulator is demonstrated for the first time. The CoFeB layers have a body-centered cubic crystal structure with the (111) crystal plane parallel to the (0001) plane of Bi2Te3. 3D mapping in the reciprocal space of high-energy electron-diffraction patterns made it possible to determine the epitaxial relationships between the film and the substrate.

Topology preserving non-rigid image registration using time-varying elasticity model for MRI brain volumes.

PubMed

Ahmad, Sahar; Khan, Muhammad Faisal

2015-12-01

In this paper, we present a new non-rigid image registration method that imposes a topology preservation constraint on the deformation. We propose to incorporate the time varying elasticity model into the deformable image matching procedure and constrain the Jacobian determinant of the transformation over the entire image domain. The motion of elastic bodies is governed by a hyperbolic partial differential equation, generally termed as elastodynamics wave equation, which we propose to use as a deformation model. We carried out clinical image registration experiments on 3D magnetic resonance brain scans from IBSR database. The results of the proposed registration approach in terms of Kappa index and relative overlap computed over the subcortical structures were compared against the existing topology preserving non-rigid image registration methods and non topology preserving variant of our proposed registration scheme. The Jacobian determinant maps obtained with our proposed registration method were qualitatively and quantitatively analyzed. The results demonstrated that the proposed scheme provides good registration accuracy with smooth transformations, thereby guaranteeing the preservation of topology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Landing Hazard Avoidance Display

NASA Technical Reports Server (NTRS)

Abernathy, Michael Franklin (Inventor); Hirsh, Robert L. (Inventor)

2016-01-01

Landing hazard avoidance displays can provide rapidly understood visual indications of where it is safe to land a vehicle and where it is unsafe to land a vehicle. Color coded maps can indicate zones in two dimensions relative to the vehicles position where it is safe to land. The map can be simply green (safe) and red (unsafe) areas with an indication of scale or can be a color coding of another map such as a surface map. The color coding can be determined in real time based on topological measurements and safety criteria to thereby adapt to dynamic, unknown, or partially known environments.

Data Mining in Cyber Operations

DTIC Science & Technology

2014-07-01

information processing units intended to mimic the network of neurons in the human brain for performing pattern recognition  Self- organizing maps (SOM...patterns are mined from in order to influence the learning model . An exploratory attack does not alter the training process , but rather uses other...New Jersey: Prentice Hall. 21) Kohonen, T. (1982). Self- organized formation of topologically correct feature maps. Biological Cybernetics , 43, 59–69

Insulator function and topological domain border strength scale with architectural protein occupancy

PubMed Central

2014-01-01

Background Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions. Results By mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals. Conclusions We identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains. PMID:24981874

The complex magnetic field topology of the cool Ap star 49 Cam

NASA Astrophysics Data System (ADS)

Silvester, J.; Kochukhov, O.; Rusomarov, N.; Wade, G. A.

2017-10-01

49 Cam is a cool magnetic chemically peculiar star that has been noted for showing strong, complex Zeeman linear polarization signatures. This paper describes magnetic and chemical surface maps obtained for 49 Cam using the Invers10 magnetic Doppler imaging code and high-resolution spectropolarimetric data in all four Stokes parameters collected with the ESPaDOnS and Narval spectropolarimeters at the Canada-France-Hawaii Telescope and Pic du Midi Observatory. The reconstructed magnetic field maps of 49 Cam show a relatively complex structure. Describing the magnetic field topology in terms of spherical harmonics, we find significant contributions of modes up to ℓ = 3, including toroidal components. Observations cannot be reproduced using a simple low-order multipolar magnetic field structure. 49 Cam exhibits a level of field complexity that has not been seen in magnetic maps of other cool Ap stars. Hence, we concluded that relatively complex magnetic fields are observed in Ap stars at both low and high effective temperatures. In addition to mapping the magnetic field, we also derive surface abundance distributions of nine chemical elements, including Ca, Sc, Ti, Cr, Fe, Ce, Pr, Nd and Eu. Comparing these abundance maps with the reconstructed magnetic field geometry, we find no clear relationship of the abundance distributions with the magnetic field for some elements. However, for other elements some distinct patterns are found. We discuss these results in the context of other recent magnetic mapping studies and theoretical predictions of radiative diffusion.

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

Universal ventricular coordinates: A generic framework for describing position within the heart and transferring data.

PubMed

Bayer, Jason; Prassl, Anton J; Pashaei, Ali; Gomez, Juan F; Frontera, Antonio; Neic, Aurel; Plank, Gernot; Vigmond, Edward J

2018-04-01

Being able to map a particular set of cardiac ventricles to a generic topologically equivalent representation has many applications, including facilitating comparison of different hearts, as well as mapping quantities and structures of interest between them. In this paper we describe Universal Ventricular Coordinates (UVC), which can be used to describe position within any biventricular heart. UVC comprise four unique coordinates that we have chosen to be intuitive, well defined, and relevant for physiological descriptions. We describe how to determine these coordinates for any volumetric mesh by illustrating how to properly assign boundary conditions and utilize solutions to Laplace's equation. Using UVC, we transferred scalar, vector, and tensor data between four unstructured ventricular meshes from three different species. Performing the mappings was very fast, on the order of a few minutes, since mesh nodes were searched in a KD tree. Distance errors in mapping mesh nodes back and forth between meshes were less than the size of an element. Analytically derived fiber directions were also mapped across meshes and compared, showing  < 5° difference over most of the ventricles. The ability to transfer gradients was also demonstrated. Topologically variable structures, like papillary muscles, required further definition outside of the UVC framework. In conclusion, UVC can aid in transferring many types of data between different biventricular geometries. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Magnification of signatures of a topological phase transition by quantum zero point motion

NASA Astrophysics Data System (ADS)

Lopes, Pedro L. e. S.; Ghaemi, Pouyan

2015-08-01

We show that the zero point motion of a vortex in superconducting doped topological insulators leads to significant changes in the electronic spectrum at the topological phase transition in this system. This topological phase transition is tuned by the doping level, and the corresponding effects are manifest in the density of states at energies which are on the order of the vortex fluctuation frequency. Although the electronic energy gap in the spectrum generated by a stationary vortex is but a small fraction of the bulk superconducting gap, the vortex fluctuation frequency may be much larger. As a result, this quantum zero point motion can induce a discontinuous change in the spectral features of the system at the topological vortex phase transition to energies which are well within the resolution of scanning tunneling microscopy. This discontinuous change is exclusive to superconducting systems in which we have a topological phase transition. Moreover, the phenomena studied in this paper present effects of Magnus forces on the vortex spectrum which are not present in the ordinary s -wave superconductors. Finally, we demonstrate explicitly that the vortex in this system is equivalent to a Kitaev chain. This allows for the mapping of the vortex fluctuating scenario in three dimensions into similar one-dimensional situations in which one may search for other novel signatures of topological phase transitions.

Enquiry into the Topology of Plasma Membrane-Localized PIN Auxin Transport Components.

PubMed

Nodzyński, Tomasz; Vanneste, Steffen; Zwiewka, Marta; Pernisová, Markéta; Hejátko, Jan; Friml, Jiří

2016-11-07

Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure-function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Stabilizing embedology: Geometry-preserving delay-coordinate maps

NASA Astrophysics Data System (ADS)

Eftekhari, Armin; Yap, Han Lun; Wakin, Michael B.; Rozell, Christopher J.

2018-02-01

Delay-coordinate mapping is an effective and widely used technique for reconstructing and analyzing the dynamics of a nonlinear system based on time-series outputs. The efficacy of delay-coordinate mapping has long been supported by Takens' embedding theorem, which guarantees that delay-coordinate maps use the time-series output to provide a reconstruction of the hidden state space that is a one-to-one embedding of the system's attractor. While this topological guarantee ensures that distinct points in the reconstruction correspond to distinct points in the original state space, it does not characterize the quality of this embedding or illuminate how the specific parameters affect the reconstruction. In this paper, we extend Takens' result by establishing conditions under which delay-coordinate mapping is guaranteed to provide a stable embedding of a system's attractor. Beyond only preserving the attractor topology, a stable embedding preserves the attractor geometry by ensuring that distances between points in the state space are approximately preserved. In particular, we find that delay-coordinate mapping stably embeds an attractor of a dynamical system if the stable rank of the system is large enough to be proportional to the dimension of the attractor. The stable rank reflects the relation between the sampling interval and the number of delays in delay-coordinate mapping. Our theoretical findings give guidance to choosing system parameters, echoing the tradeoff between irrelevancy and redundancy that has been heuristically investigated in the literature. Our initial result is stated for attractors that are smooth submanifolds of Euclidean space, with extensions provided for the case of strange attractors.

Stabilizing embedology: Geometry-preserving delay-coordinate maps.

PubMed

Eftekhari, Armin; Yap, Han Lun; Wakin, Michael B; Rozell, Christopher J

2018-02-01

Delay-coordinate mapping is an effective and widely used technique for reconstructing and analyzing the dynamics of a nonlinear system based on time-series outputs. The efficacy of delay-coordinate mapping has long been supported by Takens' embedding theorem, which guarantees that delay-coordinate maps use the time-series output to provide a reconstruction of the hidden state space that is a one-to-one embedding of the system's attractor. While this topological guarantee ensures that distinct points in the reconstruction correspond to distinct points in the original state space, it does not characterize the quality of this embedding or illuminate how the specific parameters affect the reconstruction. In this paper, we extend Takens' result by establishing conditions under which delay-coordinate mapping is guaranteed to provide a stable embedding of a system's attractor. Beyond only preserving the attractor topology, a stable embedding preserves the attractor geometry by ensuring that distances between points in the state space are approximately preserved. In particular, we find that delay-coordinate mapping stably embeds an attractor of a dynamical system if the stable rank of the system is large enough to be proportional to the dimension of the attractor. The stable rank reflects the relation between the sampling interval and the number of delays in delay-coordinate mapping. Our theoretical findings give guidance to choosing system parameters, echoing the tradeoff between irrelevancy and redundancy that has been heuristically investigated in the literature. Our initial result is stated for attractors that are smooth submanifolds of Euclidean space, with extensions provided for the case of strange attractors.

Effects of mistuning and matrix structure on the topology of frequency response curves

NASA Technical Reports Server (NTRS)

Afolabi, Dare

1989-01-01

The stability of a frequency response curve under mild perturbations of the system's matrix is investigated. Using recent developments in the theory of singularities of differentiable maps, it is shown that the stability of a response curve depends on the structure of the system's matrix. In particular, the frequency response curves of a cylic system are shown to be unstable. Consequently, slight parameter variations engendered by mistuning will induce a significant difference in the topology of the forced response curves, if the mistuning transformation crosses the bifurcation set.

Topological characterization and early detection of bifurcations and chaos in complex systems using persistent homology.

PubMed

Mittal, Khushboo; Gupta, Shalabh

2017-05-01

Early detection of bifurcations and chaos and understanding their topological characteristics are essential for safe and reliable operation of various electrical, chemical, physical, and industrial processes. However, the presence of non-linearity and high-dimensionality in system behavior makes this analysis a challenging task. The existing methods for dynamical system analysis provide useful tools for anomaly detection (e.g., Bendixson-Dulac and Poincare-Bendixson criteria can detect the presence of limit cycles); however, they do not provide a detailed topological understanding about system evolution during bifurcations and chaos, such as the changes in the number of subcycles and their positions, lifetimes, and sizes. This paper addresses this research gap by using topological data analysis as a tool to study system evolution and develop a mathematical framework for detecting the topological changes in the underlying system using persistent homology. Using the proposed technique, topological features (e.g., number of relevant k-dimensional holes, etc.) are extracted from nonlinear time series data which are useful for deeper analysis of the system behavior and early detection of bifurcations and chaos. When applied to a Logistic map, a Duffing oscillator, and a real life Op-amp based Jerk circuit, these features are shown to accurately characterize the system dynamics and detect the onset of chaos.

Transmission and visualization of large geographical maps

NASA Astrophysics Data System (ADS)

Zhang, Liqiang; Zhang, Liang; Ren, Yingchao; Guo, Zhifeng

Transmission and visualization of large geographical maps have become a challenging research issue in GIS applications. This paper presents an efficient and robust way to simplify large geographical maps using frame buffers and Voronoi diagrams. The topological relationships are kept during the simplification by removing the Voronoi diagram's self-overlapped regions. With the simplified vector maps, we establish different levels of detail (LOD) models of these maps. Then we introduce a client/server architecture which integrates our out-of-core algorithm, progressive transmission and rendering scheme based on computer graphics hardware. The architecture allows the viewers to view different regions interactively at different LODs on the network. Experimental results show that our proposed scheme provides an effective way for powerful transmission and manipulation of large maps.

Complex network approach to fractional time series

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

Manshour, Pouya

In order to extract correlation information inherited in stochastic time series, the visibility graph algorithm has been recently proposed, by which a time series can be mapped onto a complex network. We demonstrate that the visibility algorithm is not an appropriate one to study the correlation aspects of a time series. We then employ the horizontal visibility algorithm, as a much simpler one, to map fractional processes onto complex networks. The degree distributions are shown to have parabolic exponential forms with Hurst dependent fitting parameter. Further, we take into account other topological properties such as maximum eigenvalue of the adjacencymore » matrix and the degree assortativity, and show that such topological quantities can also be used to predict the Hurst exponent, with an exception for anti-persistent fractional Gaussian noises. To solve this problem, we take into account the Spearman correlation coefficient between nodes' degrees and their corresponding data values in the original time series.« less

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

PubMed Central

Brackley, Chris A.; Johnson, James; Kelly, Steven; Cook, Peter R.; Marenduzzo, Davide

2016-01-01

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green ‘transcription factors’ bind to cognate sites in strings of beads (‘chromatin’) to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster—red with red, green with green, but rarely red with green—to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent ‘bridging-induced attraction’ proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales. PMID:27060145

A novel algorithm for fully automated mapping of geospatial ontologies

NASA Astrophysics Data System (ADS)

Chaabane, Sana; Jaziri, Wassim

2018-01-01

Geospatial information is collected from different sources thus making spatial ontologies, built for the same geographic domain, heterogeneous; therefore, different and heterogeneous conceptualizations may coexist. Ontology integrating helps creating a common repository of the geospatial ontology and allows removing the heterogeneities between the existing ontologies. Ontology mapping is a process used in ontologies integrating and consists in finding correspondences between the source ontologies. This paper deals with the "mapping" process of geospatial ontologies which consist in applying an automated algorithm in finding the correspondences between concepts referring to the definitions of matching relationships. The proposed algorithm called "geographic ontologies mapping algorithm" defines three types of mapping: semantic, topological and spatial.

Fixed points of contractive mappings in b-metric-like spaces.

PubMed

Hussain, Nawab; Roshan, Jamal Rezaei; Parvaneh, Vahid; Kadelburg, Zoran

2014-01-01

We discuss topological structure of b-metric-like spaces and demonstrate a fundamental lemma for the convergence of sequences. As an application we prove certain fixed point results in the setup of such spaces for different types of contractive mappings. Finally, some periodic point results in b-metric-like spaces are obtained. Two examples are presented in order to verify the effectiveness and applicability of our main results.

Use of Biodescriptors and Chemodescriptors in Predictive Toxicology: A Mathematical/Computational Approach

DTIC Science & Technology

2005-01-01

proteomic gel analyses. The research group has explored the use of chemodescriptors calculated using high-level ab initio quantum chemical basis sets...descriptors that characterize the entire proteomics map, local descriptors that characterize a subset of the proteins present in the gel, and spectrum...techniques for analyzing the full set of proteins present in a proteomics map. 14. SUBJECT TERMS 1S. NUMBER OF PAGES Topological indices

Cardiac magnetic field map topology quantified by Kullback-Leibler entropy identifies patients with hypertrophic cardiomyopathy

NASA Astrophysics Data System (ADS)

Schirdewan, A.; Gapelyuk, A.; Fischer, R.; Koch, L.; Schütt, H.; Zacharzowsky, U.; Dietz, R.; Thierfelder, L.; Wessel, N.

2007-03-01

Hypertrophic cardiomyopathy (HCM) is a common primary inherited cardiac muscle disorder, defined clinically by the presence of unexplained left ventricular hypertrophy. The detection of affected patients remains challenging. Genetic testing is limited because only in 50%-60% of all HCM diagnoses an underlying mutation can be found. Furthermore, the disease has a varied clinical course and outcome, with many patients having little or no discernible cardiovascular symptoms, whereas others develop profound exercise limitation and recurrent arrhythmias or sudden cardiac death. Therefore prospective screening of HCM family members is strongly recommended. According to the current guidelines this includes serial echocardiographic and electrocardiographic examinations. In this study we investigated the capability of cardiac magnetic field mapping (CMFM) to detect patients suffering from HCM. We introduce for the first time a combined diagnostic approach based on map topology quantification using Kullback-Leibler (KL) entropy and regional magnetic field strength parameters. The cardiac magnetic field was recorded over the anterior chest wall using a multichannel-LT-SQUID system. CMFM was calculated based on a regular 36 point grid. We analyzed CMFM in patients with confirmed diagnosis of HCM (HCM, n =33, 43.8±13 years, 13 women, 20 men), a control group of healthy subjects (NORMAL, n =57, 39.6±8.9 years; 22 women and 35 men), and patients with confirmed cardiac hypertrophy due to arterial hypertension (HYP, n =42, 49.7±7.9 years, 15 women and 27 men). A subgroup analysis was performed between HCM patients suffering from the obstructive (HOCM, n =19) and nonobstructive (HNCM, n =14) form of the disease. KL entropy based map topology quantification alone identified HCM patients with a sensitivity of 78.8% and specificity of 86.9% (overall classification rate 84.8%). The combination of the KL parameters with a regional field strength parameter improved the overall classification rate to 87.9% (sensitivity: 84.8%, specificity: 88.9%, area under ROC curve: 0.94). KL measures applied to discriminate between HOCM and HNCM patients showed a correct classification of 78.8%. The combination of one KL and one regional parameter again improved the overall classification rate to 97%. A preliminary prospective analysis in two HCM families showed the feasibility of this diagnostic approach with a correct diagnosis of all 22 screened family members (1 HOCM, 4 HNCM, 17 normal). In conclusion, Cardiac Magnetic Field Mapping including KL entropy based topology quantifications is a suitable tool for HCM screening.

Mapping the q-voter model: From a single chain to complex networks

NASA Astrophysics Data System (ADS)

Jȩdrzejewski, Arkadiusz; Sznajd-Weron, Katarzyna; Szwabiński, Janusz

2016-03-01

We propose and compare six different ways of mapping the modified q-voter model to complex networks. Considering square lattices, Barabási-Albert, Watts-Strogatz and real Twitter networks, we ask the question if always a particular choice of the group of influence of a fixed size q leads to different behavior at the macroscopic level. Using Monte Carlo simulations we show that the answer depends on the relative average path length of the network and for real-life topologies the differences between the considered mappings may be negligible.

Planck 2013 results. XXVI. Background geometry and topology of the Universe

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Armitage-Caplan, C.; Arnaud, M.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bobin, J.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bridges, M.; Bucher, M.; Burigana, C.; Butler, R. C.; Cardoso, J.-F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, H. C.; Chiang, L.-Y.; Christensen, P. R.; Church, S.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J.-M.; Désert, F.-X.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Dupac, X.; Efstathiou, G.; Enßlin, T. A.; Eriksen, H. K.; Fabre, O.; Finelli, F.; Forni, O.; Frailis, M.; Franceschi, E.; Galeotta, S.; Ganga, K.; Giard, M.; Giardino, G.; Giraud-Héraud, Y.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Laureijs, R. J.; Lawrence, C. R.; Leahy, J. P.; Leonardi, R.; Leroy, C.; Lesgourgues, J.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maffei, B.; Maino, D.; Mandolesi, N.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Massardi, M.; Matarrese, S.; Matthai, F.; Mazzotta, P.; McEwen, J. D.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Osborne, S.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Peiris, H. V.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pogosyan, D.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Popa, L.; Poutanen, T.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Riazuelo, A.; Ricciardi, S.; Riller, T.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rowan-Robinson, M.; Rusholme, B.; Sandri, M.; Santos, D.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Starck, J.-L.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sureau, F.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Tavagnacco, D.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Varis, J.; Vielva, P.; Villa, F.; Vittorio, N.; Wade, L. A.; Wandelt, B. D.; Yvon, D.; Zacchei, A.; Zonca, A.

2014-11-01

The new cosmic microwave background (CMB) temperature maps from Planck provide the highest-quality full-sky view of the surface of last scattering available to date. This allows us to detect possible departures from the standard model of a globally homogeneous and isotropic cosmology on the largest scales. We search for correlations induced by a possible non-trivial topology with a fundamental domain intersecting, or nearly intersecting, the last scattering surface (at comoving distance χrec), both via a direct search for matched circular patterns at the intersections and by an optimal likelihood search for specific topologies. For the latter we consider flat spaces with cubic toroidal (T3), equal-sided chimney (T2) and slab (T1) topologies, three multi-connected spaces of constant positive curvature (dodecahedral, truncated cube and octahedral) and two compact negative-curvature spaces. These searches yield no detection of the compact topology with the scale below the diameter of the last scattering surface. For most compact topologies studied the likelihood maximized over the orientation of the space relative to the observed map shows some preference for multi-connected models just larger than the diameter of the last scattering surface. Since this effect is also present in simulated realizations of isotropic maps, we interpret it as the inevitable alignment of mild anisotropic correlations with chance features in a single sky realization; such a feature can also be present, in milder form, when the likelihood is marginalized over orientations. Thus marginalized, the limits on the radius ℛi of the largest sphere inscribed in topological domain (at log-likelihood-ratio Δln ℒ > -5 relative to a simply-connected flat Planck best-fit model) are: in a flat Universe, ℛi> 0.92χrec for the T3 cubic torus; ℛi> 0.71χrec for the T2 chimney; ℛi> 0.50χrec for the T1 slab; and in a positively curved Universe, ℛi> 1.03χrec for the dodecahedral space; ℛi> 1.0χrec for the truncated cube; and ℛi> 0.89χrec for the octahedral space. The limit for a wider class of topologies, i.e., those predicting matching pairs of back-to-back circles, among them tori and the three spherical cases listed above, coming from the matched-circles search, is ℛi> 0.94χrec at 99% confidence level. Similar limits apply to a wide, although not exhaustive, range of topologies. We also perform a Bayesian search for an anisotropic global Bianchi VIIh geometry. In the non-physical setting where the Bianchi cosmology is decoupled from the standard cosmology, Planck data favour the inclusion of a Bianchi component with a Bayes factor of at least 1.5 units of log-evidence. Indeed, the Bianchi pattern is quite efficient at accounting for some of the large-scale anomalies found in Planck data. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. In the physically motivated setting where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VIIh cosmology and constrain the vorticity of such models to (ω/H)0< 8.1 × 10-10 (95% confidence level).

Graph theory data for topological quantum chemistry.

PubMed

Vergniory, M G; Elcoro, L; Wang, Zhijun; Cano, Jennifer; Felser, C; Aroyo, M I; Bernevig, B Andrei; Bradlyn, Barry

2017-08-01

Topological phases of noninteracting particles are distinguished by the global properties of their band structure and eigenfunctions in momentum space. On the other hand, group theory as conventionally applied to solid-state physics focuses only on properties that are local (at high-symmetry points, lines, and planes) in the Brillouin zone. To bridge this gap, we have previously [Bradlyn et al., Nature (London) 547, 298 (2017)NATUAS0028-083610.1038/nature23268] mapped the problem of constructing global band structures out of local data to a graph construction problem. In this paper, we provide the explicit data and formulate the necessary algorithms to produce all topologically distinct graphs. Furthermore, we show how to apply these algorithms to certain "elementary" band structures highlighted in the aforementioned reference, and thus we identified and tabulated all orbital types and lattices that can give rise to topologically disconnected band structures. Finally, we show how to use the newly developed bandrep program on the Bilbao Crystallographic Server to access the results of our computation.

Observation of topological nodal fermion semimetal phase in ZrSiS

DOE PAGES

Neupane, Madhab; Belopolski, Ilya; Hosen, M. Mofazzel; ...

2016-05-11

We present that unveiling new topological phases of matter is one of the current objectives in condensed matter physics. Recent experimental discoveries of Dirac and Weyl semimetals prompt the search for other exotic phases of matter. Here we present a systematic angle-resolved photoemission spectroscopy study of ZrSiS, a prime topological nodal semimetal candidate. Our wider Brillouin zone (BZ) mapping shows multiple Fermi surface pockets such as the diamond-shaped Fermi surface, elliptical-shaped Fermi surface, and a small electron pocket encircling at the zone center (Γ) point, the M point, and the X point of the BZ, respectively. We experimentally establish themore » spinless nodal fermion semimetal phase in ZrSiS, which is supported by our first-principles calculations. Our findings evidence that the ZrSiS-type of material family is a new platform on which to explore exotic states of quantum matter; these materials are expected to provide an avenue for engineering two-dimensional topological insulator systems.« less

Dependence of Coronary 3-Dimensional Dose Maps on Coronary Topologies and Beam Set in Breast Radiation Therapy: A Study Based on CT Angiographies

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

Moignier, Alexandra, E-mail: alexandra.moignier@gmail.com; Broggio, David; Derreumaux, Sylvie

2014-05-01

Purpose: In left-side breast radiation therapy (RT), doses to the left main (LM) and left anterior descending (LAD) coronary arteries are usually assessed after delineation by prior anatomic knowledge on the treatment planning computed tomography (CT) scan. In this study, dose sensitivity due to interindividual coronary topology variation was assessed, and hot spots were located. Methods and Materials: Twenty-two detailed heart models, created from heart computed tomography angiographies, were fitted into a single representative female thorax. Two breast RT protocols were then simulated into a treatment planning system: the first protocol comprised tangential and tumoral bed beams (TGs{sub T}B) atmore » 50 + 16 Gy, the second protocol added internal mammary chain beams at 50 Gy to TGs{sub T}B (TGs{sub T}B{sub I}MC). For the heart, the LAD, and the LM, several dose indicators were calculated: dose-volume histograms, mean dose (D{sub mean}), minimal dose received by the most irradiated 2% of the volume (D{sub 2%}), and 3-dimensional (3D) dose maps. Variations of these indicators with anatomies were studied. Results: For the LM, the intermodel dispersion of D{sub mean} and D{sub 2%} was 10% and 11%, respectively, with TGs{sub T}B and 40% and 80%, respectively, with TGs{sub T}B{sub I}MC. For the LAD, these dispersions were 19% (D{sub mean}) and 49% (D{sub 2%}) with TGs{sub T}B and 35% (D{sub mean}) and 76% (D{sub 2%}) with TGs{sub T}B{sub I}MC. The 3D dose maps revealed that the internal mammary chain beams induced hot spots between 20 and 30 Gy on the LM and the proximal LAD for some coronary topologies. Without IMC beams, hot spots between 5 and 26 Gy are located on the middle and distal LAD. Conclusions: Coronary dose distributions with hot spot location and dose level can change significantly depending on coronary topology, as highlighted by 3D coronary dose maps. In clinical practice, coronary imaging may be required for a relevant coronary dose assessment, especially in cases of internal mammary chain irradiation.« less

Topological defects in electric double layers of ionic liquids at carbon interfaces

DOE PAGES

Black, Jennifer M.; Okatan, Mahmut Baris; Feng, Guang; ...

2015-06-07

The structure and properties of the electrical double layer in ionic liquids is of interest in a wide range of areas including energy storage, catalysis, lubrication, and many more. Theories describing the electrical double layer for ionic liquids have been proposed, however a full molecular level description of the double layer is lacking. To date, studies have been predominantly focused on ion distributions normal to the surface, however the 3D nature of the electrical double layer in ionic liquids requires a full picture of the double layer structure not only normal to the surface, but also in plane. Here wemore » utilize 3D force mapping to probe the in plane structure of an ionic liquid at a graphite interface and report the direct observation of the structure and properties of topological defects. The observation of ion layering at structural defects such as step-edges, reinforced by molecular dynamics simulations, defines the spatial resolution of the method. Observation of defects allows for the establishment of the universality of ionic liquid behavior vs. separation from the carbon surface and to map internal defect structure. In conclusion, these studies offer a universal pathway for probing the internal structure of topological defects in soft condensed matter on the nanometer level in three dimensions.« less

Testing trivializing maps in the Hybrid Monte Carlo algorithm

PubMed Central

Engel, Georg P.; Schaefer, Stefan

2011-01-01

We test a recent proposal to use approximate trivializing maps in a field theory to speed up Hybrid Monte Carlo simulations. Simulating the CPN−1 model, we find a small improvement with the leading order transformation, which is however compensated by the additional computational overhead. The scaling of the algorithm towards the continuum is not changed. In particular, the effect of the topological modes on the autocorrelation times is studied. PMID:21969733

Entropy of homeomorphisms on unimodal inverse limit spaces

NASA Astrophysics Data System (ADS)

Bruin, H.; Štimac, S.

2013-04-01

We prove that every self-homeomorphism h : Ks → Ks on the inverse limit space Ks of the tent map Ts with slope s \\in (\\sqrt 2, 2] has topological entropy htop(h) = |R| log s, where R \\in { Z} is such that h and σR are isotopic. Conclusions on all possible values of the entropy of homeomorphisms of the inverse limit space of a (renormalizable) quadratic map are also drawn.

Fixed Points of Contractive Mappings in b-Metric-Like Spaces

PubMed Central

Hussain, Nawab; Roshan, Jamal Rezaei

2014-01-01

We discuss topological structure of b-metric-like spaces and demonstrate a fundamental lemma for the convergence of sequences. As an application we prove certain fixed point results in the setup of such spaces for different types of contractive mappings. Finally, some periodic point results in b-metric-like spaces are obtained. Two examples are presented in order to verify the effectiveness and applicability of our main results. PMID:25143980

Building regional early flood warning systems by AI techniques

NASA Astrophysics Data System (ADS)

Chang, F. J.; Chang, L. C.; Amin, M. Z. B. M.

2017-12-01

Building early flood warning system is essential for the protection of the residents against flood hazards and make actions to mitigate the losses. This study implements AI technology for forecasting multi-step-ahead regional flood inundation maps during storm events. The methodology includes three major schemes: (1) configuring the self-organizing map (SOM) to categorize a large number of regional inundation maps into a meaningful topology; (2) building dynamic neural networks to forecast multi-step-ahead average inundated depths (AID); and (3) adjusting the weights of the selected neuron in the constructed SOM based on the forecasted AID to obtain real-time regional inundation maps. The proposed models are trained, and tested based on a large number of inundation data sets collected in regions with the most frequent and serious flooding in the river basin. The results appear that the SOM topological relationships between individual neurons and their neighbouring neurons are visible and clearly distinguishable, and the hybrid model can continuously provide multistep-ahead visible regional inundation maps with high resolution during storm events, which have relatively small RMSE values and high R2 as compared with numerical simulation data sets. The computing time is only few seconds, and thereby leads to real-time regional flood inundation forecasting and make early flood inundation warning system. We demonstrate that the proposed hybrid ANN-based model has a robust and reliable predictive ability and can be used for early warning to mitigate flood disasters.

The generalized Lyapunov theorem and its application to quantum channels

NASA Astrophysics Data System (ADS)

Burgarth, Daniel; Giovannetti, Vittorio

2007-05-01

We give a simple and physically intuitive necessary and sufficient condition for a map acting on a compact metric space to be mixing (i.e. infinitely many applications of the map transfer any input into a fixed convergency point). This is a generalization of the 'Lyapunov direct method'. First we prove this theorem in topological spaces and for arbitrary continuous maps. Finally we apply our theorem to maps which are relevant in open quantum systems and quantum information, namely quantum channels. In this context, we also discuss the relations between mixing and ergodicity (i.e. the property that there exists only a single input state which is left invariant by a single application of the map) showing that the two are equivalent when the invariant point of the ergodic map is pure.

Exploiting Surroundedness for Saliency Detection: A Boolean Map Approach.

PubMed

Zhang, Jianming; Sclaroff, Stan

2016-05-01

We demonstrate the usefulness of surroundedness for eye fixation prediction by proposing a Boolean Map based Saliency model (BMS). In our formulation, an image is characterized by a set of binary images, which are generated by randomly thresholding the image's feature maps in a whitened feature space. Based on a Gestalt principle of figure-ground segregation, BMS computes a saliency map by discovering surrounded regions via topological analysis of Boolean maps. Furthermore, we draw a connection between BMS and the Minimum Barrier Distance to provide insight into why and how BMS can properly captures the surroundedness cue via Boolean maps. The strength of BMS is verified by its simplicity, efficiency and superior performance compared with 10 state-of-the-art methods on seven eye tracking benchmark datasets.

DIGITAL LINE GRAPHS - USGS

EPA Science Inventory

USGS DLGs are digital representations of program-quadrangle format and sectional maps. All DLG data distributed by the United States Geological Survey (USGS) are DLG-Level 3 (DLG-3), which means the data contain a full range of attribute codes, have full topological structuring, ...

Lunar and planetary maps and charts available for public sale

NASA Technical Reports Server (NTRS)

1973-01-01

A catalog of lunar and planetary charts which are available from the U.S. Government Printing Office is presented. The charts are identified by the area of the lunar topology involved and the prices of each chart are shown.

3D topology of orientation columns in visual cortex revealed by functional optical coherence tomography.

PubMed

Nakamichi, Yu; Kalatsky, Valery A; Watanabe, Hideyuki; Sato, Takayuki; Rajagopalan, Uma Maheswari; Tanifuji, Manabu

2018-04-01

Orientation tuning is a canonical neuronal response property of six-layer visual cortex that is encoded in pinwheel structures with center orientation singularities. Optical imaging of intrinsic signals enables us to map these surface two-dimensional (2D) structures, whereas lack of appropriate techniques has not allowed us to visualize depth structures of orientation coding. In the present study, we performed functional optical coherence tomography (fOCT), a technique capable of acquiring a 3D map of the intrinsic signals, to study the topology of orientation coding inside the cat visual cortex. With this technique, for the first time, we visualized columnar assemblies in orientation coding that had been predicted from electrophysiological recordings. In addition, we found that the columnar structures were largely distorted around pinwheel centers: center singularities were not rigid straight lines running perpendicularly to the cortical surface but formed twisted string-like structures inside the cortex that turned and extended horizontally through the cortex. Looping singularities were observed with their respective termini accessing the same cortical surface via clockwise and counterclockwise orientation pinwheels. These results suggest that a 3D topology of orientation coding cannot be fully anticipated from 2D surface measurements. Moreover, the findings demonstrate the utility of fOCT as an in vivo mesoscale imaging method for mapping functional response properties of cortex in the depth axis. NEW & NOTEWORTHY We used functional optical coherence tomography (fOCT) to visualize three-dimensional structure of the orientation columns with millimeter range and micrometer spatial resolution. We validated vertically elongated columnar structure in iso-orientation domains. The columnar structure was distorted around pinwheel centers. An orientation singularity formed a string with tortuous trajectories inside the cortex and connected clockwise and counterclockwise pinwheel centers in the surface orientation map. The results were confirmed by comparisons with conventional optical imaging and electrophysiological recordings.

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

Fermionic Symmetry-Protected Topological Phase in a Two-Dimensional Hubbard Model

DOE PAGES

Chen, Cheng-Chien; Muechler, Lukas; Car, Roberto; ...

2016-08-25

We study the two-dimensional (2D) Hubbard model using exact diagonalization for spin-1/2 fermions on the triangular and honeycomb lattices decorated with a single hexagon per site. In certain parameter ranges, the Hubbard model maps to a quantum compass model on those lattices. On the triangular lattice, the compass model exhibits collinear stripe antiferromagnetism, implying d-density wave charge order in the original Hubbard model. On the honeycomb lattice, the compass model has a unique, quantum disordered ground state that transforms nontrivially under lattice reflection. The ground state of the Hubbard model on the decorated honeycomb lattice is thus a 2D fermionicmore » symmetry-protected topological phase. This state—protected by time-reversal and reflection symmetries—cannot be connected adiabatically to a free-fermion topological phase.« less

Topological spinon bands and vison excitations in spin-orbit coupled quantum spin liquids

NASA Astrophysics Data System (ADS)

Sonnenschein, Jonas; Reuther, Johannes

2017-12-01

Spin liquids are exotic quantum states characterized by the existence of fractional and deconfined quasiparticle excitations, referred to as spinons and visons. Their fractional nature establishes topological properties such as a protected ground-state degeneracy. This work investigates spin-orbit coupled spin liquids where, additionally, topology enters via nontrivial band structures of the spinons. We revisit the Z2 spin-liquid phases that have recently been identified in a projective symmetry-group analysis on the square lattice when spin-rotation symmetry is maximally lifted [J. Reuther et al., Phys. Rev. B 90, 174417 (2014), 10.1103/PhysRevB.90.174417]. We find that in the case of nearest-neighbor couplings only, Z2 spin liquids on the square lattice always exhibit trivial spinon bands. Adding second-neighbor terms, the simplest projective symmetry-group solution closely resembles the Bernevig-Hughes-Zhang model for topological insulators. Assuming that the emergent gauge fields are static, we investigate vison excitations, which we confirm to be deconfined in all investigated spin phases. Particularly, if the spinon bands are topological, the spinons and visons form bound states consisting of several spinon-Majorana zero modes coupling to one vison. The existence of such zero modes follows from an exact mapping between these spin phases and topological p +i p superconductors with vortices. We propose experimental probes to detect such states in real materials.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Estimating Topology of Discrete Dynamical Networks

NASA Astrophysics Data System (ADS)

Guo, Shu-Juan; Fu, Xin-Chu

2010-07-01

In this paper, by applying Lasalle's invariance principle and some results about the trace of a matrix, we propose a method for estimating the topological structure of a discrete dynamical network based on the dynamical evolution of the network. The network concerned can be directed or undirected, weighted or unweighted, and the local dynamics of each node can be nonidentical. The connections among the nodes can be all unknown or partially known. Finally, two examples, including a Hénon map and a central network, are illustrated to verify the theoretical results.

The Topographical Mapping in Drosophila Central Complex Network and Its Signal Routing

PubMed Central

Chang, Po-Yen; Su, Ta-Shun; Shih, Chi-Tin; Lo, Chung-Chuan

2017-01-01

Neural networks regulate brain functions by routing signals. Therefore, investigating the detailed organization of a neural circuit at the cellular levels is a crucial step toward understanding the neural mechanisms of brain functions. To study how a complicated neural circuit is organized, we analyzed recently published data on the neural circuit of the Drosophila central complex, a brain structure associated with a variety of functions including sensory integration and coordination of locomotion. We discovered that, except for a small number of “atypical” neuron types, the network structure formed by the identified 194 neuron types can be described by only a few simple mathematical rules. Specifically, the topological mapping formed by these neurons can be reconstructed by applying a generation matrix on a small set of initial neurons. By analyzing how information flows propagate with or without the atypical neurons, we found that while the general pattern of signal propagation in the central complex follows the simple topological mapping formed by the “typical” neurons, some atypical neurons can substantially re-route the signal pathways, implying specific roles of these neurons in sensory signal integration. The present study provides insights into the organization principle and signal integration in the central complex. PMID:28443014

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.

PubMed

Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E

2018-05-14

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Holcomb, Chris

GeoCF has greatly enhanced the utility-scale solar siting platform, Smart Power Maps, through the help of the DOE Solar Energy Technologies Office. It is now available for the entire country and includes an improved user interface and additional layers such as topology, soils, comprehensive floodplains, parcels, imagery, wells, pipelines, and more. As well, users can now draw and save maps and perform drastically improved and more relevant hydrological, transmission, and financial analyzes. Smart Power Maps has played a pivotal role in supporting the development of otherwise unknown or hard to locate ideal locations for large solar farms in the Unitedmore » States.« less

DIGITAL LINE GRAPHS - USGS 1:24,000

EPA Science Inventory

USGS DLGs are digital representations of program-quadrangle format and sectional maps. All DLG data distributed by the United States Geological Survey (USGS) are DLG-Level 3 (DLG-3), which means the data contain a full range of attribute codes, have full topological structuring, ...

DIGITAL LINE GRAPHS - USGS 1:100,000

EPA Science Inventory

USGS DLGs are digital representations of program-quadrangle format and sectional maps. All DLG data distributed by the United States Geological Survey (USGS) are DLG-Level 3 (DLG-3), which means the data contain a full range of attribute codes, have full topological structuring, ...

Uncovering Topological Structures in Unstructured Data

DTIC Science & Technology

2015-04-20

paper [4] presents an approach for constructing statistical shape models (SSMs) for aortic surfaces with the eventual goal of mapping the mean aorta ...characterize the variation pattern are found after optimizing the group-wise correspondence across the aorta training set. We use the direct

Synchronization Dynamics of Coupled Chemical Oscillators

NASA Astrophysics Data System (ADS)

Tompkins, Nathan

The synchronization dynamics of complex networks have been extensively studied over the past few decades due to their ubiquity in the natural world. Prominent examples include cardiac rhythms, circadian rhythms, the flashing of fireflies, predator/prey population dynamics, mammalian gait, human applause, pendulum clocks, the electrical grid, and of the course the brain. Detailed experiments have been done to map the topology of many of these systems and significant advances have been made to describe the mathematics of these networks. Compared to these bodies of work relatively little has been done to directly test the role of topology in the synchronization dynamics of coupled oscillators. This Dissertation develops technology to examine the dynamics due to topology within networks of discrete oscillatory components. The oscillatory system used here consists of the photo-inhibitable Belousov-Zhabotinsky (BZ) reaction water-in-oil emulsion where the oscillatory drops are diffusively coupled to one another and the topology is defined by the geometry of the diffusive connections. Ring networks are created from a close-packed 2D array of drops using the Programmable Illumination Microscope (PIM) in order to test Turing's theory of morphogenesis directly. Further technology is developed to create custom planar networks of BZ drops in more complicated topologies which can be individually perturbed using illumination from the PIM. The work presented here establishes the validity of using the BZ emulsion system with a PIM to study the topology induced effects on the synchronization dynamics of coupled chemical oscillators, tests the successes and limitations of Turing's theory of morphogenesis, and develops new technology to further probe the effects of network topology on a system of coupled oscillators. Finally, this Dissertation concludes by describing ongoing experiments which utilize this new technology to examine topology induced transitions of synchronization dynamics of diffusively coupled chemical oscillators.

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.

Membrane Topology Mapping of the Na+-Pumping NADH: Quinone Oxidoreductase from Vibrio cholerae by PhoA- Green Fluorescent Protein Fusion Analysis▿

PubMed Central

Duffy, Ellen B.; Barquera, Blanca

2006-01-01

The membrane topologies of the six subunits of Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae were determined by a combination of topology prediction algorithms and the construction of C-terminal fusions. Fusion expression vectors contained either bacterial alkaline phosphatase (phoA) or green fluorescent protein (gfp) genes as reporters of periplasmic and cytoplasmic localization, respectively. A majority of the topology prediction algorithms did not predict any transmembrane helices for NqrA. A lack of PhoA activity when fused to the C terminus of NqrA and the observed fluorescence of the green fluorescent protein C-terminal fusion confirm that this subunit is localized to the cytoplasmic side of the membrane. Analysis of four PhoA fusions for NqrB indicates that this subunit has nine transmembrane helices and that residue T236, the binding site for flavin mononucleotide (FMN), resides in the cytoplasm. Three fusions confirm that the topology of NqrC consists of two transmembrane helices with the FMN binding site at residue T225 on the cytoplasmic side. Fusion analysis of NqrD and NqrE showed almost mirror image topologies, each consisting of six transmembrane helices; the results for NqrD and NqrE are consistent with the topologies of Escherichia coli homologs YdgQ and YdgL, respectively. The NADH, flavin adenine dinucleotide, and Fe-S center binding sites of NqrF were localized to the cytoplasm. The determination of the topologies of the subunits of Na+-NQR provides valuable insights into the location of cofactors and identifies targets for mutagenesis to characterize this enzyme in more detail. The finding that all the redox cofactors are localized to the cytoplasmic side of the membrane is discussed. PMID:17041063

Drawing Road Networks with Mental Maps.

PubMed

Lin, Shih-Syun; Lin, Chao-Hung; Hu, Yan-Jhang; Lee, Tong-Yee

2014-09-01

Tourist and destination maps are thematic maps designed to represent specific themes in maps. The road network topologies in these maps are generally more important than the geometric accuracy of roads. A road network warping method is proposed to facilitate map generation and improve theme representation in maps. The basic idea is deforming a road network to meet a user-specified mental map while an optimization process is performed to propagate distortions originating from road network warping. To generate a map, the proposed method includes algorithms for estimating road significance and for deforming a road network according to various geometric and aesthetic constraints. The proposed method can produce an iconic mark of a theme from a road network and meet a user-specified mental map. Therefore, the resulting map can serve as a tourist or destination map that not only provides visual aids for route planning and navigation tasks, but also visually emphasizes the presentation of a theme in a map for the purpose of advertising. In the experiments, the demonstrations of map generations show that our method enables map generation systems to generate deformed tourist and destination maps efficiently.

Hierarchical layered and semantic-based image segmentation using ergodicity map

NASA Astrophysics Data System (ADS)

Yadegar, Jacob; Liu, Xiaoqing

2010-04-01

Image segmentation plays a foundational role in image understanding and computer vision. Although great strides have been made and progress achieved on automatic/semi-automatic image segmentation algorithms, designing a generic, robust, and efficient image segmentation algorithm is still challenging. Human vision is still far superior compared to computer vision, especially in interpreting semantic meanings/objects in images. We present a hierarchical/layered semantic image segmentation algorithm that can automatically and efficiently segment images into hierarchical layered/multi-scaled semantic regions/objects with contextual topological relationships. The proposed algorithm bridges the gap between high-level semantics and low-level visual features/cues (such as color, intensity, edge, etc.) through utilizing a layered/hierarchical ergodicity map, where ergodicity is computed based on a space filling fractal concept and used as a region dissimilarity measurement. The algorithm applies a highly scalable, efficient, and adaptive Peano- Cesaro triangulation/tiling technique to decompose the given image into a set of similar/homogenous regions based on low-level visual cues in a top-down manner. The layered/hierarchical ergodicity map is built through a bottom-up region dissimilarity analysis. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level of detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanisms for contextual topological object/region relationship generation. Experiments have been conducted within the maritime image environment where the segmented layered semantic objects include the basic level objects (i.e. sky/land/water) and deeper level objects in the sky/land/water surfaces. Experimental results demonstrate the proposed algorithm has the capability to robustly and efficiently segment images into layered semantic objects/regions with contextual topological relationships.

Communications and control for electric power systems

NASA Technical Reports Server (NTRS)

Kirkham, H.; Goettsche, A.; Niebur, D.; Friend, H.; Johnston, A.

1991-01-01

The first section of the report describes the AbNET system, a hardware and software communications system designed for distribution automation (it can also find application in substation monitoring and control). The topology of the power system fixes the topology of the communications network, which can therefore be expected to include a larger number of branch points, tap points, and interconnections. These features make this communications network unlike any other. The network operating software has to solve the problem of communicating to all the nodes of a very complex network in as reliable a way as possible even if the network is damaged, and it has to do so with minimum transmission delays and at minimum cost. The design of the operating protocols is described within the framework of the seven-layer Open System Interconnection hierarchy of the International Standards Organization. Section 2 of the report describes the development and testing of a high voltage sensor based on an electro-optic polymer. The theory of operation is reviewed. Bulk fabrication of the polymer is discussed, as well as results of testing of the electro-optic coefficient of the material. Fabrication of a complete prototype sensor suitable for use in the range 1-20 kV is described. The electro-optic polymer is shown to be an important material for fiber optic sensing applications. Appendix A is theoretical support for this work. The third section of the report presents the application of an artificial neural network, Kohonen's self-organizing feature map, for the classification of power system states. This classifier maps vectors of an N-dimensional space to a 2-dimensional neural net in a nonlinear way preserving the topological order of the input vectors. These mappings are studied using a nonlinear power system model.

Topology characterization of a benzodiazepine-binding beta-rich domain of the GABAA receptor alpha1 subunit.

PubMed

Xu, Zhiwen; Fang, Shisong; Shi, Haifeng; Li, Hoiming; Deng, Yiqun; Liao, Yinglei; Wu, Jiun-Ming; Zheng, Hui; Zhu, Huaimin; Chen, Hueih-Min; Tsang, Shui Ying; Xue, Hong

2005-10-01

Structural investigation of GABAA receptors has been limited by difficulties imposed by its trans-membrane-complex nature. In the present study, the topology of a membrane-proximal beta-rich (MPB) domain in the C139-L269 segment of the receptor alpha1 subunit was probed by mapping the benzodiazepine (BZ)-binding and epitopic sites, as well as fluorescence resonance energy transfer (FRET) analysis. Ala-scanning and semiconservative substitutions within this segment revealed the contribution of the phenyl rings of Y160 and Y210, the hydroxy group of S186 and the positive charge on R187 to BZ-binding. FRET with the bound BZ ligand indicated the proximity of Y160, S186, R187, and S206 to the BZ-binding site. On the other hand, epitope-mapping using the monoclonal antibodies (mAbs) against the MPB domain established a clustering of T172, R173, E174, Q196, and T197. Based on the lack of FRET between Trp substitutionally placed at R173 or V198 and bound BZ, this epitope-mapped cluster is located on a separate end of the folded protein from the BZ-binding site. Mutations of the five conserved Cys and Trp residues in the MPB domain gave rise to synergistic and rescuing effects on protein secondary structures and unfolding stability that point to a CCWCW-pentad, reminiscent to the CWC-triad "pin" of immunoglobulin (Ig)-like domains, important for the structural maintenance. These findings, together with secondary structure and fold predictions suggest an anti-parallel beta-strand topology with resemblance to Ig-like fold, having the BZ-binding and the epitopic residues being clustered at two different ends of the fold.

Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet.

PubMed

Yang, Q; Siganos, G; Faloutsos, M; Lonardi, S

2006-01-01

Recent research efforts have made available genome-wide, high-throughput protein-protein interaction (PPI) maps for several model organisms. This has enabled the systematic analysis of PPI networks, which has become one of the primary challenges for the system biology community. In this study, we attempt to understand better the topological structure of PPI networks by comparing them against man-made communication networks, and more specifically, the Internet. Our comparative study is based on a comprehensive set of graph metrics. Our results exhibit an interesting dichotomy. On the one hand, both networks share several macroscopic properties such as scale-free and small-world properties. On the other hand, the two networks exhibit significant topological differences, such as the cliqueishness of the highest degree nodes. We attribute these differences to the distinct design principles and constraints that both networks are assumed to satisfy. We speculate that the evolutionary constraints that favor the survivability and diversification are behind the building process of PPI networks, whereas the leading force in shaping the Internet topology is a decentralized optimization process geared towards efficient node communication.

Impact of high-frequency pumping on anomalous finite-size effects in three-dimensional topological insulators

NASA Astrophysics Data System (ADS)

Pervishko, Anastasiia A.; Yudin, Dmitry; Shelykh, Ivan A.

2018-02-01

Lowering of the thickness of a thin-film three-dimensional topological insulator down to a few nanometers results in the gap opening in the spectrum of topologically protected two-dimensional surface states. This phenomenon, which is referred to as the anomalous finite-size effect, originates from hybridization between the states propagating along the opposite boundaries. In this work, we consider a bismuth-based topological insulator and show how the coupling to an intense high-frequency linearly polarized pumping can further be used to manipulate the value of a gap. We address this effect within recently proposed Brillouin-Wigner perturbation theory that allows us to map a time-dependent problem into a stationary one. Our analysis reveals that both the gap and the components of the group velocity of the surface states can be tuned in a controllable fashion by adjusting the intensity of the driving field within an experimentally accessible range and demonstrate the effect of light-induced band inversion in the spectrum of the surface states for high enough values of the pump.

Mapping the Braiding Properties of Non-Abelian FQHE Liquids.

NASA Astrophysics Data System (ADS)

Prodan, Emil; Haldane, F. D. M.

2007-03-01

Non-Abelian FQHE (NAFQHE) states have elementary excitations that cannot be individually locally-created. When widely separated, they give rise to topological (quasi-)degeneracy of the quantum states; braiding of such non-Abelian quasiparticles (NAQP's) implements unitary transformations among the degenerate states that may be useful for ``topological quantum computing'' (TQC). We have developed a new technique for explicit computation of NAQP braiding in models exhibiting ideal NAFQHE behavior (where the topological degeneracy is exact), in particular the Moore-Read ν = 5/2 state. For systems of small numbers of NAQP's on a sphere, we have computed the non-Abelian Berry curvature and Hilbert space metric, as one NAQP is moved relative to a fixed configuration of the others, showing how the topological properties develop as the system size (NAQP separation) increases. We also studied the effect of perturbations (Coulomb interaction and substrate potentials) that lift the exact degeneracy, and become the dominant corrections when NAQP's are brought together so that quantum measurements can be made; these effects are likely to be crucial in determining whether TQC is viable in NAFQHE systems.

Flow-aggregated traffic-driven label mapping in label-switching networks

NASA Astrophysics Data System (ADS)

Nagami, Kenichi; Katsube, Yasuhiro; Esaki, Hiroshi; Nakamura, Osamu

1998-12-01

Label switching technology enables high performance, flexible, layer-3 packet forwarding based on the fixed length label information mapped to the layer-3 packet stream. A Label Switching Router (LSR) forwards layer-3 packets based on their label information mapped to the layer-3 address information as well as their layer-3 address information. This paper evaluates the required number of labels under traffic-driven label mapping policy using the real backbone traffic traces. The evaluation shows that the label mapping policy requires a large number of labels. In order to reduce the required number of labels, we propose a label mapping policy which is a traffic-driven label mapping for the traffic toward the same destination network. The evaluation shows that the proposed label mapping policy requires only about one tenth as many labels compared with the traffic-driven label mapping for the host-pair packet stream,and the topology-driven label mapping for the destination network packet stream.

Anatomy-guided joint tissue segmentation and topological correction for 6-month infant brain MRI with risk of autism.

PubMed

Wang, Li; Li, Gang; Adeli, Ehsan; Liu, Mingxia; Wu, Zhengwang; Meng, Yu; Lin, Weili; Shen, Dinggang

2018-06-01

Tissue segmentation of infant brain MRIs with risk of autism is critically important for characterizing early brain development and identifying biomarkers. However, it is challenging due to low tissue contrast caused by inherent ongoing myelination and maturation. In particular, at around 6 months of age, the voxel intensities in both gray matter and white matter are within similar ranges, thus leading to the lowest image contrast in the first postnatal year. Previous studies typically employed intensity images and tentatively estimated tissue probabilities to train a sequence of classifiers for tissue segmentation. However, the important prior knowledge of brain anatomy is largely ignored during the segmentation. Consequently, the segmentation accuracy is still limited and topological errors frequently exist, which will significantly degrade the performance of subsequent analyses. Although topological errors could be partially handled by retrospective topological correction methods, their results may still be anatomically incorrect. To address these challenges, in this article, we propose an anatomy-guided joint tissue segmentation and topological correction framework for isointense infant MRI. Particularly, we adopt a signed distance map with respect to the outer cortical surface as anatomical prior knowledge, and incorporate such prior information into the proposed framework to guide segmentation in ambiguous regions. Experimental results on the subjects acquired from National Database for Autism Research demonstrate the effectiveness to topological errors and also some levels of robustness to motion. Comparisons with the state-of-the-art methods further demonstrate the advantages of the proposed method in terms of both segmentation accuracy and topological correctness. © 2018 Wiley Periodicals, Inc.

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

Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

PubMed Central

2011-01-01

Background Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design. Results In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys. Conclusions Out of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry. PMID:21605466

Membrane topology and identification of key residues of EaDAcT, a plant MBOAT with unusual substrate specificity.

PubMed

Tran, Tam N T; Shelton, Jennifer; Brown, Susan; Durrett, Timothy P

2017-10-01

Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) catalyzes the transfer of an acetyl group from acetyl-CoA to the sn-3 position of diacylglycerol to form 3-acetyl-1,2-diacyl-sn-glycerol (acetyl-TAG). EaDAcT belongs to a small, plant-specific subfamily of the membrane bound O-acyltransferases (MBOAT) that acylate different lipid substrates. Sucrose gradient density centrifugation revealed that EaDAcT colocalizes to the same fractions as an endoplasmic reticulum (ER)-specific marker. By mapping the membrane topology of EaDAcT, we obtained an experimentally determined topology model for a plant MBOAT. The EaDAcT model contains four transmembrane domains (TMDs), with both the N- and C-termini orientated toward the lumen of the ER. In addition, there is a large cytoplasmic loop between the first and second TMDs, with the MBOAT signature region of the protein embedded in the third TMD close to the interface between the membrane and the cytoplasm. During topology mapping, we discovered two cysteine residues (C187 and C293) located on opposite sides of the membrane that are important for enzyme activity. In order to identify additional amino acid residues important for acetyltransferase activity, we isolated and characterized acetyltransferases from other acetyl-TAG-producing plants. Among them, the acetyltransferase from Euonymus fortunei possessed the highest activity in vivo and in vitro. Mutagenesis of conserved amino acids revealed that S253, H257, D258 and V263 are essential for EaDAcT activity. Alteration of residues unique to the acetyltransferases did not alter the unique acyl donor specificity of EaDAcT, suggesting that multiple amino acids are important for substrate recognition. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Numerical grid generation techniques. [conference

NASA Technical Reports Server (NTRS)

1980-01-01

The state of the art in topology and flow geometry is presented. Solution techniques for partial differential equations are reviewed and included developments in coordinate transformations, conformal mapping, and invariant imbeddings. Applications of these techniques in fluid mechanics, flow geometry, boundary value problems, and fluidics are presented.

Primitives for Active Internet Topology Mapping: Toward High-Frequency Characterization

DTIC Science & Technology

2010-11-03

that a tension exists between the two conflict- ing goals of reducing probing traffic and capturing dynamic forwarding paths. Many networks deploy...perform alias resolution to future work. Acknowledgments The authors would like to thank Young Hyun, k. claffy and CAIDA for measurement

Mapping Multiplex Hubs in Human Functional Brain Networks

PubMed Central

De Domenico, Manlio; Sasai, Shuntaro; Arenas, Alex

2016-01-01

Typical brain networks consist of many peripheral regions and a few highly central ones, i.e., hubs, playing key functional roles in cerebral inter-regional interactions. Studies have shown that networks, obtained from the analysis of specific frequency components of brain activity, present peculiar architectures with unique profiles of region centrality. However, the identification of hubs in networks built from different frequency bands simultaneously is still a challenging problem, remaining largely unexplored. Here we identify each frequency component with one layer of a multiplex network and face this challenge by exploiting the recent advances in the analysis of multiplex topologies. First, we show that each frequency band carries unique topological information, fundamental to accurately model brain functional networks. We then demonstrate that hubs in the multiplex network, in general different from those ones obtained after discarding or aggregating the measured signals as usual, provide a more accurate map of brain's most important functional regions, allowing to distinguish between healthy and schizophrenic populations better than conventional network approaches. PMID:27471443

Geometrical and topological issues in octree based automatic meshing

NASA Technical Reports Server (NTRS)

Saxena, Mukul; Perucchio, Renato

1987-01-01

Finite element meshes derived automatically from solid models through recursive spatial subdivision schemes (octrees) can be made to inherit the hierarchical structure and the spatial addressability intrinsic to the underlying grid. These two properties, together with the geometric regularity that can also be built into the mesh, make octree based meshes ideally suited for efficient analysis and self-adaptive remeshing and reanalysis. The element decomposition of the octal cells that intersect the boundary of the domain is discussed. The problem, central to octree based meshing, is solved by combining template mapping and element extraction into a procedure that utilizes both constructive solid geometry and boundary representation techniques. Boundary cells that are not intersected by the edge of the domain boundary are easily mapped to predefined element topology. Cells containing edges (and vertices) are first transformed into a planar polyhedron and then triangulated via element extractor. The modeling environments required for the derivation of planar polyhedra and for element extraction are analyzed.

Fracton-Elasticity Duality

NASA Astrophysics Data System (ADS)

Pretko, Michael; Radzihovsky, Leo

2018-05-01

Motivated by recent studies of fractons, we demonstrate that elasticity theory of a two-dimensional quantum crystal is dual to a fracton tensor gauge theory, providing a concrete manifestation of the fracton phenomenon in an ordinary solid. The topological defects of elasticity theory map onto charges of the tensor gauge theory, with disclinations and dislocations corresponding to fractons and dipoles, respectively. The transverse and longitudinal phonons of crystals map onto the two gapless gauge modes of the gauge theory. The restricted dynamics of fractons matches with constraints on the mobility of lattice defects. The duality leads to numerous predictions for phases and phase transitions of the fracton system, such as the existence of gauge theory counterparts to the (commensurate) crystal, supersolid, hexatic, and isotropic fluid phases of elasticity theory. Extensions of this duality to generalized elasticity theories provide a route to the discovery of new fracton models. As a further consequence, the duality implies that fracton phases are relevant to the study of interacting topological crystalline insulators.

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.

Spatial fluctuations of helical Dirac fermions on the surface of topological insulators

NASA Astrophysics Data System (ADS)

Beidenkopf, Haim

2013-03-01

Strong topological insulators are materials that host exotic states on their surfaces due to a topological band inversion in their bulk band structure. These surface states have Dirac dispersion as if they were massless relativistic particles, and are assured to remain metallic by time reversal symmetry. The helical spin texture associated with the Dirac dispersion prohibits backscattering, which we have imaged using scanning tunneling microscopy (STM) and spectroscopic mappings. This topological protection can be lifted by time-reversal breaking perturbations that induce a gap at the Dirac point and cant the helical spin texture. Massive Dirac electrons had been visualized by angular resolved photo emission spectroscopy in magnetically doped topological insulators. While we do not identify a gapped spectrum in our STM measurements of similar compounds, we do find a dominating electrostatic response to the charged content of those dopants. In their presence the Dirac spectrum exhibits strong spatial fluctuations. As a result translational invariance is broken over a characteristic length scale and the Dirac-point energy is only locally defined. Possible global manifestations of these local fluctuations will be discussed, as well as alternative avenues for breaking time reversal symmetry while maintaining the integrity of the Dirac spectrum. This work was supported by NSF, NSF-MRSEC, and DARPA.

Homological Order in Three and Four dimensions: Wilson Algebra, Entanglement Entropy and Twist Defects

NASA Astrophysics Data System (ADS)

Roy, Abhishek; Chen, Xiao; Teo, Jeffrey

2013-03-01

We investigate homological orders in two, three and four dimensions by studying Zk toric code models on simplicial, cellular or in general differential complexes. The ground state degeneracy is obtained from Wilson loop and surface operators, and the homological intersection form. We compute these for a series of closed 3 and 4 dimensional manifolds and study the projective representations of mapping class groups (modular transformations). Braiding statistics between point and string excitations in (3+1)-dimensions or between dual string excitations in (4+1)-dimensions are topologically determined by the higher dimensional linking number, and can be understood by an effective topological field theory. An algorithm for calculating entanglemnent entropy of any bipartition of closed manifolds is presented, and its topological signature is completely characterized homologically. Extrinsic twist defects (or disclinations) are studied in 2,3 and 4 dimensions and are shown to carry exotic fusion and braiding properties. Simons Fellowship

Robustness against non-magnetic impurities in topological superconductors

NASA Astrophysics Data System (ADS)

Nagai, Y.; Ota, Y.; Machida, M.

2014-12-01

We study the robustness against non-magnetic impurities in a three-dimensional topological superconductor, focusing on an effective model (massive Dirac Bogoliubov-de Gennes (BdG) Hamiltonian with s-wave on-site pairing) of CuxBi2Se3 with the parameter set determined by the first-principles calculation. With the use of the self-consistent T- matrix approximation for impurity scattering, we discuss the impurity-concentration dependence of the zero-energy density of states. We show that a single material variable, measuring relativistic effects in the Dirac-BdG Hamiltonian, well characterizes the numerical results. In the nonrelativistic limit, the odd-parity fully-gapped topological superconductivity is fragile against non-magnetic impurities, since this superconductivity can be mapped onto the p-wave superconductivity. On the other hand, in the ultrarelativistic limit, the superconductivity is robust against the non-magnetic impurities, since the effective model has the s-wave superconductivity. We derive the effective Hamiltonian in the both limit.

Asymptotically locally Euclidean/Kaluza-Klein stationary vacuum black holes in five dimensions

NASA Astrophysics Data System (ADS)

Khuri, Marcus; Weinstein, Gilbert; Yamada, Sumio

2018-05-01

We produce new examples, both explicit and analytical, of bi-axisymmetric stationary vacuum black holes in five dimensions. A novel feature of these solutions is that they are asymptotically locally Euclidean, in which spatial cross-sections at infinity have lens space L(p,q) topology, or asymptotically Kaluza-Klein so that spatial cross-sections at infinity are topologically S^1× S^2. These are nondegenerate black holes of cohomogeneity 2, with any number of horizon components, where the horizon cross-section topology is any one of the three admissible types: S^3, S^1× S^2, or L(p,q). Uniqueness of these solutions is also established. Our method is to solve the relevant harmonic map problem with prescribed singularities, having target symmetric space SL(3,{R})/SO(3). In addition, we analyze the possibility of conical singularities and find a large family for which geometric regularity is guaranteed.

Analysis of recurrent patterns in toroidal magnetic fields.

PubMed

Sanderson, Allen R; Chen, Guoning; Tricoche, Xavier; Pugmire, David; Kruger, Scott; Breslau, Joshua

2010-01-01

In the development of magnetic confinement fusion which will potentially be a future source for low cost power, physicists must be able to analyze the magnetic field that confines the burning plasma. While the magnetic field can be described as a vector field, traditional techniques for analyzing the field's topology cannot be used because of its Hamiltonian nature. In this paper we describe a technique developed as a collaboration between physicists and computer scientists that determines the topology of a toroidal magnetic field using fieldlines with near minimal lengths. More specifically, we analyze the Poincaré map of the sampled fieldlines in a Poincaré section including identifying critical points and other topological features of interest to physicists. The technique has been deployed into an interactive parallel visualization tool which physicists are using to gain new insight into simulations of magnetically confined burning plasmas.

Correlation between topological structure and its properties in dynamic singular vector fields.

PubMed

Vasilev, Vasyl; Soskin, Marat

2016-04-20

A new technique for establishment of topology measurements for static and dynamic singular vector fields is elaborated. It is based on precise measurement of the 3D landscape of ellipticity distribution for a checked singular optical field with C points on the tops of ellipticity hills. Vector fields possess three-component topology: areas with right-hand (RH) and left-hand (LH) ellipses, and delimiting those L lines as the singularities of handedness. The azimuth map of polarization ellipses is common for both RH and LH ellipses of vector fields and do not feel L lines. The strict rules were confirmed experimentally, which define the connection between the sign of underlying optical vortices and morphological parameters of upper-lying C points. Percolation phenomena explain their realization in-between singular vector fields and long duration of their chains of 10³  s order.

Topological sound in active-liquid metamaterials

NASA Astrophysics Data System (ADS)

Souslov, Anton; van Zuiden, Benjamin C.; Bartolo, Denis; Vitelli, Vincenzo

2017-11-01

Liquids composed of self-propelled particles have been experimentally realized using molecular, colloidal or macroscopic constituents. These active liquids can flow spontaneously even in the absence of an external drive. Unlike spontaneous active flow, the propagation of density waves in confined active liquids is not well explored. Here, we exploit a mapping between density waves on top of a chiral flow and electrons in a synthetic gauge field to lay out design principles for artificial structures termed topological active metamaterials. We design metamaterials that break time-reversal symmetry using lattices composed of annular channels filled with a spontaneously flowing active liquid. Such active metamaterials support topologically protected sound modes that propagate unidirectionally, without backscattering, along either sample edges or domain walls and despite overdamped particle dynamics. Our work illustrates how parity-symmetry breaking in metamaterial structure combined with microscopic irreversibility of active matter leads to novel functionalities that cannot be achieved using only passive materials.

Discovery of stable skyrmionic state in ferroelectric nanocomposites

NASA Astrophysics Data System (ADS)

Nahas, Y.; Prokhorenko, S.; Louis, L.; Gui, Z.; Kornev, I.; Bellaiche, L.

2015-10-01

Non-coplanar swirling field textures, or skyrmions, are now widely recognized as objects of both fundamental interest and technological relevance. So far, skyrmions were amply investigated in magnets, where due to the presence of chiral interactions, these topological objects were found to be intrinsically stabilized. Ferroelectrics on the other hand, lacking such chiral interactions, were somewhat left aside in this quest. Here we demonstrate, via the use of a first-principles-based framework, that skyrmionic configuration of polarization can be extrinsically stabilized in ferroelectric nanocomposites. The interplay between the considered confined geometry and the dipolar interaction underlying the ferroelectric phase instability induces skyrmionic configurations. The topological structure of the obtained electrical skyrmion can be mapped onto the topology of domain-wall junctions. Furthermore, the stabilized electrical skyrmion can be as small as a few nanometers, thus revealing prospective skyrmion-based applications of ferroelectric nanocomposites.

Topodynamics of metastable brains

NASA Astrophysics Data System (ADS)

Tozzi, Arturo; Peters, James F.; Fingelkurts, Andrew A.; Fingelkurts, Alexander A.; Marijuán, Pedro C.

2017-07-01

The brain displays both the anatomical features of a vast amount of interconnected topological mappings as well as the functional features of a nonlinear, metastable system at the edge of chaos, equipped with a phase space where mental random walks tend towards lower energetic basins. Nevertheless, with the exception of some advanced neuro-anatomic descriptions and present-day connectomic research, very few studies have been addressing the topological path of a brain embedded or embodied in its external and internal environment. Herein, by using new formal tools derived from algebraic topology, we provide an account of the metastable brain, based on the neuro-scientific model of Operational Architectonics of brain-mind functioning. We introduce a ;topodynamic; description that shows how the relationships among the countless intertwined spatio-temporal levels of brain functioning can be assessed in terms of projections and mappings that take place on abstract structures, equipped with different dimensions, curvatures and energetic constraints. Such a topodynamical approach, apart from providing a biologically plausible model of brain function that can be operationalized, is also able to tackle the issue of a long-standing dichotomy: it throws indeed a bridge between the subjective, immediate datum of the naïve complex of sensations and mentations and the objective, quantitative, data extracted from experimental neuro-scientific procedures. Importantly, it opens the door to a series of new predictions and future directions of advancement for neuroscientific research.

Steenrod homotopy

NASA Astrophysics Data System (ADS)

Melikhov, Sergey A.

2009-06-01

Steenrod homotopy theory is a natural framework for doing algebraic topology on general spaces in terms of algebraic topology of polyhedra; or from a different viewpoint, it studies the topology of the \\lim^1 functor (for inverse sequences of groups). This paper is primarily concerned with the case of compacta, in which Steenrod homotopy coincides with strong shape. An attempt is made to simplify the foundations of the theory and to clarify and improve some of its major results. With geometric tools such as Milnor's telescope compactification, comanifolds (=mock bundles), and the Pontryagin-Thom construction, new simple proofs are obtained for results by Barratt-Milnor, Geoghegan-Krasinkiewicz, Dydak, Dydak-Segal, Krasinkiewicz-Minc, Cathey, Mittag-Leffler-Bourbaki, Fox, Eda-Kawamura, Edwards-Geoghegan, Jussila, and for three unpublished results by Shchepin. An error in Lisitsa's proof of the `Hurewicz theorem in Steenrod homotopy' is corrected. It is shown that over compacta, R.H. Fox's overlayings are equivalent to I.M. James' uniform covering maps. Other results include: \\bullet A morphism between inverse sequences of countable (possibly non-Abelian) groups that induces isomorphisms on \\lim and \\lim^1 is invertible in the pro-category. This implies the `Whitehead theorem in Steenrod homotopy', thereby answering two questions of Koyama. \\bullet If X is an LC_{n-1}-compactum, n\\ge 1, then its n-dimensional Steenrod homotopy classes are representable by maps S^n\\to\

Equivalence between the Arquès-Walsh sequence formula and the number of connected Feynman diagrams for every perturbation order in the fermionic many-body problem

NASA Astrophysics Data System (ADS)

Castro, E.

2018-02-01

From the perturbative expansion of the exact Green function, an exact counting formula is derived to determine the number of different types of connected Feynman diagrams. This formula coincides with the Arquès-Walsh sequence formula in the rooted map theory, supporting the topological connection between Feynman diagrams and rooted maps. A classificatory summing-terms approach is used, in connection to discrete mathematical theory.

An efficient approach to the travelling salesman problem using self-organizing maps.

PubMed

Vieira, Frederico Carvalho; Dória Neto, Adrião Duarte; Costa, José Alfredo Ferreira

2003-04-01

This paper presents an approach to the well-known Travelling Salesman Problem (TSP) using Self-Organizing Maps (SOM). The SOM algorithm has interesting topological information about its neurons configuration on cartesian space, which can be used to solve optimization problems. Aspects of initialization, parameters adaptation, and complexity analysis of the proposed SOM based algorithm are discussed. The results show an average deviation of 3.7% from the optimal tour length for a set of 12 TSP instances.

Efficient morse decompositions of vector fields.

PubMed

Chen, Guoning; Mischaikow, Konstantin; Laramee, Robert S; Zhang, Eugene

2008-01-01

Existing topology-based vector field analysis techniques rely on the ability to extract the individual trajectories such as fixed points, periodic orbits, and separatrices that are sensitive to noise and errors introduced by simulation and interpolation. This can make such vector field analysis unsuitable for rigorous interpretations. We advocate the use of Morse decompositions, which are robust with respect to perturbations, to encode the topological structures of a vector field in the form of a directed graph, called a Morse connection graph (MCG). While an MCG exists for every vector field, it need not be unique. Previous techniques for computing MCG's, while fast, are overly conservative and usually results in MCG's that are too coarse to be useful for the applications. To address this issue, we present a new technique for performing Morse decomposition based on the concept of tau-maps, which typically provides finer MCG's than existing techniques. Furthermore, the choice of tau provides a natural tradeoff between the fineness of the MCG's and the computational costs. We provide efficient implementations of Morse decomposition based on tau-maps, which include the use of forward and backward mapping techniques and an adaptive approach in constructing better approximations of the images of the triangles in the meshes used for simulation.. Furthermore, we propose the use of spatial tau-maps in addition to the original temporal tau-maps. These techniques provide additional trade-offs between the quality of the MCGs and the speed of computation. We demonstrate the utility of our technique with various examples in the plane and on surfaces including engine simulation data sets.

From the currency rate quotations onto strings and brane world scenarios

NASA Astrophysics Data System (ADS)

Horváth, D.; Pincak, R.

2012-11-01

In the paper, we study the projections of the real exchange rate dynamics onto the string-like topology. Our approach is inspired by the contemporary movements in the string theory. The string map of data is defined here by the boundary conditions, characteristic length, real valued and the method of redistribution of information. As a practical matter, this map represents the detrending and data standardization procedure. We introduced maps onto 1-end-point and 2-end-point open strings that satisfy the Dirichlet and Neumann boundary conditions. The questions of the choice of extra-dimensions, symmetries, duality and ways to the partial compactification are discussed. Subsequently, we pass to higher dimensional and more complex objects. The 2D-Brane was suggested which incorporated bid-ask spreads. Polarization by the spread was considered which admitted analyzing arbitrage opportunities on the market where transaction costs are taken into account. The model of the rotating string which naturally yields calculation of angular momentum is suitable for tracking of several currency pairs. The systematic way which allows one suggest more structured maps suitable for a simultaneous study of several currency pairs was analyzed by means of the Gâteaux generalized differential calculus. The effect of the string and brane maps on test data was studied by comparing their mean statistical characteristics. The study revealed notable differences between topologies. We review the dependence on the characteristic string length, mean fluctuations and properties of the intra-string statistics. The study explores the coupling of the string amplitude and volatility. The possible utilizations of the string theory approach in financial markets are slight.

Magnetic End States in a Strongly Interacting One-Dimensional Topological Kondo Insulator

DOE PAGES

Lobos, Alejandro M.; Dobry, Ariel O.; Galitski, Victor

2015-05-22

Topological Kondo insulators are strongly correlated materials where itinerant electrons hybridize with localized spins, giving rise to a topologically nontrivial band structure. Here, we use nonperturbative bosonization and renormalization-group techniques to study theoretically a one-dimensional topological Kondo insulator, described as a Kondo-Heisenberg model, where the Heisenberg spin-1/2 chain is coupled to a Hubbard chain through a Kondo exchange interaction in the p-wave channel (i.e., a strongly correlated version of the prototypical Tamm-Schockley model).We derive and solve renormalization-group equations at two-loop order in the Kondo parameter, and find that, at half filling, the charge degrees of freedom in the Hubbard chainmore » acquire a Mott gap, even in the case of a noninteracting conduction band (Hubbard parameter U = 0). Furthermore, at low enough temperatures, the system maps onto a spin-1/2 ladder with local ferromagnetic interactions along the rungs, effectively locking the spin degrees of freedom into a spin-1 chain with frozen charge degrees of freedom. This structure behaves as a spin-1 Haldane chain, a prototypical interacting topological spin model, and features two magnetic spin-1/2 end states for chains with open boundary conditions. In conclusion, our analysis allows us to derive an insightful connection between topological Kondo insulators in one spatial dimension and the well-known physics of the Haldane chain, showing that the ground state of the former is qualitatively different from the predictions of the naive mean-field theory.« less

Live-cell topology assessment of URG7, MRP6{sub 102} and SP-C using glycosylatable green fluorescent protein in mammalian cells

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

Lee, Hunsang; Lara, Patricia; Ostuni, Angela

2014-08-08

Highlights: • Glycosylatable GFP (gGFP) is developed for the use in mammalian cells. • gGFP selectively loses its fluorescence upon N-linked glycosylation in the ER lumen. • Differential fluorescence/glycosylation pattern probes membrane protein topology. • Membrane topology of URG7, MRP6{sub 102}, and SP-C was determined by gGFP tagging in vivo. - Abstract: Experimental tools to determine membrane topology of a protein are rather limited in higher eukaryotic organisms. Here, we report the use of glycosylatable GFP (gGFP) as a sensitive and versatile membrane topology reporter in mammalian cells. gGFP selectively loses its fluorescence upon N-linked glycosylation in the ER lumen.more » Thus, positive fluorescence signal assigns location of gGFP to the cytosol whereas no fluorescence signal and a glycosylated status of gGFP map the location of gGFP to the ER lumen. By using mammalian gGFP, the membrane topology of disease-associated membrane proteins, URG7, MRP6{sub 102}, SP-C(Val) and SP-C(Leu) was confirmed. URG7 is partially targeted to the ER, and inserted in C{sub in} form. MRP6{sub 102} and SP-C(Leu/Val) are inserted into the membrane in C{sub out} form. A minor population of untargeted SP-C is removed by proteasome dependent quality control system.« less

Horseshoes in a Chaotic System with Only One Stable Equilibrium

NASA Astrophysics Data System (ADS)

Huan, Songmei; Li, Qingdu; Yang, Xiao-Song

To confirm the numerically demonstrated chaotic behavior in a chaotic system with only one stable equilibrium reported by Wang and Chen, we resort to Poincaré map technique and present a rigorous computer-assisted verification of horseshoe chaos by virtue of topological horseshoes theory.

Automatic Correction Algorithm of Hyfrology Feature Attribute in National Geographic Census

NASA Astrophysics Data System (ADS)

Li, C.; Guo, P.; Liu, X.

2017-09-01

A subset of the attributes of hydrologic features data in national geographic census are not clear, the current solution to this problem was through manual filling which is inefficient and liable to mistakes. So this paper proposes an automatic correction algorithm of hydrologic features attribute. Based on the analysis of the structure characteristics and topological relation, we put forward three basic principles of correction which include network proximity, structure robustness and topology ductility. Based on the WJ-III map workstation, we realize the automatic correction of hydrologic features. Finally, practical data is used to validate the method. The results show that our method is highly reasonable and efficient.

Effective equilibrium picture in the x y model with exponentially correlated noise

NASA Astrophysics Data System (ADS)

Paoluzzi, Matteo; Marconi, Umberto Marini Bettolo; Maggi, Claudio

2018-02-01

We study the effect of exponentially correlated noise on the x y model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time τ , indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.

Exact folded-band chaotic oscillator.

PubMed

Corron, Ned J; Blakely, Jonathan N

2012-06-01

An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

Effective equilibrium picture in the xy model with exponentially correlated noise.

PubMed

Paoluzzi, Matteo; Marconi, Umberto Marini Bettolo; Maggi, Claudio

2018-02-01

We study the effect of exponentially correlated noise on the xy model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time τ, indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.

Conformal Nets II: Conformal Blocks

NASA Astrophysics Data System (ADS)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Automatic Aircraft Structural Topology Generation for Multidisciplinary Optimization and Weight Estimation

NASA Technical Reports Server (NTRS)

Sensmeier, Mark D.; Samareh, Jamshid A.

2005-01-01

An approach is proposed for the application of rapid generation of moderate-fidelity structural finite element models of air vehicle structures to allow more accurate weight estimation earlier in the vehicle design process. This should help to rapidly assess many structural layouts before the start of the preliminary design phase and eliminate weight penalties imposed when actual structure weights exceed those estimated during conceptual design. By defining the structural topology in a fully parametric manner, the structure can be mapped to arbitrary vehicle configurations being considered during conceptual design optimization. A demonstration of this process is shown for two sample aircraft wing designs.

Investigation of the resistive switching in AgxAsS2 layer by conductive AFM

NASA Astrophysics Data System (ADS)

Zhang, Bo; Kutalek, Petr; Knotek, Petr; Hromadko, Ludek; Macak, Jan M.; Wagner, Tomas

2016-09-01

In this paper, a study of resistive switching in AgxAsS2 layer, based on a utilization of conductive atomic force microscope (AFM), is reported. As the result of biasing, two distinct regions were created on the surface (the conductive region and non-conductive region). Both were analysed from the spread current maps. The volume change, corresponding to the growth of Ag particles, was derived from the topological maps, recorded simultaneously with the current maps. Based on the results, a model explaining the mechanism of the Ag particle and Ag filament formation was proposed from the distribution of charge carriers and Ag ions.

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Topological Schemas of Memory Spaces.

PubMed

Babichev, Andrey; Dabaghian, Yuri A

2018-01-01

Hippocampal cognitive map-a neuronal representation of the spatial environment-is widely discussed in the computational neuroscience literature for decades. However, more recent studies point out that hippocampus plays a major role in producing yet another cognitive framework-the memory space-that incorporates not only spatial, but also non-spatial memories. Unlike the cognitive maps, the memory spaces, broadly understood as "networks of interconnections among the representations of events," have not yet been studied from a theoretical perspective. Here we propose a mathematical approach that allows modeling memory spaces constructively, as epiphenomena of neuronal spiking activity and thus to interlink several important notions of cognitive neurophysiology. First, we suggest that memory spaces have a topological nature-a hypothesis that allows treating both spatial and non-spatial aspects of hippocampal function on equal footing. We then model the hippocampal memory spaces in different environments and demonstrate that the resulting constructions naturally incorporate the corresponding cognitive maps and provide a wider context for interpreting spatial information. Lastly, we propose a formal description of the memory consolidation process that connects memory spaces to the Morris' cognitive schemas-heuristic representations of the acquired memories, used to explain the dynamics of learning and memory consolidation in a given environment. The proposed approach allows evaluating these constructs as the most compact representations of the memory space's structure.

Communication Characterization and Optimization of Applications Using Topology-Aware Task Mapping on Large Supercomputers

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

Sreepathi, Sarat; D'Azevedo, Eduardo; Philip, Bobby

On large supercomputers, the job scheduling systems may assign a non-contiguous node allocation for user applications depending on available resources. With parallel applications using MPI (Message Passing Interface), the default process ordering does not take into account the actual physical node layout available to the application. This contributes to non-locality in terms of physical network topology and impacts communication performance of the application. In order to mitigate such performance penalties, this work describes techniques to identify suitable task mapping that takes the layout of the allocated nodes as well as the application's communication behavior into account. During the first phasemore » of this research, we instrumented and collected performance data to characterize communication behavior of critical US DOE (United States - Department of Energy) applications using an augmented version of the mpiP tool. Subsequently, we developed several reordering methods (spectral bisection, neighbor join tree etc.) to combine node layout and application communication data for optimized task placement. We developed a tool called mpiAproxy to facilitate detailed evaluation of the various reordering algorithms without requiring full application executions. This work presents a comprehensive performance evaluation (14,000 experiments) of the various task mapping techniques in lowering communication costs on Titan, the leadership class supercomputer at Oak Ridge National Laboratory.« less

Structure-Function Network Mapping and Its Assessment via Persistent Homology

PubMed Central

2017-01-01

Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal. We demonstrate that our approach can uncover the direct and indirect structural paths for predicting functional connectivity, and our network similarity measure outperforms other currently available methods. We systematically validate our approach with (1) a comparison of regularized vs. non-regularized procedures, (2) a null model of the degree-preserving random rewired structural matrix, (3) different network types (binary vs. weighted matrices), and (4) different brain parcellation schemes (low vs. high resolutions). Finally, we evaluate the scalability of our method with relatively large matrices (2514x2514) of structural and functional connectivity obtained from 12 healthy human subjects measured non-invasively while at rest. Our results reveal a nonlinear structure-function relationship, suggesting that the resting-state functional connectivity depends on direct structural connections, as well as relatively parsimonious indirect connections via polysynaptic pathways. PMID:28046127

Chaos and Fractals in C-K Map

NASA Astrophysics Data System (ADS)

Wang, Xing-Yuan; Liang, Qing-Yong; Meng, Juan

The characteristic of the fixed points of the Carotid-Kundalini (C-K) map is investigated and the boundary equation of the first bifurcation of the C-K map in the parameter plane is given. Based on the studies of the phase graph, the power spectrum, the correlation dimension and the Lyapunov exponents, the paper reveals the general features of the C-K map transforming from regularity. Meanwhile, using the periodic scanning technology proposed by Welstead and Cromer, a series of Mandelbrot-Julia (M-J) sets of the complex C-K map are constructed. The symmetry of M-J set and the topological inflexibility of distributing of periodic region in the Mandelbrot set are investigated. By founding the whole portray of Julia sets based on Mandelbrot set qualitatively, we find out that Mandelbrot sets contain abundant information of structure of Julia sets.

Connected components of irreducible maps and 1D quantum phases

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

Szehr, Oleg, E-mail: oleg.szehr@posteo.de; Wolf, Michael M., E-mail: wolf@ma.tum.de

We investigate elementary topological properties of sets of completely positive (CP) maps that arise in quantum Perron-Frobenius theory. We prove that the set of primitive CP maps of fixed Kraus rank is path-connected and we provide a complete classification of the connected components of irreducible CP maps at given Kraus rank and fixed peripheral spectrum in terms of a multiplicity index. These findings are then applied to analyse 1D quantum phases by studying equivalence classes of translational invariant matrix product states that correspond to the connected components of the respective CP maps. Our results extend the previously obtained picture inmore » that they do not require blocking of physical sites, they lead to analytic paths, and they allow us to decompose into ergodic components and to study the breaking of translational symmetry.« less

Interval data clustering using self-organizing maps based on adaptive Mahalanobis distances.

PubMed

Hajjar, Chantal; Hamdan, Hani

2013-10-01

The self-organizing map is a kind of artificial neural network used to map high dimensional data into a low dimensional space. This paper presents a self-organizing map for interval-valued data based on adaptive Mahalanobis distances in order to do clustering of interval data with topology preservation. Two methods based on the batch training algorithm for the self-organizing maps are proposed. The first method uses a common Mahalanobis distance for all clusters. In the second method, the algorithm starts with a common Mahalanobis distance per cluster and then switches to use a different distance per cluster. This process allows a more adapted clustering for the given data set. The performances of the proposed methods are compared and discussed using artificial and real interval data sets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Aerostructural Shape and Topology Optimization of Aircraft Wings

NASA Astrophysics Data System (ADS)

James, Kai

A series of novel algorithms for performing aerostructural shape and topology optimization are introduced and applied to the design of aircraft wings. An isoparametric level set method is developed for performing topology optimization of wings and other non-rectangular structures that must be modeled using a non-uniform, body-fitted mesh. The shape sensitivities are mapped to computational space using the transformation defined by the Jacobian of the isoparametric finite elements. The mapped sensitivities are then passed to the Hamilton-Jacobi equation, which is solved on a uniform Cartesian grid. The method is derived for several objective functions including mass, compliance, and global von Mises stress. The results are compared with SIMP results for several two-dimensional benchmark problems. The method is also demonstrated on a three-dimensional wingbox structure subject to fixed loading. It is shown that the isoparametric level set method is competitive with the SIMP method in terms of the final objective value as well as computation time. In a separate problem, the SIMP formulation is used to optimize the structural topology of a wingbox as part of a larger MDO framework. Here, topology optimization is combined with aerodynamic shape optimization, using a monolithic MDO architecture that includes aerostructural coupling. The aerodynamic loads are modeled using a three-dimensional panel method, and the structural analysis makes use of linear, isoparametric, hexahedral elements. The aerodynamic shape is parameterized via a set of twist variables representing the jig twist angle at equally spaced locations along the span of the wing. The sensitivities are determined analytically using a coupled adjoint method. The wing is optimized for minimum drag subject to a compliance constraint taken from a 2 g maneuver condition. The results from the MDO algorithm are compared with those of a sequential optimization procedure in order to quantify the benefits of the MDO approach. While the sequentially optimized wing exhibits a nearly-elliptical lift distribution, the MDO design seeks to push a greater portion of the load toward the root, thus reducing the structural deflection, and allowing for a lighter structure. By exploiting this trade-off, the MDO design achieves a 42% lower drag than the sequential result.

Direct Bio-printing with Heterogeneous Topology Design.

PubMed

Ahsan, Amm Nazmul; Xie, Ruinan; Khoda, Bashir

2017-01-01

Bio-additive manufacturing is a promising tool to fabricate porous scaffold structures for expediting the tissue regeneration processes. Unlike the most traditional bulk material objects, the microstructures of tissue and organs are mostly highly anisotropic, heterogeneous, and porous in nature. However, modelling the internal heterogeneity of tissues/organs structures in the traditional CAD environment is difficult and oftentimes inaccurate. Besides, the de facto STL conversion of bio-models introduces loss of information and piles up more errors in each subsequent step (build orientation, slicing, tool-path planning) of the bio-printing process plan. We are proposing a topology based scaffold design methodology to accurately represent the heterogeneous internal architecture of tissues/organs. An image analysis technique is used that digitizes the topology information contained in medical images of tissues/organs. A weighted topology reconstruction algorithm is implemented to represent the heterogeneity with parametric functions. The parametric functions are then used to map the spatial material distribution. The generated information is directly transferred to the 3D bio-printer and heterogeneous porous tissue scaffold structure is manufactured without STL file. The proposed methodology is implemented to verify the effectiveness of the approach and the designed example structure is bio-fabricated with a deposition based bio-additive manufacturing system.

Diversity of Knot Solitons in Liquid Crystals Manifested by Linking of Preimages in Torons and Hopfions

NASA Astrophysics Data System (ADS)

Ackerman, Paul J.; Smalyukh, Ivan I.

2017-01-01

Topological solitons are knots in continuous physical fields classified by nonzero Hopf index values. Despite arising in theories that span many branches of physics, from elementary particles to condensed matter and cosmology, they remain experimentally elusive and poorly understood. We introduce a method of experimental and numerical analysis of such localized structures in liquid crystals that, similar to the mathematical Hopf maps, relates all points of the medium's order parameter space to their closed-loop preimages within the three-dimensional solitons. We uncover a surprisingly large diversity of naturally occurring and laser-generated topologically nontrivial solitons with differently knotted nematic fields, which previously have not been realized in theories and experiments alike. We discuss the implications of the liquid crystal's nonpolar nature on the knot soliton topology and how the medium's chirality, confinement, and elastic anisotropy help to overcome the constraints of the Hobart-Derrick theorem, yielding static three-dimensional solitons without or with additional defects. Our findings will establish chiral nematics as a model system for experimental exploration of topological solitons and may impinge on understanding of such nonsingular field configurations in other branches of physics, as well as may lead to technological applications.

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

A topological approach unveils system invariances and broken symmetries in the brain.

PubMed

Tozzi, Arturo; Peters, James F

2016-05-01

Symmetries are widespread invariances underscoring countless systems, including the brain. A symmetry break occurs when the symmetry is present at one level of observation but is hidden at another level. In such a general framework, a concept from algebraic topology, namely, the Borsuk-Ulam theorem (BUT), comes into play and sheds new light on the general mechanisms of nervous symmetries. The BUT tells us that we can find, on an n-dimensional sphere, a pair of opposite points that have the same encoding on an n - 1 sphere. This mapping makes it possible to describe both antipodal points with a single real-valued vector on a lower dimensional sphere. Here we argue that this topological approach is useful for the evaluation of hidden nervous symmetries. This means that symmetries can be found when evaluating the brain in a proper dimension, although they disappear (are hidden or broken) when we evaluate the same brain only one dimension lower. In conclusion, we provide a topological methodology for the evaluation of the most general features of brain activity, i.e., the symmetries, cast in a physical/biological fashion that has the potential to be operationalized. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees.

PubMed

Aberer, Andre J; Stamatakis, Alexandros; Ronquist, Fredrik

2016-01-01

Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees using primitive transformations or re-mappings of old branch lengths. This reduces acceptance rates and presumably slows down convergence and mixing. Here, we explore branch proposals that do not rely on old branch lengths but instead are based on approximations of the conditional posterior. Using a diverse set of empirical data sets, we show that most conditional branch posteriors can be accurately approximated via a [Formula: see text] distribution. We empirically determine the relationship between the logarithmic conditional posterior density, its derivatives, and the characteristics of the branch posterior. We use these relationships to derive an independence sampler for proposing branches with an acceptance ratio of ~90% on most data sets. This proposal samples branches between 2× and 3× more efficiently than traditional proposals with respect to the effective sample size per unit of runtime. We also compare the performance of standard topology proposals with hybrid proposals that use the new independence sampler to update those branches that are most affected by the topological change. Our results show that hybrid proposals can sometimes noticeably decrease the number of generations necessary for topological convergence. Inconsistent performance gains indicate that branch updates are not the limiting factor in improving topological convergence for the currently employed set of proposals. However, our independence sampler might be essential for the construction of novel tree proposals that apply more radical topology changes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Circles-in-the-sky searches and observable cosmic topology in a flat universe

NASA Astrophysics Data System (ADS)

Mota, B.; Rebouças, M. J.; Tavakol, R.

2010-05-01

In a universe with a detectable nontrivial spatial topology, the last scattering surface contains pairs of matching circles with the same distribution of temperature fluctuations—the so-called circles-in-the-sky. Searches for nearly antipodal circles-in-the-sky in maps of cosmic microwave background radiation have so far been unsuccessful. This negative outcome, along with recent theoretical results concerning the detectability of nearly flat compact topologies, is sufficient to exclude a detectable nontrivial topology for most observers in very nearly flat positively and negatively curved universes, whose total matter-energy density satisfies 0<|Ωtot-1|≲10-5. Here, we investigate the consequences of these searches for observable nontrivial topologies if the Universe turns out to be exactly flat (Ωtot=1). We demonstrate that in this case, the conclusions deduced from such searches can be radically different. We show that, although there is no characteristic topological scale in the flat manifolds, for all multiply-connected orientable flat manifolds, it is possible to directly study the action of the holonomies in order to obtain a general upper bound on the angle that characterizes the deviation from antipodicity of pairs of matching circles associated with the shortest closed geodesic. This bound is valid for all observers and all possible values of the compactification length parameters. We also show that in a flat universe, there are observers for whom the circles-in-the-sky searches already undertaken are insufficient to exclude the possibility of a detectable nontrivial spatial topology. It is remarkable how such small variations in the spatial curvature of the Universe, which are effectively indistinguishable geometrically, can have such a drastic effect on the detectability of cosmic topology. Another important outcome of our results is that they offer a framework with which to make statistical inferences from future circles-in-the-sky searches on whether the Universe is exactly flat.

Interfacing 1990 US Census TIGER map files with New S graphics software. [Topologically Integrated Geographic Encoding and Referencing (TIGER)

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

Rizzardi, M.; Mohr, M.S.; Merrill, D.W.

1992-07-01

In 1990, the United States Bureau of the Census released detailed geographic base files known as TIGER/Line (Topologically Integrated Geographic Encoding and Referencing) which contain detail on the physical features and census tract boundaries of every county in the United States. The TIGER database is attractive for two reasons. First, it is publicly available through the Bureau of the Census on tape or cd-rom for a minimal fee. Second, it contains 24 billion characters of data which describe geographic features of interest to the Census Bureau such as coastlines, hydrography, transportation networks, political boundaries, etc. Unfortunately, the large TIGER databasemore » only provides raw alphanumeric data; no utility software, graphical or otherwise, is included. On the other hand New S, a popular statistical software package by AT T, has easily operated functions that permit advanced graphics in conjunction with data analysis. New S has the ability to plot contours, lines, segments, and points. However, of special interest is the New S function map and its options. Using the map function, which requires polygons as input, census tracts can be quickly selected, plotted, shaded, etc. New S graphics combined with the TIGER database has obvious potential. This paper reports on our efforts to use the TIGER map files with New S, especially to construct census tract maps of counties. While census tract boundaries are inherently polygonal, they are not organized as such in the TIGER database. This conversion of the TIGER line'' format into New S polygon/polyline'' format is one facet of the work reported here. Also we discuss the selection and extraction of auxiliary geographic information from TIGER files for graphical display using New S.« less

Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells.

PubMed

Lee, Song-Yi; Kang, Myeong-Gyun; Shin, Sanghee; Kwak, Chulhwan; Kwon, Taejoon; Seo, Jeong Kon; Kim, Jong-Seo; Rhee, Hyun-Woo

2017-03-15

The inner mitochondrial membrane (IMM) proteome plays a central role in maintaining mitochondrial physiology and cellular metabolism. Various important biochemical reactions such as oxidative phosphorylation, metabolite production, and mitochondrial biogenesis are conducted by the IMM proteome, and mitochondria-targeted therapeutics have been developed for IMM proteins, which is deeply related for various human metabolic diseases including cancer and neurodegenerative diseases. However, the membrane topology of the IMM proteome remains largely unclear because of the lack of methods to evaluate it in live cells in a high-throughput manner. In this article, we reveal the in vivo topological direction of 135 IMM proteins, using an in situ-generated radical probe with genetically targeted peroxidase (APEX). Owing to the short lifetime of phenoxyl radicals generated in situ by submitochondrial targeted APEX and the impermeability of the IMM to small molecules, the solvent-exposed tyrosine residues of both the matrix and intermembrane space (IMS) sides of IMM proteins were exclusively labeled with the radical probe in live cells by Matrix-APEX and IMS-APEX, respectively and identified by mass spectrometry. From this analysis, we confirmed 58 IMM protein topologies and we could determine the topological direction of 77 IMM proteins whose topology at the IMM has not been fully characterized. We also found several IMM proteins (e.g., LETM1 and OXA1) whose topological information should be revised on the basis of our results. Overall, our identification of structural information on the mitochondrial inner-membrane proteome can provide valuable insights for the architecture and connectome of the IMM proteome in live cells.

Neural Representation of Spatial Topology in the Rodent Hippocampus

PubMed Central

Chen, Zhe; Gomperts, Stephen N.; Yamamoto, Jun; Wilson, Matthew A.

2014-01-01

Pyramidal cells in the rodent hippocampus often exhibit clear spatial tuning in navigation. Although it has been long suggested that pyramidal cell activity may underlie a topological code rather than a topographic code, it remains unclear whether an abstract spatial topology can be encoded in the ensemble spiking activity of hippocampal place cells. Using a statistical approach developed previously, we investigate this question and related issues in greater details. We recorded ensembles of hippocampal neurons as rodents freely foraged in one and two-dimensional spatial environments, and we used a “decode-to-uncover” strategy to examine the temporally structured patterns embedded in the ensemble spiking activity in the absence of observed spatial correlates during periods of rodent navigation or awake immobility. Specifically, the spatial environment was represented by a finite discrete state space. Trajectories across spatial locations (“states”) were associated with consistent hippocampal ensemble spiking patterns, which were characterized by a state transition matrix. From this state transition matrix, we inferred a topology graph that defined the connectivity in the state space. In both one and two-dimensional environments, the extracted behavior patterns from the rodent hippocampal population codes were compared against randomly shuffled spike data. In contrast to a topographic code, our results support the efficiency of topological coding in the presence of sparse sample size and fuzzy space mapping. This computational approach allows us to quantify the variability of ensemble spiking activity, to examine hippocampal population codes during off-line states, and to quantify the topological complexity of the environment. PMID:24102128

Chaotic attractors of relaxation oscillators

NASA Astrophysics Data System (ADS)

Guckenheimer, John; Wechselberger, Martin; Young, Lai-Sang

2006-03-01

We develop a general technique for proving the existence of chaotic attractors for three-dimensional vector fields with two time scales. Our results connect two important areas of dynamical systems: the theory of chaotic attractors for discrete two-dimensional Henon-like maps and geometric singular perturbation theory. Two-dimensional Henon-like maps are diffeomorphisms that limit on non-invertible one-dimensional maps. Wang and Young formulated hypotheses that suffice to prove the existence of chaotic attractors in these families. Three-dimensional singularly perturbed vector fields have return maps that are also two-dimensional diffeomorphisms limiting on one-dimensional maps. We describe a generic mechanism that produces folds in these return maps and demonstrate that the Wang-Young hypotheses are satisfied. Our analysis requires a careful study of the convergence of the return maps to their singular limits in the Ck topology for k >= 3. The theoretical results are illustrated with a numerical study of a variant of the forced van der Pol oscillator.

Computerized mappings of the cerebral cortex: a multiresolution flattening method and a surface-based coordinate system

NASA Technical Reports Server (NTRS)

Drury, H. A.; Van Essen, D. C.; Anderson, C. H.; Lee, C. W.; Coogan, T. A.; Lewis, J. W.

1996-01-01

We present a new method for generating two-dimensional maps of the cerebral cortex. Our computerized, two-stage flattening method takes as its input any well-defined representation of a surface within the three-dimensional cortex. The first stage rapidly converts this surface to a topologically correct two-dimensional map, without regard for the amount of distortion introduced. The second stage reduces distortions using a multiresolution strategy that makes gross shape changes on a coarsely sampled map and further shape refinements on progressively finer resolution maps. We demonstrate the utility of this approach by creating flat maps of the entire cerebral cortex in the macaque monkey and by displaying various types of experimental data on such maps. We also introduce a surface-based coordinate system that has advantages over conventional stereotaxic coordinates and is relevant to studies of cortical organization in humans as well as non-human primates. Together, these methods provide an improved basis for quantitative studies of individual variability in cortical organization.

Design of an image encryption scheme based on a multiple chaotic map

NASA Astrophysics Data System (ADS)

Tong, Xiao-Jun

2013-07-01

In order to solve the problem that chaos is degenerated in limited computer precision and Cat map is the small key space, this paper presents a chaotic map based on topological conjugacy and the chaotic characteristics are proved by Devaney definition. In order to produce a large key space, a Cat map named block Cat map is also designed for permutation process based on multiple-dimensional chaotic maps. The image encryption algorithm is based on permutation-substitution, and each key is controlled by different chaotic maps. The entropy analysis, differential analysis, weak-keys analysis, statistical analysis, cipher random analysis, and cipher sensibility analysis depending on key and plaintext are introduced to test the security of the new image encryption scheme. Through the comparison to the proposed scheme with AES, DES and Logistic encryption methods, we come to the conclusion that the image encryption method solves the problem of low precision of one dimensional chaotic function and has higher speed and higher security.

US GeoData

USGS Publications Warehouse

,

1992-01-01

US GeoData tapes are computer tapes which contain cartographic data in digital form. The 1:2,000,000-scale data are available in two forms. The graphic form can be used to generate computer-plotted maps. The content and scale of the maps can be varied to meet your needs. The topologically-structured form of US GeoData is suitable for input to geographic information systems for use in spatial analysis and geographic studies. Both forms must be used in conjunction with appropriate software. US GeoData tapes offer convenience, accuracy, flexibility, and cost effectiveness to many map users. Business, industry, and government users who are involved in network planning and analysis, transportation, demography, land use, or any activity where data can be related to, or plotted on a map will find US GeoData a valuable resource.

Predicting perturbation patterns from the topology of biological networks.

PubMed

Santolini, Marc; Barabási, Albert-László

2018-06-20

High-throughput technologies, offering an unprecedented wealth of quantitative data underlying the makeup of living systems, are changing biology. Notably, the systematic mapping of the relationships between biochemical entities has fueled the rapid development of network biology, offering a suitable framework to describe disease phenotypes and predict potential drug targets. However, our ability to develop accurate dynamical models remains limited, due in part to the limited knowledge of the kinetic parameters underlying these interactions. Here, we explore the degree to which we can make reasonably accurate predictions in the absence of the kinetic parameters. We find that simple dynamically agnostic models are sufficient to recover the strength and sign of the biochemical perturbation patterns observed in 87 biological models for which the underlying kinetics are known. Surprisingly, a simple distance-based model achieves 65% accuracy. We show that this predictive power is robust to topological and kinetic parameter perturbations, and we identify key network properties that can increase up to 80% the recovery rate of the true perturbation patterns. We validate our approach using experimental data on the chemotactic pathway in bacteria, finding that a network model of perturbation spreading predicts with ∼80% accuracy the directionality of gene expression and phenotype changes in knock-out and overproduction experiments. These findings show that the steady advances in mapping out the topology of biochemical interaction networks opens avenues for accurate perturbation spread modeling, with direct implications for medicine and drug development.

Classical impurities and boundary Majorana zero modes in quantum chains

NASA Astrophysics Data System (ADS)

Müller, Markus; Nersesyan, Alexander A.

2016-09-01

We study the response of classical impurities in quantum Ising chains. The Z2 degeneracy they entail renders the existence of two decoupled Majorana modes at zero energy, an exact property of a finite system at arbitrary values of its bulk parameters. We trace the evolution of these modes across the transition from the disordered phase to the ordered one and analyze the concomitant qualitative changes of local magnetic properties of an isolated impurity. In the disordered phase, the two ground states differ only close to the impurity, and they are related by the action of an explicitly constructed quasi-local operator. In this phase the local transverse spin susceptibility follows a Curie law. The critical response of a boundary impurity is logarithmically divergent and maps to the two-channel Kondo problem, while it saturates for critical bulk impurities, as well as in the ordered phase. The results for the Ising chain translate to the related problem of a resonant level coupled to a 1d p-wave superconductor or a Peierls chain, whereby the magnetic order is mapped to topological order. We find that the topological phase always exhibits a continuous impurity response to local fields as a result of the level repulsion of local levels from the boundary Majorana zero mode. In contrast, the disordered phase generically features a discontinuous magnetization or charging response. This difference constitutes a general thermodynamic fingerprint of topological order in phases with a bulk gap.

A case study in bifurcation theory

NASA Astrophysics Data System (ADS)

Khmou, Youssef

This short paper is focused on the bifurcation theory found in map functions called evolution functions that are used in dynamical systems. The most well-known example of discrete iterative function is the logistic map that puts into evidence bifurcation and chaotic behavior of the topology of the logistic function. We propose a new iterative function based on Lorentizan function and its generalized versions, based on numerical study, it is found that the bifurcation of the Lorentzian function is of second-order where it is characterized by the absence of chaotic region.

Robot Competence Development by Constructive Learning

NASA Astrophysics Data System (ADS)

Meng, Q.; Lee, M. H.; Hinde, C. J.

This paper presents a constructive learning approach for developing sensor-motor mapping in autonomous systems. The system’s adaptation to environment changes is discussed and three methods are proposed to deal with long term and short term changes. The proposed constructive learning allows autonomous systems to develop network topology and adjust network parameters. The approach is supported by findings from psychology and neuroscience especially during infants cognitive development at early stages. A growing radial basis function network is introduced as a computational substrate for sensory-motor mapping learning. Experiments are conducted on a robot eye/hand coordination testbed and results show the incremental development of sensory-motor mapping and its adaptation to changes such as in tool-use.

Robot Competence Development by Constructive Learning

NASA Astrophysics Data System (ADS)

Meng, Q.; Lee, M. H.; Hinde, C. J.

This paper presents a constructive learning approach for developing sensor-motor mapping in autonomous systems. The system's adaptation to environment changes is discussed and three methods are proposed to deal with long term and short term changes. The proposed constructive learning allows autonomous systems to develop network topology and adjust network parameters. The approach is supported by findings from psychology and neuroscience especially during infants cognitive development at early stages. A growing radial basis function network is introduced as a computational substrate for sensory-motor mapping learning. Experiments are conducted on a robot eye/hand coordination testbed and results show the incremental development of sensory-motor mapping and its adaptation to changes such as in tool-use.

Multiwavelength Characteristics of Microflares

NASA Astrophysics Data System (ADS)

Poduval, Bala; Schmelz, J. T.

2016-10-01

We present the multiwavelength characteristic of microflare detected in the SDO/AIA and IRIS images using the Automated Microevent-finding Code (AMC). We have catalogued independent events with information such as location on the disk, size, lifetime and peak flux, and obtained their frequency distribution. We mapped these events to other wavelengths, using their location information, to study their associated features, and infer the temperature characteristics and evolution. Moreover, we obtained their magnetic topologies by mapping the microflare locations on to the HMI photospheric magnetic field synoptic maps. Further, we analyzed the filtered brightness profiles and light curves for each event to classify them. Finally, we carried out a differential emission measure (DEM) analysis to study their temperature characteristics.

A cognitive robotic system based on the Soar cognitive architecture for mobile robot navigation, search, and mapping missions

NASA Astrophysics Data System (ADS)

Hanford, Scott D.

Most unmanned vehicles used for civilian and military applications are remotely operated or are designed for specific applications. As these vehicles are used to perform more difficult missions or a larger number of missions in remote environments, there will be a great need for these vehicles to behave intelligently and autonomously. Cognitive architectures, computer programs that define mechanisms that are important for modeling and generating domain-independent intelligent behavior, have the potential for generating intelligent and autonomous behavior in unmanned vehicles. The research described in this presentation explored the use of the Soar cognitive architecture for cognitive robotics. The Cognitive Robotic System (CRS) has been developed to integrate software systems for motor control and sensor processing with Soar for unmanned vehicle control. The CRS has been tested using two mobile robot missions: outdoor navigation and search in an indoor environment. The use of the CRS for the outdoor navigation mission demonstrated that a Soar agent could autonomously navigate to a specified location while avoiding obstacles, including cul-de-sacs, with only a minimal amount of knowledge about the environment. While most systems use information from maps or long-range perceptual capabilities to avoid cul-de-sacs, a Soar agent in the CRS was able to recognize when a simple approach to avoiding obstacles was unsuccessful and switch to a different strategy for avoiding complex obstacles. During the indoor search mission, the CRS autonomously and intelligently searches a building for an object of interest and common intersection types. While searching the building, the Soar agent builds a topological map of the environment using information about the intersections the CRS detects. The agent uses this topological model (along with Soar's reasoning, planning, and learning mechanisms) to make intelligent decisions about how to effectively search the building. Once the object of interest has been detected, the Soar agent uses the topological map to make decisions about how to efficiently return to the location where the mission began. Additionally, the CRS can send an email containing step-by-step directions using the intersections in the environment as landmarks that describe a direct path from the mission's start location to the object of interest. The CRS has displayed several characteristics of intelligent behavior, including reasoning, planning, learning, and communication of learned knowledge, while autonomously performing two missions. The CRS has also demonstrated how Soar can be integrated with common robotic motor and perceptual systems that complement the strengths of Soar for unmanned vehicles and is one of the few systems that use perceptual systems such as occupancy grid, computer vision, and fuzzy logic algorithms with cognitive architectures for robotics. The use of these perceptual systems to generate symbolic information about the environment during the indoor search mission allowed the CRS to use Soar's planning and learning mechanisms, which have rarely been used by agents to control mobile robots in real environments. Additionally, the system developed for the indoor search mission represents the first known use of a topological map with a cognitive architecture on a mobile robot. The ability to learn both a topological map and production rules allowed the Soar agent used during the indoor search mission to make intelligent decisions and behave more efficiently as it learned about its environment. While the CRS has been applied to two different missions, it has been developed with the intention that it be extended in the future so it can be used as a general system for mobile robot control. The CRS can be expanded through the addition of new sensors and sensor processing algorithms, development of Soar agents with more production rules, and the use of new architectural mechanisms in Soar.

Using Pipe Cleaners to Bring the Tree of Life to Life

ERIC Educational Resources Information Center

Halverson, Kristy L.

2010-01-01

Phylogenetic trees, such as the "Tree of Life," are commonly found in biology textbooks and are often used in teaching. Because students often struggle to understand these diagrams, I developed a simple, inexpensive classroom model. Made of pipe cleaners, it is easily manipulated to rotate branches, compare topologies, map complete lineages,…

Automated Network Mapping and Topology Verification

DTIC Science & Technology

2016-06-01

collection of information includes amplifying data about the networked devices such as hardware details, logical addressing schemes, 7 operating ...collection of information, including suggestions for reducing this burden, to Washington headquarters Services, Directorate for Information Operations ...maximum 200 words) The current military reliance on computer networks for operational missions and administrative duties makes network

Cleavage Mapping the Topology of Protein Folding Intermediates

DTIC Science & Technology

1995-03-13

1993). 29. Nakano, T., Antonino , L. C, Fox, R. O. & Fink, A. L. Effect of proline mutation on the stability and kinetics of folding of...Biochem. 62, 653-683. Nakano, T., Antonino , L. C., Fox, R. O., & Fink, A. L. (1993) Biochemistry 32, 2534-2541. Nozaki, Y. (1972) Methods Enzymol. 26, 43

An investigation of condition mapping and plot proportion calculation issues

Treesearch

Demetrios Gatziolis

2007-01-01

A systematic examination of Forest Inventory and Analysis condition data collected under the annual inventory protocol in the Pacific Northwest region between 2000 and 2004 revealed the presence of errors both in condition topology and plot proportion computations. When plots were compiled to generate population estimates, proportion errors were found to cause...

Cochlea segmentation using iterated random walks with shape prior

NASA Astrophysics Data System (ADS)

Ruiz Pujadas, Esmeralda; Kjer, Hans Martin; Vera, Sergio; Ceresa, Mario; González Ballester, Miguel Ángel

2016-03-01

Cochlear implants can restore hearing to deaf or partially deaf patients. In order to plan the intervention, a model from high resolution µCT images is to be built from accurate cochlea segmentations and then, adapted to a patient-specific model. Thus, a precise segmentation is required to build such a model. We propose a new framework for segmentation of µCT cochlear images using random walks where a region term is combined with a distance shape prior weighted by a confidence map to adjust its influence according to the strength of the image contour. Then, the region term can take advantage of the high contrast between the background and foreground and the distance prior guides the segmentation to the exterior of the cochlea as well as to less contrasted regions inside the cochlea. Finally, a refinement is performed preserving the topology using a topological method and an error control map to prevent boundary leakage. We tested the proposed approach with 10 datasets and compared it with the latest techniques with random walks and priors. The experiments suggest that this method gives promising results for cochlea segmentation.

An automated 3D reconstruction method of UAV images

NASA Astrophysics Data System (ADS)

Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

2015-10-01

In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

Topological Frequency Conversion in Strongly Driven Quantum Systems

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

Martin, Ivar; Refael, Gil; Halperin, Bertrand

When a physical system is subjected to a strong external multi-frequency drive, its dynamics can be conveniently represented in the multi-dimensional Floquet lattice. The number of the Floquet lattice dimensions equals the number of irrationally-related drive frequencies, and the evolution occurs in response to a built-in effective \\electric" field, whose components are proportional to the corresponding drive frequencies. The mapping allows to engineer and study temporal analogs of many real-space phenomena. Here we focus on the specifc example of a two-level system under two-frequency drive that induces topologically nontrivial band structure in the 2D Floquet space. The observable consequence ofmore » such construction is quantized pumping of energy between the sources with frequencies w 1 and w 2. Finally, when the system is initialized into a Floquet band with the Chern number C, the pumping occurs at the rate P 12 = – P 21 = ( C/2π)hw 1w 2, an exact counterpart of the transverse current in a conventional topological insulator.« less

Observation of Polarization Vortices in Momentum Space

NASA Astrophysics Data System (ADS)

Zhang, Yiwen; Chen, Ang; Liu, Wenzhe; Hsu, Chia Wei; Wang, Bo; Guan, Fang; Liu, Xiaohan; Shi, Lei; Lu, Ling; Zi, Jian

2018-05-01

The vortex, a fundamental topological excitation featuring the in-plane winding of a vector field, is important in various areas such as fluid dynamics, liquid crystals, and superconductors. Although commonly existing in nature, vortices were observed exclusively in real space. Here, we experimentally observed momentum-space vortices as the winding of far-field polarization vectors in the first Brillouin zone of periodic plasmonic structures. Using homemade polarization-resolved momentum-space imaging spectroscopy, we mapped out the dispersion, lifetime, and polarization of all radiative states at the visible wavelengths. The momentum-space vortices were experimentally identified by their winding patterns in the polarization-resolved isofrequency contours and their diverging radiative quality factors. Such polarization vortices can exist robustly on any periodic systems of vectorial fields, while they are not captured by the existing topological band theory developed for scalar fields. Our work provides a new way for designing high-Q plasmonic resonances, generating vector beams, and studying topological photonics in the momentum space.

Verification of LANDSAT imagery for morphametric and topological studies of drainage basins in a section of the western plateau of Sao Paulo State: Tiete-Aguapei watershed. M.S. Thesis; [Brazil

NASA Technical Reports Server (NTRS)

Parada, N. D. J. (Principal Investigator); Camargo, J. C. G.

1982-01-01

The potential of using LANDSAT MSS imagery for morphometric and topological studies of drainage basins was verified. Using Tiete and Aguapei watershed (Western Plateau) as the test site because of its homogeneous landscape. Morphometric variables collected for ten drainage basins include: circularity index; river density; drainage density; topographic texture; areal and index length; basin parameter; and main river length 1st order and 2nd order channel length. The topographical variables determined were: order; magnitude; bifuraction ratio; weighted bifuraction ratio; number of segments; number of linking; trajectory length; and topological diameter. Data were collected on topographical maps at the scale of 1:250,000 and 1:59,000 and on LANDSAT imagery at the scale of 1:250,000. The results which were summarized on tables for further analysis, show that LANDSAT imagery can supply the lack of topographic charts for drainage studies.

Reconceiving the hippocampal map as a topological template

PubMed Central

Dabaghian, Yuri; Brandt, Vicky L; Frank, Loren M

2014-01-01

The role of the hippocampus in spatial cognition is incontrovertible yet controversial. Place cells, initially thought to be location-specifiers, turn out to respond promiscuously to a wide range of stimuli. Here we test the idea, which we have recently demonstrated in a computational model, that the hippocampal place cells may ultimately be interested in a space's topological qualities (its connectivity) more than its geometry (distances and angles); such higher-order functioning would be more consistent with other known hippocampal functions. We recorded place cell activity in rats exploring morphing linear tracks that allowed us to dissociate the geometry of the track from its topology. The resulting place fields preserved the relative sequence of places visited along the track but did not vary with the metrical features of the track or the direction of the rat's movement. These results suggest a reinterpretation of previous studies and new directions for future experiments. DOI: http://dx.doi.org/10.7554/eLife.03476.001 PMID:25141375

Making sense of sparse rating data in collaborative filtering via topographic organization of user preference patterns.

PubMed

Polcicová, Gabriela; Tino, Peter

2004-01-01

We introduce topographic versions of two latent class models (LCM) for collaborative filtering. Latent classes are topologically organized on a square grid. Topographic organization of latent classes makes orientation in rating/preference patterns captured by the latent classes easier and more systematic. The variation in film rating patterns is modelled by multinomial and binomial distributions with varying independence assumptions. In the first stage of topographic LCM construction, self-organizing maps with neural field organized according to the LCM topology are employed. We apply our system to a large collection of user ratings for films. The system can provide useful visualization plots unveiling user preference patterns buried in the data, without loosing potential to be a good recommender model. It appears that multinomial distribution is most adequate if the model is regularized by tight grid topologies. Since we deal with probabilistic models of the data, we can readily use tools from probability and information theories to interpret and visualize information extracted by our system.

Topological Frequency Conversion in Strongly Driven Quantum Systems

DOE PAGES

Martin, Ivar; Refael, Gil; Halperin, Bertrand

2017-10-16

When a physical system is subjected to a strong external multi-frequency drive, its dynamics can be conveniently represented in the multi-dimensional Floquet lattice. The number of the Floquet lattice dimensions equals the number of irrationally-related drive frequencies, and the evolution occurs in response to a built-in effective \\electric" field, whose components are proportional to the corresponding drive frequencies. The mapping allows to engineer and study temporal analogs of many real-space phenomena. Here we focus on the specifc example of a two-level system under two-frequency drive that induces topologically nontrivial band structure in the 2D Floquet space. The observable consequence ofmore » such construction is quantized pumping of energy between the sources with frequencies w 1 and w 2. Finally, when the system is initialized into a Floquet band with the Chern number C, the pumping occurs at the rate P 12 = – P 21 = ( C/2π)hw 1w 2, an exact counterpart of the transverse current in a conventional topological insulator.« less

Developing an eBook-Integrated High-Fidelity Mobile App Prototype for Promoting Child Motor Skills and Taxonomically Assessing Children's Emotional Responses Using Face and Sound Topology.

PubMed

Brown, William; Liu, Connie; John, Rita Marie; Ford, Phoebe

2014-01-01

Developing gross and fine motor skills and expressing complex emotion is critical for child development. We introduce "StorySense", an eBook-integrated mobile app prototype that can sense face and sound topologies and identify movement and expression to promote children's motor skills and emotional developmental. Currently, most interactive eBooks on mobile devices only leverage "low-motor" interaction (i.e. tapping or swiping). Our app senses a greater breath of motion (e.g. clapping, snapping, and face tracking), and dynamically alters the storyline according to physical responses in ways that encourage the performance of predetermined motor skills ideal for a child's gross and fine motor development. In addition, our app can capture changes in facial topology, which can later be mapped using the Facial Action Coding System (FACS) for later interpretation of emotion. StorySense expands the human computer interaction vocabulary for mobile devices. Potential clinical applications include child development, physical therapy, and autism.

Observation of Polarization Vortices in Momentum Space.

PubMed

Zhang, Yiwen; Chen, Ang; Liu, Wenzhe; Hsu, Chia Wei; Wang, Bo; Guan, Fang; Liu, Xiaohan; Shi, Lei; Lu, Ling; Zi, Jian

2018-05-04

The vortex, a fundamental topological excitation featuring the in-plane winding of a vector field, is important in various areas such as fluid dynamics, liquid crystals, and superconductors. Although commonly existing in nature, vortices were observed exclusively in real space. Here, we experimentally observed momentum-space vortices as the winding of far-field polarization vectors in the first Brillouin zone of periodic plasmonic structures. Using homemade polarization-resolved momentum-space imaging spectroscopy, we mapped out the dispersion, lifetime, and polarization of all radiative states at the visible wavelengths. The momentum-space vortices were experimentally identified by their winding patterns in the polarization-resolved isofrequency contours and their diverging radiative quality factors. Such polarization vortices can exist robustly on any periodic systems of vectorial fields, while they are not captured by the existing topological band theory developed for scalar fields. Our work provides a new way for designing high-Q plasmonic resonances, generating vector beams, and studying topological photonics in the momentum space.

Effect of strong disorder on three-dimensional chiral topological insulators: Phase diagrams, maps of the bulk invariant, and existence of topological extended bulk states

NASA Astrophysics Data System (ADS)

Song, Juntao; Fine, Carolyn; Prodan, Emil

2014-11-01

The effect of strong disorder on chiral-symmetric three-dimensional lattice models is investigated via analytical and numerical methods. The phase diagrams of the models are computed using the noncommutative winding number, as functions of disorder strength and model's parameters. The localized/delocalized characteristic of the quantum states is probed with level statistics analysis. Our study reconfirms the accurate quantization of the noncommutative winding number in the presence of strong disorder, and its effectiveness as a numerical tool. Extended bulk states are detected above and below the Fermi level, which are observed to undergo the so-called "levitation and pair annihilation" process when the system is driven through a topological transition. This suggests that the bulk invariant is carried by these extended states, in stark contrast with the one-dimensional case where the extended states are completely absent and the bulk invariant is carried by the localized states.

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.

Sensor-Motor Maps for Describing Linear Reflex Composition in Hopping.

PubMed

Schumacher, Christian; Seyfarth, André

2017-01-01

In human and animal motor control several sensory organs contribute to a network of sensory pathways modulating the motion depending on the task and the phase of execution to generate daily motor tasks such as locomotion. To better understand the individual and joint contribution of reflex pathways in locomotor tasks, we developed a neuromuscular model that describes hopping movements. In this model, we consider the influence of proprioceptive length (LFB), velocity (VFB) and force feedback (FFB) pathways of a leg extensor muscle on hopping stability, performance and efficiency (metabolic effort). Therefore, we explore the space describing the blending of the monosynaptic reflex pathway gains. We call this reflex parameter space a sensor-motor map . The sensor-motor maps are used to visualize the functional contribution of sensory pathways in multisensory integration. We further evaluate the robustness of these sensor-motor maps to changes in tendon elasticity, body mass, segment length and ground compliance. The model predicted that different reflex pathway compositions selectively optimize specific hopping characteristics (e.g., performance and efficiency). Both FFB and LFB were pathways that enable hopping. FFB resulted in the largest hopping heights, LFB enhanced hopping efficiency and VFB had the ability to disable hopping. For the tested case, the topology of the sensor-motor maps as well as the location of functionally optimal compositions were invariant to changes in system designs (tendon elasticity, body mass, segment length) or environmental parameters (ground compliance). Our results indicate that different feedback pathway compositions may serve different functional roles. The topology of the sensor-motor map was predicted to be robust against changes in the mechanical system design indicating that the reflex system can use different morphological designs, which does not apply for most robotic systems (for which the control often follows a specific design). Consequently, variations in body mechanics are permitted with consistent compositions of sensory feedback pathways. Given the variability in human body morphology, such variations are highly relevant for human motor control.

Do rivers really obey power-laws? Using continuous high resolution measurements to define bankfull channel and evaluate downstream hydraulic-scaling over large changes in drainage area

NASA Astrophysics Data System (ADS)

Scher, C.; Tennant, C.; Larsen, L.; Bellugi, D. G.

2016-12-01

Advances in remote-sensing technology allow for cost-effective, accurate, high-resolution mapping of river-channel topography and shallow aquatic bathymetry over large spatial scales. A combination of near-infrared and green spectra airborne laser swath mapping was used to map river channel bathymetry and watershed geometry over 90+ river-kilometers (75-1175 km2) of the Greys River in Wyoming. The day of flight wetted channel was identified from green LiDAR returns, and more than 1800 valley-bottom cross-sections were extracted at regular 50-m intervals. The bankfull channel geometry was identified using a "watershed-based" algorithm that incrementally filled local minima to a "spill" point, thereby constraining areas of local convergence and delineating all the potential channels along the cross-section for each distinct "spill stage." Multiple potential channels in alluvial floodplains and lack of clearly defined channel banks in bedrock reaches challenge identification of the bankfull channel based on topology alone. Here we combine a variety of topological measures, geometrical considerations, and stage levels to define a stage-dependent bankfull channel geometry, and compare the results with day of flight wetted channel data. Initial results suggest that channel hydraulic geometry and basin hydrology power-law scaling may not accurately capture downstream channel adjustments for rivers draining complex mountain topography.

How MAP kinase modules function as robust, yet adaptable, circuits.

PubMed

Tian, Tianhai; Harding, Angus

2014-01-01

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.

How MAP kinase modules function as robust, yet adaptable, circuits

PubMed Central

Tian, Tianhai; Harding, Angus

2014-01-01

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution. PMID:25483189

Reverse bifurcation and fractal of the compound logistic map

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Liang, Qingyong

2008-07-01

The nature of the fixed points of the compound logistic map is researched and the boundary equation of the first bifurcation of the map in the parameter space is given out. Using the quantitative criterion and rule of chaotic system, the paper reveal the general features of the compound logistic map transforming from regularity to chaos, the following conclusions are shown: (1) chaotic patterns of the map may emerge out of double-periodic bifurcation and (2) the chaotic crisis phenomena and the reverse bifurcation are found. At the same time, we analyze the orbit of critical point of the compound logistic map and put forward the definition of Mandelbrot-Julia set of compound logistic map. We generalize the Welstead and Cromer's periodic scanning technology and using this technology construct a series of Mandelbrot-Julia sets of compound logistic map. We investigate the symmetry of Mandelbrot-Julia set and study the topological inflexibility of distributing of period region in the Mandelbrot set, and finds that Mandelbrot set contain abundant information of structure of Julia sets by founding the whole portray of Julia sets based on Mandelbrot set qualitatively.

Stability and perturbations of countable Markov maps

NASA Astrophysics Data System (ADS)

Jordan, Thomas; Munday, Sara; Sahlsten, Tuomas

2018-04-01

Let T and , , be countable Markov maps such that the branches of converge pointwise to the branches of T, as . We study the stability of various quantities measuring the singularity (dimension, Hölder exponent etc) of the topological conjugacy between and T when . This is a well-understood problem for maps with finitely-many branches, and the quantities are stable for small ɛ, that is, they converge to their expected values if . For the infinite branch case their stability might be expected to fail, but we prove that even in the infinite branch case the quantity is stable under some natural regularity assumptions on and T (under which, for instance, the Hölder exponent of fails to be stable). Our assumptions apply for example in the case of Gauss map, various Lüroth maps and accelerated Manneville-Pomeau maps when varying the parameter α. For the proof we introduce a mass transportation method from the cusp that allows us to exploit thermodynamical ideas from the finite branch case. Dedicated to the memory of Bernd O Stratmann

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

PubMed Central

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-01-01

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root mean square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases. PMID:22417139

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-06-14

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.

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.

Topological mappings of video and audio data.

PubMed

Fyfe, Colin; Barbakh, Wesam; Ooi, Wei Chuan; Ko, Hanseok

2008-12-01

We review a new form of self-organizing map which is based on a nonlinear projection of latent points into data space, identical to that performed in the Generative Topographic Mapping (GTM).(1) But whereas the GTM is an extension of a mixture of experts, this model is an extension of a product of experts.(2) We show visualisation and clustering results on a data set composed of video data of lips uttering 5 Korean vowels. Finally we note that we may dispense with the probabilistic underpinnings of the product of experts and derive the same algorithm as a minimisation of mean squared error between the prototypes and the data. This leads us to suggest a new algorithm which incorporates local and global information in the clustering. Both ot the new algorithms achieve better results than the standard Self-Organizing Map.

Area of Stochastic Scrape-Off Layer for a Single-Null Divertor Tokamak Using Simple Map

NASA Astrophysics Data System (ADS)

Fisher, Tiffany; Verma, Arun; Punjabi, Alkesh

1996-11-01

The magnetic topology of a single-null divertor tokamak is represented by Simple Map (Punjabi A, Verma A and Boozer A, Phys Rev Lett), 69, 3322 (1992) and J Plasma Phys, 52, 91 (1994). The Simple map is characterized by a single parameter k representing the toroidal asymmetry. The width of the stochastic scrape-off layer and its area varies with the map parameter k. We calculate the area of the stochastic scrape-off layer for different k's and obtain a parametric expression for the area in terms of k and y _LastGoodSurface(k). This work is supported by US DOE OFES. Tiffany Fisher is a HU CFRT Summer Fusion High school Workshop Scholar from New Bern High School in North Carolina. She is supported by NASA SHARP Plus Program.

Real topological entropy versus metric entropy for birational measure-preserving transformations

NASA Astrophysics Data System (ADS)

Abarenkova, N.; Anglès d'Auriac, J.-Ch.; Boukraa, S.; Maillard, J.-M.

2000-10-01

We consider a family of birational measure-preserving transformations of two complex variables, depending on one parameter for which simple rational expressions for the dynamical zeta function have been conjectured, together with an equality between the topological entropy and the logarithm of the Arnold complexity (divided by the number of iterations). Similar results have been obtained for the adaptation of these two concepts to dynamical systems of real variables, yielding to introduce a “real topological entropy” and a “real Arnold complexity”. We try to compare, here, the Kolmogorov-Sinai metric entropy and this real Arnold complexity, or real topological entropy, on this particular example of a one-parameter dependent birational transformation of two variables. More precisely, we analyze, using an infinite precision calculation, the Lyapunov characteristic exponents for various values of the parameter of the birational transformation, in order to compare these results with the ones for the real Arnold complexity. We find a quite surprising result: for this very birational example, and, in fact, for a large set of birational measure-preserving mappings generated by involutions, the Lyapunov characteristic exponents seem to be equal to zero or, at least, extremely small, for all the orbits we have considered, and for all values of the parameter. Birational measure-preserving transformations, generated by involutions, could thus allow to better understand the difference between the topological description and the probabilistic description of discrete dynamical systems. Many birational measure-preserving transformations, generated by involutions, seem to provide examples of discrete dynamical systems which can be topologically chaotic while they are metrically almost quasi-periodic. Heuristically, this can be understood as a consequence of the fact that their orbits seem to form some kind of “transcendental foliation” of the two-dimensional space of variables.

Nonlinear functional approximation with networks using adaptive neurons

NASA Technical Reports Server (NTRS)

Tawel, Raoul

1992-01-01

A novel mathematical framework for the rapid learning of nonlinear mappings and topological transformations is presented. It is based on allowing the neuron's parameters to adapt as a function of learning. This fully recurrent adaptive neuron model (ANM) has been successfully applied to complex nonlinear function approximation problems such as the highly degenerate inverse kinematics problem in robotics.

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

PubMed

Chartier, Sylvain; Giguère, Gyslain; Langlois, Dominic

2009-01-01

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

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.

PubMed

Dorier, Julien; Goundaroulis, Dimos; Benedetti, Fabrizio; Stasiak, Andrzej

2018-05-02

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds. Knoto-ID is written in C ++ and includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID. julien.dorier@sib.swiss.

Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis

PubMed Central

Reuter, Martin; Wolter, Franz-Erich; Shenton, Martha; Niethammer, Marc

2009-01-01

This paper proposes the use of the surface based Laplace-Beltrami and the volumetric Laplace eigenvalues and -functions as shape descriptors for the comparison and analysis of shapes. These spectral measures are isometry invariant and therefore allow for shape comparisons with minimal shape pre-processing. In particular, no registration, mapping, or remeshing is necessary. The discriminatory power of the 2D surface and 3D solid methods is demonstrated on a population of female caudate nuclei (a subcortical gray matter structure of the brain, involved in memory function, emotion processing, and learning) of normal control subjects and of subjects with schizotypal personality disorder. The behavior and properties of the Laplace-Beltrami eigenvalues and -functions are discussed extensively for both the Dirichlet and Neumann boundary condition showing advantages of the Neumann vs. the Dirichlet spectra in 3D. Furthermore, topological analyses employing the Morse-Smale complex (on the surfaces) and the Reeb graph (in the solids) are performed on selected eigenfunctions, yielding shape descriptors, that are capable of localizing geometric properties and detecting shape differences by indirectly registering topological features such as critical points, level sets and integral lines of the gradient field across subjects. The use of these topological features of the Laplace-Beltrami eigenfunctions in 2D and 3D for statistical shape analysis is novel. PMID:20161035

Hippocampal Replay Captures the Unique Topological Structure of a Novel Environment

PubMed Central

Wu, Xiaojing

2014-01-01

Hippocampal place-cell replay has been proposed as a fundamental mechanism of learning and memory, which might support navigational learning and planning. An important hypothesis of relevance to these proposed functions is that the information encoded in replay should reflect the topological structure of experienced environments; that is, which places in the environment are connected with which others. Here we report several attributes of replay observed in rats exploring a novel forked environment that support the hypothesis. First, we observed that overlapping replays depicting divergent trajectories through the fork recruited the same population of cells with the same firing rates to represent the common portion of the trajectories. Second, replay tended to be directional and to flip the represented direction at the fork. Third, replay-associated sharp-wave–ripple events in the local field potential exhibited substructure that mapped onto the maze topology. Thus, the spatial complexity of our recording environment was accurately captured by replay: the underlying neuronal activities reflected the bifurcating shape, and both directionality and associated ripple structure reflected the segmentation of the maze. Finally, we observed that replays occurred rapidly after small numbers of experiences. Our results suggest that hippocampal replay captures learned information about environmental topology to support a role in navigation. PMID:24806672

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.

Topological features of the Sokolov integrable case on the Lie algebra so(3,1)

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

Novikov, D V

2014-08-31

The integrable Sokolov case on so(3,1){sup ⋆} is investigated. This is a Hamiltonian system with two degrees of freedom, in which the Hamiltonian and the additional integral are homogeneous polynomials of degrees 2 and 4, respectively. It is an interesting feature of this system that connected components of common level surfaces of the Hamiltonian and the additional integral turn out to be noncompact. The critical points of the moment map and their indices are found, the bifurcation diagram is constructed, and the topology of noncompact level surfaces is determined, that is, the closures of solutions of the Sokolov system on so(3,1)more » are described. Bibliography: 24 titles.« less

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

Imprints of spherical nontrivial topologies on the cosmic microwave background.

PubMed

Niarchou, Anastasia; Jaffe, Andrew

2007-08-24

The apparent low power in the cosmic microwave background (CMB) temperature anisotropy power spectrum derived from the Wilkinson Microwave Anisotropy Probe motivated us to consider the possibility of a nontrivial topology. We focus on simple spherical multiconnected manifolds and discuss their implications for the CMB in terms of the power spectrum, maps, and the correlation matrix. We perform a Bayesian model comparison against the fiducial best-fit cold dark matter model with a cosmological constant based both on the power spectrum and the correlation matrix to assess their statistical significance. We find that the first-year power spectrum shows a slight preference for the truncated cube space, but the three-year data show no evidence for any of these spaces.

Valley switch in a graphene superlattice due to pseudo-Andreev reflection

NASA Astrophysics Data System (ADS)

Beenakker, C. W. J.; Gnezdilov, N. V.; Dresselhaus, E.; Ostroukh, V. P.; Herasymenko, Y.; Adagideli, I.; Tworzydło, J.

2018-06-01

Dirac electrons in graphene have a valley degree of freedom that is being explored as a carrier of information. In that context of "valleytronics" one seeks to coherently manipulate the valley index. Here, we show that reflection from a superlattice potential can provide a valley switch: Electrons approaching a pristine-graphene-superlattice-graphene interface near normal incidence are reflected in the opposite valley. We identify the topological origin of this valley switch, by mapping the problem onto that of Andreev reflection from a topological superconductor, with the electron-hole degree of freedom playing the role of the valley index. The valley switch is ideal at a symmetry point of the superlattice potential, but remains close to 100% in a broad parameter range.

Optimal design of tunable phononic bandgap plates under equibiaxial stretch

NASA Astrophysics Data System (ADS)

Hedayatrasa, Saeid; Abhary, Kazem; Uddin, M. S.; Guest, James K.

2016-05-01

Design and application of phononic crystal (PhCr) acoustic metamaterials has been a topic with tremendous growth of interest in the last decade due to their promising capabilities to manipulate acoustic and elastodynamic waves. Phononic controllability of waves through a particular PhCr is limited only to the spectrums located within its fixed bandgap frequency. Hence the ability to tune a PhCr is desired to add functionality over its variable bandgap frequency or for switchability. Deformation induced bandgap tunability of elastomeric PhCr solids and plates with prescribed topology have been studied by other researchers. Principally the internal stress state and distorted geometry of a deformed phononic crystal plate (PhP) changes its effective stiffness and leads to deformation induced tunability of resultant modal band structure. Thus the microstructural topology of a PhP can be altered so that specific tunability features are met through prescribed deformation. In the present study novel tunable PhPs of this kind with optimized bandgap efficiency-tunability of guided waves are computationally explored and evaluated. Low loss transmission of guided waves throughout thin walled structures makes them ideal for fabrication of low loss ultrasound devices and structural health monitoring purposes. Various tunability targets are defined to enhance or degrade complete bandgaps of plate waves through macroscopic tensile deformation. Elastomeric hyperelastic material is considered which enables recoverable micromechanical deformation under tuning finite stretch. Phononic tunability through stable deformation of phononic lattice is specifically required and so any topology showing buckling instability under assumed deformation is disregarded. Nondominated sorting genetic algorithm (GA) NSGA-II is adopted for evolutionary multiobjective topology optimization of hypothesized tunable PhP with square symmetric unit-cell and relevant topologies are analyzed through finite element method. Following earlier studies by the authors, specialized GA algorithm, topology mapping, assessment and analysis techniques are employed to get feasible porous topologies of assumed thick PhP, efficiently.

Fixed Point Results for G-α-Contractive Maps with Application to Boundary Value Problems

PubMed Central

Roshan, Jamal Rezaei

2014-01-01

We unify the concepts of G-metric, metric-like, and b-metric to define new notion of generalized b-metric-like space and discuss its topological and structural properties. In addition, certain fixed point theorems for two classes of G-α-admissible contractive mappings in such spaces are obtained and some new fixed point results are derived in corresponding partially ordered space. Moreover, some examples and an application to the existence of a solution for the first-order periodic boundary value problem are provided here to illustrate the usability of the obtained results. PMID:24895655

Self-organizing adaptive map: autonomous learning of curves and surfaces from point samples.

PubMed

Piastra, Marco

2013-05-01

Competitive Hebbian Learning (CHL) (Martinetz, 1993) is a simple and elegant method for estimating the topology of a manifold from point samples. The method has been adopted in a number of self-organizing networks described in the literature and has given rise to related studies in the fields of geometry and computational topology. Recent results from these fields have shown that a faithful reconstruction can be obtained using the CHL method only for curves and surfaces. Within these limitations, these findings constitute a basis for defining a CHL-based, growing self-organizing network that produces a faithful reconstruction of an input manifold. The SOAM (Self-Organizing Adaptive Map) algorithm adapts its local structure autonomously in such a way that it can match the features of the manifold being learned. The adaptation process is driven by the defects arising when the network structure is inadequate, which cause a growth in the density of units. Regions of the network undergo a phase transition and change their behavior whenever a simple, local condition of topological regularity is met. The phase transition is eventually completed across the entire structure and the adaptation process terminates. In specific conditions, the structure thus obtained is homeomorphic to the input manifold. During the adaptation process, the network also has the capability to focus on the acquisition of input point samples in critical regions, with a substantial increase in efficiency. The behavior of the network has been assessed experimentally with typical data sets for surface reconstruction, including suboptimal conditions, e.g. with undersampling and noise. Copyright © 2012 Elsevier Ltd. All rights reserved.

Topology reduction in deep convolutional feature extraction networks

NASA Astrophysics Data System (ADS)

Wiatowski, Thomas; Grohs, Philipp; Bölcskei, Helmut

2017-08-01

Deep convolutional neural networks (CNNs) used in practice employ potentially hundreds of layers and 10,000s of nodes. Such network sizes entail significant computational complexity due to the large number of convolutions that need to be carried out; in addition, a large number of parameters needs to be learned and stored. Very deep and wide CNNs may therefore not be well suited to applications operating under severe resource constraints as is the case, e.g., in low-power embedded and mobile platforms. This paper aims at understanding the impact of CNN topology, specifically depth and width, on the network's feature extraction capabilities. We address this question for the class of scattering networks that employ either Weyl-Heisenberg filters or wavelets, the modulus non-linearity, and no pooling. The exponential feature map energy decay results in Wiatowski et al., 2017, are generalized to O(a-N), where an arbitrary decay factor a > 1 can be realized through suitable choice of the Weyl-Heisenberg prototype function or the mother wavelet. We then show how networks of fixed (possibly small) depth N can be designed to guarantee that ((1 - ɛ) · 100)% of the input signal's energy are contained in the feature vector. Based on the notion of operationally significant nodes, we characterize, partly rigorously and partly heuristically, the topology-reducing effects of (effectively) band-limited input signals, band-limited filters, and feature map symmetries. Finally, for networks based on Weyl-Heisenberg filters, we determine the prototype function bandwidth that minimizes - for fixed network depth N - the average number of operationally significant nodes per layer.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

PubMed

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

PubMed Central

DeBlasio, Stacy L.; Chavez, Juan D.; Alexander, Mariko M.; Ramsey, John; Eng, Jimmy K.; Mahoney, Jaclyn; Gray, Stewart M.; Bruce, James E.

2015-01-01

ABSTRACT Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection—hallmarks of host-pathogen interactions—were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. PMID:26656710

Magnetic Doppler imaging of the chemically peculiar star HD 125248

NASA Astrophysics Data System (ADS)

Rusomarov, N.; Kochukhov, O.; Ryabchikova, T.; Ilyin, I.

2016-04-01

Context. Intermediate-mass, chemically peculiar stars with strong magnetic fields provide an excellent opportunity to study the topology of their surface magnetic fields and the interplay between magnetic geometries and abundance inhomogeneities in the atmospheres of these stars. Aims: We reconstruct detailed maps of the surface magnetic field and abundance distributions for the magnetic Ap star HD 125248. Methods: We performed the analysis based on phase-resolved, four Stokes parameter spectropolarimetric observations obtained with the HARPSpol instrument. These data were interpreted with the help of magnetic Doppler imaging techniques and model atmospheres taking the effects of strong magnetic fields and nonsolar chemical composition into account. Results: We improved the atmospheric parameters of the star, Teff = 9850 ± 250 K and log g = 4.05 ± 0.10. We performed detailed abundance analysis, which confirmed that HD 125248 has abundances typical of other Ap stars, and discovered significant vertical stratification effects for the Fe II and Cr II ions. We computed LSD Stokes profiles using several line masks corresponding to Fe-peak and rare earth elements, and studied their behavior with rotational phase. Combining previous longitudinal field measurements with our own observations, we improved the rotational period of the star Prot = 9.29558 ± 0.00006 d. Magnetic Doppler imaging of HD 125248 showed that its magnetic field is mostly poloidal and quasi-dipolar with two large spots of different polarity and field strength. The chemical maps of Fe, Cr, Ce, Nd, Gd, and Ti show abundance contrasts of 0.9-3.5 dex. Among these elements, the Fe abundance map does not show high-contrast features. Cr is overabundant around the negative magnetic pole and has 3.5 dex abundance range. The rare earth elements and Ti are overabundant near the positive magnetic pole. Conclusions: The magnetic field of HD 125248 has strong deviations from the classical oblique dipole field geometry. A comparison of the magnetic field topology of HD 125248 with the results derived for other stars using four Stokes magnetic Doppler imaging suggests evidence that the field topology becomes simpler with increasing age. The abundance maps show weak correlation with magnetic field geometry, but they do not agree with the theoretical atomic diffusion calculations, which predict element accumulation in the horizontal field regions. Based on observations collected at the European Southern Observatory, Chile (ESO programs 088.D-0066, 090.D-0256).

Reconstruction of phase maps from the configuration of phase singularities in two-dimensional manifolds.

PubMed

Herlin, Antoine; Jacquemet, Vincent

2012-05-01

Phase singularity analysis provides a quantitative description of spiral wave patterns observed in chemical or biological excitable media. The configuration of phase singularities (locations and directions of rotation) is easily derived from phase maps in two-dimensional manifolds. The question arises whether one can construct a phase map with a given configuration of phase singularities. The existence of such a phase map is guaranteed provided that the phase singularity configuration satisfies a certain constraint associated with the topology of the supporting medium. This paper presents a constructive mathematical approach to numerically solve this problem in the plane and on the sphere as well as in more general geometries relevant to atrial anatomy including holes and a septal wall. This tool can notably be used to create initial conditions with a controllable spiral wave configuration for cardiac propagation models and thus help in the design of computer experiments in atrial electrophysiology.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics-innervated tissues.

PubMed

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M

2016-09-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could have important impacts on fundamental scientific and clinical studies, yet realization is hampered by a lack of effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and a submillisecond temporal resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multisite stimulation and mapping to actively manipulate the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics innervated tissues

PubMed Central

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M.

2016-01-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could impact broadly fundamental scientific and clinical studies, yet realization lacks effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and sub-millisecond time-resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues, and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multi-site stimulation and mapping to manipulate actively the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics. PMID:27347837

Pore configuration landscape of granular crystallization.

PubMed

Saadatfar, M; Takeuchi, H; Robins, V; Francois, N; Hiraoka, Y

2017-05-12

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Pore configuration landscape of granular crystallization

PubMed Central

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-01-01

Uncovering grain-scale mechanisms that underlie the disorder–order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics. PMID:28497794

Pore configuration landscape of granular crystallization

NASA Astrophysics Data System (ADS)

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-05-01

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution.

PubMed

Mozziconacci, Julien; Koszul, Romain

2015-08-21

The fine three-dimensional structure of the nucleosomal fiber has remained elusive to genome-wide chromosome conformation capture (3C) approaches. A new study mapping contacts at the single nucleosome level (Micro-C) reveals topological interacting domains along budding yeast chromosomes. These domains encompass one to five consecutive genes and are delimited by highly active promoters.

Can single molecule localization microscopy be used to map closely spaced RGD nanodomains?

PubMed Central

Nicovich, Philip R.; Soeriyadi, Alexander; Nieves, Daniel J.; Gooding, J. Justin; Gaus, Katharina

2017-01-01

Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers. We first determined the topology of the block copolymer with atomic force microscopy (AFM) and then imaged the localization of individual RGD peptides with direct stochastic optical reconstruction microscopy (dSTORM). To compare the data, we analyzed the dSTORM data with DBSCAN (density-based spatial clustering application with noise). The ligand distribution and polymer topology are not necessary identical since peptides may attach to the polymer outside the nanodomains and/or coupling and detection of peptides within the nanodomains is incomplete. We therefore performed simulations to explore the extent to which nanodomains could be mapped with dSTORM. We found that successful detection of nanodomains by dSTORM was influenced by the inter-domain spacing and the localization precision of individual fluorophores, and less by non-specific absorption of ligands to the substratum. For example, under our imaging conditions, DBSCAN identification of nanodomains spaced further than 50 nm apart was largely independent of background localisations, while nanodomains spaced closer than 50 nm required a localization precision of ~11 nm to correctly estimate the modal nearest neighbor distance (NDD) between nanodomains. We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision. PMID:28723958

Innovative High-Accuracy Lidar Bathymetric Technique for the Frequent Measurement of River Systems

NASA Astrophysics Data System (ADS)

Gisler, A.; Crowley, G.; Thayer, J. P.; Thompson, G. S.; Barton-Grimley, R. A.

2015-12-01

Lidar (light detection and ranging) provides absolute depth and topographic mapping capability compared to other remote sensing methods, which is useful for mapping rapidly changing environments such as riverine systems. Effectiveness of current lidar bathymetric systems is limited by the difficulty in unambiguously identifying backscattered lidar signals from the water surface versus the bottom, limiting their depth resolution to 0.3-0.5 m. Additionally these are large, bulky systems that are constrained to expensive aircraft-mounted platforms and use waveform-processing techniques requiring substantial computation time. These restrictions are prohibitive for many potential users. A novel lidar device has been developed that allows for non-contact measurements of water depth down to 1 cm with an accuracy and precision of < 1 cm by exploiting the polarization properties of the light-surface interaction. This system can transition seamlessly from ranging over land to shallow to deep water allowing for shoreline charting, measuring water volume, mapping bottom topology, and identifying submerged objects. The scalability of the technique opens up the ability for handheld or UAS-mounted lidar bathymetric systems, which provides for potential applications currently unavailable to the community. The high laser pulse repetition rate allows for very fine horizontal resolution while the photon-counting technique permits real-time depth measurement and object detection. The enhanced measurement capability, portability, scalability, and relatively low-cost creates the opportunity to perform frequent high-accuracy monitoring and measuring of aquatic environments which is crucial for understanding how rivers evolve over many timescales. Results from recent campaigns measuring water depth in flowing creeks and murky ponds will be presented which demonstrate that the method is not limited by rough water surfaces and can map underwater topology through moderately turbid water.

Innovative Technique for High-Accuracy Remote Monitoring of Surface Water

NASA Astrophysics Data System (ADS)

Gisler, A.; Barton-Grimley, R. A.; Thayer, J. P.; Crowley, G.

2016-12-01

Lidar (light detection and ranging) provides absolute depth and topographic mapping capability compared to other remote sensing methods, which is useful for mapping rapidly changing environments such as riverine systems and agricultural waterways. Effectiveness of current lidar bathymetric systems is limited by the difficulty in unambiguously identifying backscattered lidar signals from the water surface versus the bottom, limiting their depth resolution to 0.3-0.5 m. Additionally these are large, bulky systems that are constrained to expensive aircraft-mounted platforms and use waveform-processing techniques requiring substantial computation time. These restrictions are prohibitive for many potential users. A novel lidar device has been developed that allows for non-contact measurements of water depth down to 1 cm with an accuracy and precision of < 1 cm by exploiting the polarization properties of the light-surface interaction. This system can transition seamlessly from ranging over land to shallow to deep water allowing for shoreline charting, measuring water volume, mapping bottom topology, and identifying submerged objects. The scalability of the technique opens up the ability for handheld or UAS-mounted lidar bathymetric systems, which provides for potential applications currently unavailable to the community. The high laser pulse repetition rate allows for very fine horizontal resolution while the photon-counting technique permits real-time depth measurement and object detection. The enhanced measurement capability, portability, scalability, and relatively low-cost creates the opportunity to perform frequent high-accuracy monitoring and measuring of aquatic environments which is crucial for monitoring water resources on fast timescales. Results from recent campaigns measuring water depth in flowing creeks and murky ponds will be presented which demonstrate that the method is not limited by rough water surfaces and can map underwater topology through moderately turbid water.

Developing an eBook-Integrated High-Fidelity Mobile App Prototype for Promoting Child Motor Skills and Taxonomically Assessing Children’s Emotional Responses Using Face and Sound Topology

PubMed Central

Brown, William; Liu, Connie; John, Rita Marie; Ford, Phoebe

2014-01-01

Developing gross and fine motor skills and expressing complex emotion is critical for child development. We introduce “StorySense”, an eBook-integrated mobile app prototype that can sense face and sound topologies and identify movement and expression to promote children’s motor skills and emotional developmental. Currently, most interactive eBooks on mobile devices only leverage “low-motor” interaction (i.e. tapping or swiping). Our app senses a greater breath of motion (e.g. clapping, snapping, and face tracking), and dynamically alters the storyline according to physical responses in ways that encourage the performance of predetermined motor skills ideal for a child’s gross and fine motor development. In addition, our app can capture changes in facial topology, which can later be mapped using the Facial Action Coding System (FACS) for later interpretation of emotion. StorySense expands the human computer interaction vocabulary for mobile devices. Potential clinical applications include child development, physical therapy, and autism. PMID:25954336

Spatial Charge Inhomogeneity and Defect States in Topological Dirac Semimetal Thin Films

NASA Astrophysics Data System (ADS)

Edmonds, Mark; Collins, James; Hellerstedt, Jack; Yudhistira, Indra; Rodrigues, Joao Nuno Barbosa; Gomes, Lidia Carvalho; Adam, Shaffique; Fuhrer, Michael

Dirac materials are characterized by a charge neutrality point, where the system breaks into electron/hole puddles. In graphene, substrate disorder drives fluctuations in EF, necessitating ultra-clean substrates to observe Dirac point physics. Three-dimensional topological Dirac semimetals (TDS) obviate the substrate, and should show reduced EF fluctuations due to better metallic screening and higher dielectric constants. Yet, the local response of the charge carriers in a TDS to various perturbations has yet to be explored. Here we map the potential fluctuations in TDS 20nm Na3Bi films grown via MBE using scanning tunneling microscopy/spectroscopy. The potential fluctuations are significantly smaller than room temperature (ΔEF 5 meV = 60 K) and comparable to the highest quality graphene on h-BN; far smaller than graphene on SiO2,or the Dirac surface state of a topological insulator. This observation bodes well for exploration of Dirac point physics in TDS materials. Furthermore, surface Na vacancies show a bound resonance state close to the Dirac point with large spatial extent, a possible analogue to resonant impurities in graphene.

MAGNETIC TOPOLOGY OF A NAKED SUNSPOT: IS IT REALLY NAKED?

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

Sainz Dalda, A.; Vargas Dominguez, S.; Tarbell, T. D.

The high spatial, temporal, and spectral resolution achieved by Hinode instruments gives much better understanding of the behavior of some elusive solar features, such as pores and naked sunspots. Their fast evolution and, in some cases, their small sizes have made their study difficult. The moving magnetic features (MMFs) have been studied during the last 40 years. They have been always associated with sunspots, especially with the penumbra. However, a recent observation of a naked sunspot (one with no penumbra) has shown MMF activity. The authors of this reported observation expressed their reservations about the explanation given to the bipolarmore » MMF activity as an extension of the penumbral filaments into the moat. How can this type of MMF exist when a penumbra does not? In this Letter, we study the full magnetic and (horizontal) velocity topology of the same naked sunspot, showing how the existence of a magnetic field topology similar to that observed in sunspots can explain these MMFs, even when the intensity map of the naked sunspot does not show a penumbra.« less

Hyperbolic Harmonic Mapping for Surface Registration

PubMed Central

Shi, Rui; Zeng, Wei; Su, Zhengyu; Jiang, Jian; Damasio, Hanna; Lu, Zhonglin; Wang, Yalin; Yau, Shing-Tung; Gu, Xianfeng

2016-01-01

Automatic computation of surface correspondence via harmonic map is an active research field in computer vision, computer graphics and computational geometry. It may help document and understand physical and biological phenomena and also has broad applications in biometrics, medical imaging and motion capture inducstries. Although numerous studies have been devoted to harmonic map research, limited progress has been made to compute a diffeomorphic harmonic map on general topology surfaces with landmark constraints. This work conquers this problem by changing the Riemannian metric on the target surface to a hyperbolic metric so that the harmonic mapping is guaranteed to be a diffeomorphism under landmark constraints. The computational algorithms are based on Ricci flow and nonlinear heat diffusion methods. The approach is general and robust. We employ our algorithm to study the constrained surface registration problem which applies to both computer vision and medical imaging applications. Experimental results demonstrate that, by changing the Riemannian metric, the registrations are always diffeomorphic and achieve relatively high performance when evaluated with some popular surface registration evaluation standards. PMID:27187948

Data-driven cluster reinforcement and visualization in sparsely-matched self-organizing maps.

PubMed

Manukyan, Narine; Eppstein, Margaret J; Rizzo, Donna M

2012-05-01

A self-organizing map (SOM) is a self-organized projection of high-dimensional data onto a typically 2-dimensional (2-D) feature map, wherein vector similarity is implicitly translated into topological closeness in the 2-D projection. However, when there are more neurons than input patterns, it can be challenging to interpret the results, due to diffuse cluster boundaries and limitations of current methods for displaying interneuron distances. In this brief, we introduce a new cluster reinforcement (CR) phase for sparsely-matched SOMs. The CR phase amplifies within-cluster similarity in an unsupervised, data-driven manner. Discontinuities in the resulting map correspond to between-cluster distances and are stored in a boundary (B) matrix. We describe a new hierarchical visualization of cluster boundaries displayed directly on feature maps, which requires no further clustering beyond what was implicitly accomplished during self-organization in SOM training. We use a synthetic benchmark problem and previously published microbial community profile data to demonstrate the benefits of the proposed methods.

Co-location and Self-Similar Topologies of Urban Infrastructure Networks

NASA Astrophysics Data System (ADS)

Klinkhamer, Christopher; Zhan, Xianyuan; Ukkusuri, Satish; Elisabeth, Krueger; Paik, Kyungrock; Rao, Suresh

2016-04-01

The co-location of urban infrastructure is too obvious to be easily ignored. For reasons of practicality, reliability, and eminent domain, the spatial locations of many urban infrastructure networks, including drainage, sanitary sewers, and road networks, are well correlated. However, important questions dealing with correlations in the network topologies of differing infrastructure types remain unanswered. Here, we have extracted randomly distributed, nested subnets from the urban drainage, sanitary sewer, and road networks in two distinctly different cities: Amman, Jordan; and Indianapolis, USA. Network analyses were performed for each randomly chosen subnet (location and size), using a dual-mapping approach (Hierarchical Intersection Continuity Negotiation). Topological metrics for each infrastructure type were calculated and compared for all subnets in a given city. Despite large differences in the climate, governance, and populace of the two cities, and functional properties of the different infrastructure types, these infrastructure networks are shown to be highly spatially homogenous. Furthermore, strong correlations are found between topological metrics of differing types of surface and subsurface infrastructure networks. Also, the network topologies of each infrastructure type for both cities are shown to exhibit self-similar characteristics (i.e., power law node-degree distributions, [p(k) = ak-γ]. These findings can be used to assist city planners and engineers either expanding or retrofitting existing infrastructure, or in the case of developing countries, building new cities from the ground up. In addition, the self-similar nature of these infrastructure networks holds significant implications for the vulnerability of these critical infrastructure networks to external hazards and ways in which network resilience can be improved.

Martian low-altitude magnetic topology deduced from MAVEN/SWEA observations

NASA Astrophysics Data System (ADS)

Xu, Shaosui; Mitchell, David; Liemohn, Michael; Fang, Xiaohua; Ma, Yingjuan; Luhmann, Janet; Brain, David; Steckiewicz, Morgane; Mazelle, Christian; Connerney, Jack; Jakosky, Bruce

2017-02-01

The Mars Atmosphere and Volatile Evolution mission has obtained comprehensive particle and magnetic field measurements. The Solar Wind Electron Analyzer provides electron energy-pitch angle distributions along the spacecraft trajectory that can be used to infer magnetic topology. This study presents pitch angle-resolved electron energy shape parameters that can distinguish photoelectrons from solar wind electrons, which we use to deduce the Martian magnetic topology and connectivity to the dayside ionosphere. Magnetic topology in the Mars environment is mapped in three dimensions for the first time. At low altitudes (<400 km) in sunlight, the northern hemisphere is found to be dominated by closed field lines (both ends intersecting the collisional atmosphere), with more day-night connections through cross-terminator closed field lines than in the south. Although draped field lines with 100 km amplitude vertical fluctuations that intersect the electron exobase ( 160-220 km) in two locations could appear to be closed at the spacecraft, a more likely explanation is provided by crustal magnetic fields, which naturally have the required geometry. Around 30% of the time, we observe open field lines from 200 to 400 km, which implies three distinct topological layers over the northern hemisphere: closed field lines below 200 km, open field lines with foot points at lower latitudes that pass over the northern hemisphere from 200 to 400 km, and draped interplanetary magnetic field above 400 km. This study also identifies open field lines with one end attached to the dayside ionosphere and the other end connected with the solar wind, providing a path for ion outflow.

Probing Twisted Magnetic Field Using Microwave Observations in an M Class Solar Flare on 11 February, 2014

NASA Astrophysics Data System (ADS)

Sharykin, I. N.; Kuznetsov, A. A.; Myshyakov, I. I.

2018-02-01

This work demonstrates the possibility of magnetic-field topology investigations using microwave polarimetric observations. We study a solar flare of GOES M1.7 class that occurred on 11 February, 2014. This flare revealed a clear signature of spatial inversion of the radio-emission polarization sign. We show that the observed polarization pattern can be explained by nonthermal gyrosynchrotron emission from the twisted magnetic structure. Using observations of the Reuven Ramaty High Energy Solar Spectroscopic Imager, Nobeyama Radio Observatory, Radio Solar Telescope Network, and Solar Dynamics Observatory, we have determined the parameters of nonthermal electrons and thermal plasma and identified the magnetic structure where the flare energy release occurred. To reconstruct the coronal magnetic field, we use nonlinear force-free field (NLFFF) and potential magnetic-field approaches. Radio emission of nonthermal electrons is simulated by the GX Simulator code using the extrapolated magnetic field and the parameters of nonthermal electrons and thermal plasma inferred from the observations; the model radio maps and spectra are compared with observations. We have found that the potential-magnetic-field approach fails to explain the observed circular polarization pattern; on the other hand, the Stokes-V map is successfully explained by assuming nonthermal electrons to be distributed along the twisted magnetic structure determined by the NLFFF extrapolation approach. Thus, we show that the radio-polarization maps can be used for diagnosing the topology of the flare magnetic structures where nonthermal electrons are injected.

Complex Road Intersection Modelling Based on Low-Frequency GPS Track Data

NASA Astrophysics Data System (ADS)

Huang, J.; Deng, M.; Zhang, Y.; Liu, H.

2017-09-01

It is widely accepted that digital map becomes an indispensable guide for human daily traveling. Traditional road network maps are produced in the time-consuming and labour-intensive ways, such as digitizing printed maps and extraction from remote sensing images. At present, a large number of GPS trajectory data collected by floating vehicles makes it a reality to extract high-detailed and up-to-date road network information. Road intersections are often accident-prone areas and very critical to route planning and the connectivity of road networks is mainly determined by the topological geometry of road intersections. A few studies paid attention on detecting complex road intersections and mining the attached traffic information (e.g., connectivity, topology and turning restriction) from massive GPS traces. To the authors' knowledge, recent studies mainly used high frequency (1 s sampling rate) trajectory data to detect the crossroads regions or extract rough intersection models. It is still difficult to make use of low frequency (20-100 s) and easily available trajectory data to modelling complex road intersections geometrically and semantically. The paper thus attempts to construct precise models for complex road intersection by using low frequency GPS traces. We propose to firstly extract the complex road intersections by a LCSS-based (Longest Common Subsequence) trajectory clustering method, then delineate the geometry shapes of complex road intersections by a K-segment principle curve algorithm, and finally infer the traffic constraint rules inside the complex intersections.

Detecting and Quantifying Topography in Neural Maps

PubMed Central

Yarrow, Stuart; Razak, Khaleel A.; Seitz, Aaron R.; Seriès, Peggy

2014-01-01

Topographic maps are an often-encountered feature in the brains of many species, yet there are no standard, objective procedures for quantifying topography. Topographic maps are typically identified and described subjectively, but in cases where the scale of the map is close to the resolution limit of the measurement technique, identifying the presence of a topographic map can be a challenging subjective task. In such cases, an objective topography detection test would be advantageous. To address these issues, we assessed seven measures (Pearson distance correlation, Spearman distance correlation, Zrehen's measure, topographic product, topological correlation, path length and wiring length) by quantifying topography in three classes of cortical map model: linear, orientation-like, and clusters. We found that all but one of these measures were effective at detecting statistically significant topography even in weakly-ordered maps, based on simulated noisy measurements of neuronal selectivity and sparse sampling of the maps. We demonstrate the practical applicability of these measures by using them to examine the arrangement of spatial cue selectivity in pallid bat A1. This analysis shows that significantly topographic arrangements of interaural intensity difference and azimuth selectivity exist at the scale of individual binaural clusters. PMID:24505279

Continuous properties of the data-to-solution map for a generalized μ-Camassa-Holm integrable equation

NASA Astrophysics Data System (ADS)

Yu, Shengqi

2018-05-01

This work studies a generalized μ-type integrable equation with both quadratic and cubic nonlinearities; the μ-Camassa-Holm and modified μ-Camassa-Holm equations are members of this family of equations. It has been shown that the Cauchy problem for this generalized μ-Camassa-Holm integrable equation is locally well-posed for initial data u0 ∈ Hs, s > 5/2. In this work, we further investigate the continuity properties to this equation. It is proved in this work that the data-to-solution map of the proposed equation is not uniformly continuous. It is also found that the solution map is Hölder continuous in the Hr-topology when 0 ≤ r < s with Hölder exponent α depending on both s and r.

Rapid Assessment of Aircraft Structural Topologies for Multidisciplinary Optimization and Weight Estimation

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Sensmeier, mark D.; Stewart, Bret A.

2006-01-01

Algorithms for rapid generation of moderate-fidelity structural finite element models of air vehicle structures to allow more accurate weight estimation earlier in the vehicle design process have been developed. Application of these algorithms should help to rapidly assess many structural layouts before the start of the preliminary design phase and eliminate weight penalties imposed when actual structure weights exceed those estimated during conceptual design. By defining the structural topology in a fully parametric manner, the structure can be mapped to arbitrary vehicle configurations being considered during conceptual design optimization. Recent enhancements to this approach include the porting of the algorithms to a platform-independent software language Python, and modifications to specifically consider morphing aircraft-type configurations. Two sample cases which illustrate these recent developments are presented.

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

Kozlov, I K

In this paper we study topological properties of an integrable case for Euler's equations on the Lie algebra so(4), which can be regarded as an analogue of the classical Kovalevskaya case in rigid body dynamics. In particular, for all values of the parameters of the system under consideration, the bifurcation diagrams of the momentum mapping are constructed, the types of critical points of rank 0 are determined, the bifurcations of Liouville tori are described, and the loop molecules are computed for all singular points of the bifurcation diagrams. It follows from the obtained results that some topological properties of the classicalmore » Kovalevskaya case can be obtained from the corresponding properties of the considered integrable case on the Lie algebra so(4) by taking a natural limit. Bibliography: 21 titles.« less

The magnetic fields of Ap stars from high resolution Stokes IQUV spectropolarimetry

NASA Astrophysics Data System (ADS)

Silvester, James

In this thesis we describe the acquisition of high resolution time resolved spectropolarimetric observations of 7 (bright and well understood) Ap stars in Stokes IQUV using the ESPaDOnS and Narval spectropolarimeters at the Canada-France-Hawaii Telescope and the 2m Telescope Bernard Lyot at Pic du Midi Observatory. We compare these observations with those obtained a decade earlier using the MuSiCoS spectropolarimeter to confirm consistency with the older data and provide evidence that both ESPaDOnS and Narval perform as expected in all Stokes parameters. We demonstrate that our refined longitudinal magnetic field and linear polarisation measurements for these 7 stars are of much greater quality than was previously obtained with MuSiCoS and that the global magnetic properties of these stars are stable over a long timescale. The ultimate aim of these new data is to provide a basis from which mapping of both the magnetic field and abundance structures can be performed on our target stars. We then describe magnetic field mapping of the Ap star alpha 2 CVn using these data. This mapping is achieved with the use of tomographic inversion of Doppler-broadened Stokes IQUV profiles of a large variety of spectral lines using the INVERS10 Magnetic Doppler imaging code. We show that not only are the new magnetic field maps of alpha 2 CVn consistent with a previous generation of maps of alpha 2 CVn, but that the same magnetic field topology can be derived from a variety of atomic line sets. This indicates that the magnetic field we derive for alpha2 CVn is a realistic representation of the star's true magnetic topology. Finally we investigate surface abundance structures for alpha 2 CVn for various chemical elements. We investigate the correlation between the location of these abundance features and the magnetic field of alpha 2 CVn. We will demonstrate that whilst the magnetic field plays a role in the formation of abundance structures, the current theoretical framework does not fully explain what we find from our maps. Ultimately this work motivates future mapping of Ap stars by confirming the reliability of both the instrument and associated data and the mapping technique itself.

Geologic map of the Zarkashan-Anguri copper and gold deposits, Ghazni Province, Afghanistan, modified from the 1968 original map compilation of E.P. Meshcheryakov and V.P. Sayapin

USGS Publications Warehouse

Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geological map of the area of Zarkashan-Anguri gold deposits, scale 1:50,000, which was compiled by E.P. Meshcheryakov and V.P. Sayapin in 1968. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original document and related reports and also visited the field area in April 2010. This modified map, which includes a cross section, illustrates the geologic setting of the Zarkashan-Anguri copper and gold deposits. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross section and includes modifications based on our examination of that and other documents, and based on observations made and sampling undertaken during our field visit. (Refer to the Introduction and the References in the Map PDF for an explanation of our methodology and for complete citations of the original map and related reports.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map.

Evolution families of conformal mappings with fixed points and the Löwner-Kufarev equation

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

Goryainov, V V

2015-01-31

The paper is concerned with evolution families of conformal mappings of the unit disc to itself that fix an interior point and a boundary point. Conditions are obtained for the evolution families to be differentiable, and an existence and uniqueness theorem for an evolution equation is proved. A convergence theorem is established which describes the topology of locally uniform convergence of evolution families in terms of infinitesimal generating functions. The main result in this paper is the embedding theorem which shows that any conformal mapping of the unit disc to itself with two fixed points can be embedded into a differentiable evolution familymore » of such mappings. This result extends the range of the parametric method in the theory of univalent functions. In this way the problem of the mutual change of the derivative at an interior point and the angular derivative at a fixed point on the boundary is solved for a class of mappings of the unit disc to itself. In particular, the rotation theorem is established for this class of mappings. Bibliography: 27 titles.« less

Algebraic grid generation using tensor product B-splines. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Saunders, B. V.

1985-01-01

Finite difference methods are more successful if the accompanying grid has lines which are smooth and nearly orthogonal. The development of an algorithm which produces such a grid when given the boundary description. Topological considerations in structuring the grid generation mapping are discussed. The concept of the degree of a mapping and how it can be used to determine what requirements are necessary if a mapping is to produce a suitable grid is examined. The grid generation algorithm uses a mapping composed of bicubic B-splines. Boundary coefficients are chosen so that the splines produce Schoenberg's variation diminishing spline approximation to the boundary. Interior coefficients are initially chosen to give a variation diminishing approximation to the transfinite bilinear interpolant of the function mapping the boundary of the unit square onto the boundary grid. The practicality of optimizing the grid by minimizing a functional involving the Jacobian of the grid generation mapping at each interior grid point and the dot product of vectors tangent to the grid lines is investigated. Grids generated by using the algorithm are presented.

Robot Acquisition of Active Maps Through Teleoperation and Vector Space Analysis

NASA Technical Reports Server (NTRS)

Peters, Richard Alan, II

2003-01-01

The work performed under this contract was in the area of intelligent robotics. The problem being studied was the acquisition of intelligent behaviors by a robot. The method was to acquire action maps that describe tasks as sequences of reflexive behaviors. Action maps (a.k.a. topological maps) are graphs whose nodes represent sensorimotor states and whose edges represent the motor actions that cause the robot to proceed from one state to the next. The maps were acquired by the robot after being teleoperated or otherwise guided by a person through a task several times. During a guided task, the robot records all its sensorimotor signals. The signals from several task trials are partitioned into episodes of static behavior. The corresponding episodes from each trial are averaged to produce a task description as a sequence of characteristic episodes. The sensorimotor states that indicate episode boundaries become the nodes, and the static behaviors, the edges. It was demonstrated that if compound maps are constructed from a set of tasks then the robot can perform new tasks in which it was never explicitly trained.

Small-World Brain Networks Revisited

PubMed Central

Bassett, Danielle S.; Bullmore, Edward T.

2016-01-01

It is nearly 20 years since the concept of a small-world network was first quantitatively defined, by a combination of high clustering and short path length; and about 10 years since this metric of complex network topology began to be widely applied to analysis of neuroimaging and other neuroscience data as part of the rapid growth of the new field of connectomics. Here, we review briefly the foundational concepts of graph theoretical estimation and generation of small-world networks. We take stock of some of the key developments in the field in the past decade and we consider in some detail the implications of recent studies using high-resolution tract-tracing methods to map the anatomical networks of the macaque and the mouse. In doing so, we draw attention to the important methodological distinction between topological analysis of binary or unweighted graphs, which have provided a popular but simple approach to brain network analysis in the past, and the topology of weighted graphs, which retain more biologically relevant information and are more appropriate to the increasingly sophisticated data on brain connectivity emerging from contemporary tract-tracing and other imaging studies. We conclude by highlighting some possible future trends in the further development of weighted small-worldness as part of a deeper and broader understanding of the topology and the functional value of the strong and weak links between areas of mammalian cortex. PMID:27655008

Category-Selectivity in Human Visual Cortex Follows Cortical Topology: A Grouped icEEG Study

PubMed Central

Conner, Christopher Richard; Whaley, Meagan Lee; Baboyan, Vatche George; Tandon, Nitin

2016-01-01

Neuroimaging studies suggest that category-selective regions in higher-order visual cortex are topologically organized around specific anatomical landmarks: the mid-fusiform sulcus (MFS) in the ventral temporal cortex (VTC) and lateral occipital sulcus (LOS) in the lateral occipital cortex (LOC). To derive precise structure-function maps from direct neural signals, we collected intracranial EEG (icEEG) recordings in a large human cohort (n = 26) undergoing implantation of subdural electrodes. A surface-based approach to grouped icEEG analysis was used to overcome challenges from sparse electrode coverage within subjects and variable cortical anatomy across subjects. The topology of category-selectivity in bilateral VTC and LOC was assessed for five classes of visual stimuli—faces, animate non-face (animals/body-parts), places, tools, and words—using correlational and linear mixed effects analyses. In the LOC, selectivity for living (faces and animate non-face) and non-living (places and tools) classes was arranged in a ventral-to-dorsal axis along the LOS. In the VTC, selectivity for living and non-living stimuli was arranged in a latero-medial axis along the MFS. Written word-selectivity was reliably localized to the intersection of the left MFS and the occipito-temporal sulcus. These findings provide direct electrophysiological evidence for topological information structuring of functional representations within higher-order visual cortex. PMID:27272936

Visibility in the topology of complex networks

NASA Astrophysics Data System (ADS)

Tsiotas, Dimitrios; Charakopoulos, Avraam

2018-09-01

Taking its inspiration from the visibility algorithm, which was proposed by Lacasa et al. (2008) to convert a time-series into a complex network, this paper develops and proposes a novel expansion of this algorithm that allows generating a visibility graph from a complex network instead of a time-series that is currently applicable. The purpose of this approach is to apply the idea of visibility from the field of time-series to complex networks in order to interpret the network topology as a landscape. Visibility in complex networks is a multivariate property producing an associated visibility graph that maps the ability of a node "to see" other nodes in the network that lie beyond the range of its neighborhood, in terms of a control-attribute. Within this context, this paper examines the visibility topology produced by connectivity (degree) in comparison with the original (source) network, in order to detect what patterns or forces describe the mechanism under which a network is converted to a visibility graph. The overall analysis shows that visibility is a property that increases the connectivity in networks, it may contribute to pattern recognition (among which the detection of the scale-free topology) and it is worth to be applied to complex networks in order to reveal the potential of signal processing beyond the range of its neighborhood. Generally, this paper promotes interdisciplinary research in complex networks providing new insights to network science.

Looking for trees in the forest: summary tree from posterior samples

PubMed Central

2013-01-01

Background Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. Results We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the “truth”, i.e to the tree used to generate the sequences. Conclusions Our simulations indicate that no single method is “best”. Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree. PMID:24093883

Looking for trees in the forest: summary tree from posterior samples.

PubMed

Heled, Joseph; Bouckaert, Remco R

2013-10-04

Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the "truth", i.e to the tree used to generate the sequences. Our simulations indicate that no single method is "best". Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree.

Thermodynamic phase transitions for Pomeau-Manneville maps

NASA Astrophysics Data System (ADS)

Venegeroles, Roberto

2012-08-01

We study phase transitions in the thermodynamic description of Pomeau-Manneville intermittent maps from the point of view of infinite ergodic theory, which deals with diverging measure dynamical systems. For such systems, we use a distributional limit theorem to provide both a powerful tool for calculating thermodynamic potentials as also an understanding of the dynamic characteristics at each instability phase. In particular, topological pressure and Rényi entropy are calculated exactly for such systems. Finally, we show the connection of the distributional limit theorem with non-Gaussian fluctuations of the algorithmic complexity proposed by Gaspard and Wang [Proc. Natl. Acad. Sci. USA10.1073/pnas.85.13.4591 85, 4591 (1988)].

Modeling Political Populations with Bacteria

NASA Astrophysics Data System (ADS)

Cleveland, Chris; Liao, David

2011-03-01

Results from lattice-based simulations of micro-environments with heterogeneous nutrient resources reveal that competition between wild-type and GASP rpoS819 strains of E. Coli offers mutual benefit, particularly in nutrient deprived regions. Our computational model spatially maps bacteria populations and energy sources onto a set of 3D lattices that collectively resemble the topology of North America. By implementing Wright-Fishcer re- production into a probabilistic leap-frog scheme, we observe populations of wild-type and GASP rpoS819 cells compete for resources and, yet, aid each other's long term survival. The connection to how spatial political ideologies map in a similar way is discussed.

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

Baker, J.E.

Many robotic operations, e.g., mapping, scanning, feature following, etc., require accurate surface following of arbitrary targets. This paper presents a versatile surface following and mapping system designed to promote hardware, software and application independence, modular development, and upward expandability. These goals are met by: a full, a priori specification of the hardware and software interfaces; a modular system architecture; and a hierarchical surface-data analysis method, permitting application specific tuning at each conceptual level of topological abstraction. This surface following system was fully designed and independently of any specific robotic host, then successfully integrated with and demonstrated on a completely amore » priori unknown, real-time robotic system. 7 refs.« less

FIP bias in a sigmoidal active region

NASA Astrophysics Data System (ADS)

Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, Lidia; Green, L. M.; Steed, K.; Carlyle, J.

2014-01-01

We investigate first ionization potential (FIP) bias levels in an anemone active region (AR) - coronal hole (CH) complex using an abundance map derived from Hinode/EIS spectra. The detailed, spatially resolved abundance map has a large field of view covering 359'' × 485''. Plasma with high FIP bias, or coronal abundances, is concentrated at the footpoints of the AR loops whereas the surrounding CH has a low FIP bias, ~1, i.e. photospheric abundances. A channel of low FIP bias is located along the AR's main polarity inversion line containing a filament where ongoing flux cancellation is observed, indicating a bald patch magnetic topology characteristic of a sigmoid/flux rope configuration.

Cubic polynomial maps with periodic critical orbit, Part II

NASA Astrophysics Data System (ADS)

Bonifant, Araceli; Kiwi, Jan; Milnor, John

The parameter space S_p for monic centered cubic polynomial maps with a marked critical point of period p is a smooth affine algebraic curve whose genus increases rapidly with p . Each S_p consists of a compact connectedness locus together with finitely many escape regions, each of which is biholomorphic to a punctured disk and is characterized by an essentially unique Puiseux series. This note will describe the topology of S_p , and of its smooth compactification, in terms of these escape regions. In particular, it computes the Euler characteristic. It concludes with a discussion of the real sub-locus of S_p .

Application of a Topological Metric for Assessing Numerical Ocean Models with Satellite Observations

NASA Astrophysics Data System (ADS)

Morey, S. L.; Dukhovskoy, D. S.; Hiester, H. R.; Garcia-Pineda, O. G.; MacDonald, I. R.

2015-12-01

Satellite-based sensors provide a vast amount of observational data over the world ocean. Active microwave radars measure changes in sea surface height and backscattering from surface waves. Data from passive radiometers sensing emissions in multiple spectral bands can directly measure surface temperature, be combined with other data sources to estimate salinity, or processed to derive estimates of optically significant quantities, such as concentrations of biochemical properties. Estimates of the hydrographic variables can be readily used for assimilation or assessment of hydrodynamic ocean models. Optical data, however, have been underutilized in ocean circulation modeling. Qualitative assessments of oceanic fronts and other features commonly associated with changes in optically significant quantities are often made through visual comparison. This project applies a topological approach, borrowed from the field of computer image recognition, to quantitatively evaluate ocean model simulations of features that are related to quantities inferred from satellite imagery. The Modified Hausdorff Distance (MHD) provides a measure of the similarity of two shapes. Examples of applications of the MHD to assess ocean circulation models are presented. The first application assesses several models' representation of the freshwater plume structure from the Mississippi River, which is associated with a significant expression of color, using a satellite-derived ocean color index. Even though the variables being compared (salinity and ocean color index) differ, the MHD allows contours of the fields to be compared topologically. The second application assesses simulations of surface oil transport driven by winds and ocean model currents using surface oil maps derived from synthetic aperture radar backscatter data. In this case, maps of time composited oil coverage are compared between the simulations and satellite observations.

Ambiguity assessment of small-angle scattering curves from monodisperse systems.

PubMed

Petoukhov, Maxim V; Svergun, Dmitri I

2015-05-01

A novel approach is presented for an a priori assessment of the ambiguity associated with spherically averaged single-particle scattering. The approach is of broad interest to the structural biology community, allowing the rapid and model-independent assessment of the inherent non-uniqueness of three-dimensional shape reconstruction from scattering experiments on solutions of biological macromolecules. One-dimensional scattering curves recorded from monodisperse systems are nowadays routinely utilized to generate low-resolution particle shapes, but the potential ambiguity of such reconstructions remains a major issue. At present, the (non)uniqueness can only be assessed by a posteriori comparison and averaging of repetitive Monte Carlo-based shape-determination runs. The new a priori ambiguity measure is based on the number of distinct shape categories compatible with a given data set. For this purpose, a comprehensive library of over 14,000 shape topologies has been generated containing up to seven beads closely packed on a hexagonal grid. The computed scattering curves rescaled to keep only the shape topology rather than the overall size information provide a `scattering map' of this set of shapes. For a given scattering data set, one rapidly obtains the number of neighbours in the map and the associated shape topologies such that in addition to providing a quantitative ambiguity measure the algorithm may also serve as an alternative shape-analysis tool. The approach has been validated in model calculations on geometrical bodies and its usefulness is further demonstrated on a number of experimental X-ray scattering data sets from proteins in solution. A quantitative ambiguity score (a-score) is introduced to provide immediate and convenient guidance to the user on the uniqueness of the ab initio shape reconstruction from the given data set.

A Methodology to Develop Entrepreneurial Networks: The Tech Ecosystem of Six African Cities

DTIC Science & Technology

2014-11-01

Information Center. Greve, A. and Salaff, J. W. (2003), Social Networks and Entrepreneurship . Entrepreneurship Theory and Practice, 28: 1–22. doi...methodology enables us to accurately measure social capital and circumvents the massive effort of mapping an individual’s social network before...locating the social resources in it. 15. SUBJECT TERMS Network Analysis, Economic Networks, Network Topology, Network Classification 16. SECURITY

MemAxes Visualization Software

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

Hardware advancements such as Intel's PEBS and AMD's IBS, as well as software developments such as the perf_event API in Linux have made available the acquisition of memory access samples with performance information. MemAxes is a visualization and analysis tool for memory access sample data. By mapping the samples to their associated code, variables, node topology, and application dataset, MemAxes provides intuitive views of the data.

Effective Integration of Earth Observation Data and Flood Modeling for Rapid Disaster Response: The Texas 2015 Case

NASA Astrophysics Data System (ADS)

Schumann, G.

2016-12-01

Routinely obtaining real-time 2-D inundation patterns of a flood event at a meaningful spatial resolution and over large scales is at the moment only feasible with either operational aircraft flights or satellite imagery. Of course having model simulations of floodplain inundation available to complement the remote sensing data is highly desirable, for both event re-analysis and forecasting event inundation. Using the Texas 2015 flood disaster, we demonstrate the value of multi-scale EO data for large scale 2-D floodplain inundation modeling and forecasting. A dynamic re-analysis of the Texas 2015 flood disaster was run using a 2-D flood model developed for accurate large scale simulations. We simulated the major rivers entering the Gulf of Mexico and used flood maps produced from both optical and SAR satellite imagery to examine regional model sensitivities and assess associated performance. It was demonstrated that satellite flood maps can complement model simulations and add value, although this is largely dependent on a number of important factors, such as image availability, regional landscape topology, and model uncertainty. In the preferred case where model uncertainty is high, landscape topology is complex (i.e. urbanized coastal area) and satellite flood maps are available (in case of SAR for instance), satellite data can significantly reduce model uncertainty by identifying the "best possible" model parameter set. However, most often the situation is occurring where model uncertainty is low and spatially contiguous flooding can be mapped from satellites easily enough, such as in rural large inland river floodplains. Consequently, not much value from satellites can be added. Nevertheless, where a large number of flood maps are available, model credibility can be increased substantially. In the case presented here this was true for at least 60% of the many thousands of kilometers of river flow length simulated, where satellite flood maps existed. The next steps of this project is to employ a technique termed "targeted observation" approach, which is an assimilation based procedure that allows quantifying the impact observations have on model predictions at the local scale and also along the entire river system, when assimilated with the model at specific "overpass" locations.

Growing a hypercubical output space in a self-organizing feature map.

PubMed

Bauer, H U; Villmann, T

1997-01-01

Neural maps project data from an input space onto a neuron position in a (often lower dimensional) output space grid in a neighborhood preserving way, with neighboring neurons in the output space responding to neighboring data points in the input space. A map-learning algorithm can achieve an optimal neighborhood preservation only, if the output space topology roughly matches the effective structure of the data in the input space. We here present a growth algorithm, called the GSOM or growing self-organizing map, which enhances a widespread map self-organization process, Kohonen's self-organizing feature map (SOFM), by an adaptation of the output space grid during learning. The GSOM restricts the output space structure to the shape of a general hypercubical shape, with the overall dimensionality of the grid and its extensions along the different directions being subject of the adaptation. This constraint meets the demands of many larger information processing systems, of which the neural map can be a part. We apply our GSOM-algorithm to three examples, two of which involve real world data. Using recently developed methods for measuring the degree of neighborhood preservation in neural maps, we find the GSOM-algorithm to produce maps which preserve neighborhoods in a nearly optimal fashion.

Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

PubMed Central

Aguirre, Jacobo; Buldú, Javier M.; Stich, Michael; Manrubia, Susanna C.

2011-01-01

The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence) and phenotype (approximated by the secondary structure fold) are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 412 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described. PMID:22028856

Individual tree crown delineation using localized contour tree method and airborne LiDAR data in coniferous forests

NASA Astrophysics Data System (ADS)

Wu, Bin; Yu, Bailang; Wu, Qiusheng; Huang, Yan; Chen, Zuoqi; Wu, Jianping

2016-10-01

Individual tree crown delineation is of great importance for forest inventory and management. The increasing availability of high-resolution airborne light detection and ranging (LiDAR) data makes it possible to delineate the crown structure of individual trees and deduce their geometric properties with high accuracy. In this study, we developed an automated segmentation method that is able to fully utilize high-resolution LiDAR data for detecting, extracting, and characterizing individual tree crowns with a multitude of geometric and topological properties. The proposed approach captures topological structure of forest and quantifies topological relationships of tree crowns by using a graph theory-based localized contour tree method, and finally segments individual tree crowns by analogy of recognizing hills from a topographic map. This approach consists of five key technical components: (1) derivation of canopy height model from airborne LiDAR data; (2) generation of contours based on the canopy height model; (3) extraction of hierarchical structures of tree crowns using the localized contour tree method; (4) delineation of individual tree crowns by segmenting hierarchical crown structure; and (5) calculation of geometric and topological properties of individual trees. We applied our new method to the Medicine Bow National Forest in the southwest of Laramie, Wyoming and the HJ Andrews Experimental Forest in the central portion of the Cascade Range of Oregon, U.S. The results reveal that the overall accuracy of individual tree crown delineation for the two study areas achieved 94.21% and 75.07%, respectively. Our method holds great potential for segmenting individual tree crowns under various forest conditions. Furthermore, the geometric and topological attributes derived from our method provide comprehensive and essential information for forest management.

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.

Schizophrenia‐like topological changes in the structural connectome of individuals with subclinical psychotic experiences

PubMed Central

Caeyenberghs, Karen; Dutt, Anirban; Zammit, Stanley; Evans, C. John; Reichenberg, Abraham; Lewis, Glyn; David, Anthony S.; Jones, Derek K.

2015-01-01

Abstract Schizophrenia is often regarded as a “dysconnectivity” disorder and recent work using graph theory has been used to better characterize dysconnectivity of the structural connectome in schizophrenia. However, there are still little data on the topology of connectomes in less severe forms of the condition. Such analysis will identify topological markers of less severe disease states and provide potential predictors of further disease development. Individuals with psychotic experiences (PEs) were identified from a population‐based cohort without relying on participants presenting to clinical services. Such individuals have an increased risk of developing clinically significant psychosis. 123 individuals with PEs and 125 controls were scanned with diffusion‐weighted MRI. Whole‐brain structural connectomes were derived and a range of global and local GT‐metrics were computed. Global efficiency and density were significantly reduced in individuals with PEs. Local efficiency was reduced in a number of regions, including critical network hubs. Further analysis of functional subnetworks showed differential impairment of the default mode network. An additional analysis of pair‐wise connections showed no evidence of differences in individuals with PEs. These results are consistent with previous findings in schizophrenia. Reduced efficiency in critical core hubs suggests the brains of individuals with PEs may be particularly predisposed to dysfunction. The absence of any detectable effects in pair‐wise connections illustrates that, at less severe stages of psychosis, white‐matter alterations are subtle and only manifest when examining network topology. This study indicates that topology could be a sensitive biomarker for early stages of psychotic illness. Hum Brain Mapp 36:2629–2643, 2015.© 2015 TheAuthors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:25832856

Decay of random correlation functions for unimodal maps

NASA Astrophysics Data System (ADS)

Baladi, Viviane; Benedicks, Michael; Maume-Deschamps, Véronique

2000-10-01

Since the pioneering results of Jakobson and subsequent work by Benedicks-Carleson and others, it is known that quadratic maps tfa( χ) = a - χ2 admit a unique absolutely continuous invariant measure for a positive measure set of parameters a. For topologically mixing tfa, Young and Keller-Nowicki independently proved exponential decay of correlation functions for this a.c.i.m. and smooth observables. We consider random compositions of small perturbations tf + ωt, with tf = tfa or another unimodal map satisfying certain nonuniform hyperbolicity axioms, and ωt chosen independently and identically in [-ɛ, ɛ]. Baladi-Viana showed exponential mixing of the associated Markov chain, i.e., averaging over all random itineraries. We obtain stretched exponential bounds for the random correlation functions of Lipschitz observables for the sample measure μωof almost every itinerary.

Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, L.; Allen, F. H.; Vercauteren, D. P.

1995-04-01

A computational method is described for mapping the volume within the DNA double helix accessible to a groove-binding antibiotic, netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to be a good representation of the electron density function at various resolutions; while at the atomic level the ellipsoid method gives results which are in close agreement with those from the conventional, spherical, van der Waals approach.

Shape information from a critical point analysis of calculated electron density maps: Application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, Laurence; Allen, Frank H.

1994-06-01

A computational method is described for mapping the volume within the DNA double helix accessible to the groove-binding antibiotic netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to give a good representation of the electron density function at various resolutions. At the atomic level, the ellipsoid method gives results which are in close agreement with those from the conventional spherical van der Waals approach.

Communications and control for electric power systems: Power flow classification for static security assessment

NASA Technical Reports Server (NTRS)

Niebur, D.; Germond, A.

1993-01-01

This report investigates the classification of power system states using an artificial neural network model, Kohonen's self-organizing feature map. The ultimate goal of this classification is to assess power system static security in real-time. Kohonen's self-organizing feature map is an unsupervised neural network which maps N-dimensional input vectors to an array of M neurons. After learning, the synaptic weight vectors exhibit a topological organization which represents the relationship between the vectors of the training set. This learning is unsupervised, which means that the number and size of the classes are not specified beforehand. In the application developed in this report, the input vectors used as the training set are generated by off-line load-flow simulations. The learning algorithm and the results of the organization are discussed.

Squeezed Dirac and topological magnons in a bosonic honeycomb optical lattice

NASA Astrophysics Data System (ADS)

Owerre, S. A.; Nsofini, J.

2017-11-01

Quantum information storage using charge-neutral quasiparticles is expected to play a crucial role in the future of quantum computers. In this regard, magnons or collective spin-wave excitations in solid-state materials are promising candidates in the future of quantum computing. Here, we study the quantum squeezing of Dirac and topological magnons in a bosonic honeycomb optical lattice with spin-orbit interaction by utilizing the mapping to quantum spin-1/2 XYZ Heisenberg model on the honeycomb lattice with discrete Z2 symmetry and a Dzyaloshinskii-Moriya interaction. We show that the squeezed magnons can be controlled by the Z2 anisotropy and demonstrate how the noise in the system is periodically modified in the ferromagnetic and antiferromagnetic phases of the model. Our results also apply to solid-state honeycomb (anti)ferromagnetic insulators.

Squeezed Dirac and Topological Magnons in a Bosonic Honeycomb Optical Lattice.

PubMed

Owerre, Solomon; Nsofini, Joachim

2017-09-20

Quantum information storage using charge-neutral quasiparticles are expected to play a crucial role in the future of quantum computers. In this regard, magnons or collective spin-wave excitations in solid-state materials are promising candidates in the future of quantum computing. Here, we study the quantum squeezing of Dirac and topological magnons in a bosonic honeycomb optical lattice with spin-orbit interaction by utilizing the mapping to quantum spin-$1/2$ XYZ Heisenberg model on the honeycomb lattice with discrete Z$_2$ symmetry and a Dzyaloshinskii-Moriya interaction. We show that the squeezed magnons can be controlled by the Z$_2$ anisotropy and demonstrate how the noise in the system is periodically modified in the ferromagnetic and antiferromagnetic phases of the model. Our results also apply to solid-state honeycomb (anti)ferromagnetic insulators. . © 2017 IOP Publishing Ltd.

Squeezed Dirac and topological magnons in a bosonic honeycomb optical lattice.

PubMed

Owerre, S A; Nsofini, J

2017-10-19

Quantum information storage using charge-neutral quasiparticles is expected to play a crucial role in the future of quantum computers. In this regard, magnons or collective spin-wave excitations in solid-state materials are promising candidates in the future of quantum computing. Here, we study the quantum squeezing of Dirac and topological magnons in a bosonic honeycomb optical lattice with spin-orbit interaction by utilizing the mapping to quantum spin-[Formula: see text] XYZ Heisenberg model on the honeycomb lattice with discrete Z 2 symmetry and a Dzyaloshinskii-Moriya interaction. We show that the squeezed magnons can be controlled by the Z 2 anisotropy and demonstrate how the noise in the system is periodically modified in the ferromagnetic and antiferromagnetic phases of the model. Our results also apply to solid-state honeycomb (anti)ferromagnetic insulators.

Topology of the South African stock market network across the 2008 financial crisis

NASA Astrophysics Data System (ADS)

Majapa, Mohamed; Gossel, Sean Joss

2016-03-01

This study uses the cross-correlations in the daily closing prices of the South African Top 100 companies listed on the JSE All share index (ALSI) from June 2003 to June 2013 to compute minimum spanning tree maps. In addition to the full sample, the analysis also uses three sub-periods to investigate the topological evolution before, during, and after the 2008 financial crisis. The findings show that although there is substantial clustering and homogeneity on the JSE, the most connected nodes are in the financial and resources sectors. The sub-sample results further reveal that the JSE network tree shrank in the run-up to, and during the financial crisis, and slowly expanded afterwards. In addition, the different clusters in the network are connected by various nodes that are significantly affected by diversification and credit market dynamics.

Organizing symmetry-protected topological phases by layering and symmetry reduction: A minimalist perspective

NASA Astrophysics Data System (ADS)

Xiong, Charles Zhaoxi; Alexandradinata, A.

2018-03-01

It is demonstrated that fermionic/bosonic symmetry-protected topological (SPT) phases across different dimensions and symmetry classes can be organized using geometric constructions that increase dimensions and symmetry-reduction maps that change symmetry groups. Specifically, it is shown that the interacting classifications of SPT phases with and without glide symmetry fit into a short exact sequence, so that the classification with glide is constrained to be a direct sum of cyclic groups of order 2 or 4. Applied to fermionic SPT phases in the Wigner-Dyson class AII, this implies that the complete interacting classification in the presence of glide is Z4⊕Z2⊕Z2 in three dimensions. In particular, the hourglass-fermion phase recently realized in the band insulator KHgSb must be robust to interactions. Generalizations to spatiotemporal glide symmetries are discussed.

Anomaly clustering in hyperspectral images

NASA Astrophysics Data System (ADS)

Doster, Timothy J.; Ross, David S.; Messinger, David W.; Basener, William F.

2009-05-01

The topological anomaly detection algorithm (TAD) differs from other anomaly detection algorithms in that it uses a topological/graph-theoretic model for the image background instead of modeling the image with a Gaussian normal distribution. In the construction of the model, TAD produces a hard threshold separating anomalous pixels from background in the image. We build on this feature of TAD by extending the algorithm so that it gives a measure of the number of anomalous objects, rather than the number of anomalous pixels, in a hyperspectral image. This is done by identifying, and integrating, clusters of anomalous pixels via a graph theoretical method combining spatial and spectral information. The method is applied to a cluttered HyMap image and combines small groups of pixels containing like materials, such as those corresponding to rooftops and cars, into individual clusters. This improves visualization and interpretation of objects.

A Symbolic Dynamics Perspective of Conway’s Game of Life

NASA Astrophysics Data System (ADS)

Chen, Fangyue; Chen, Bo; Guan, Junbiao; Jin, Weifeng

An interesting question is whether the intrinsic complexity of the gliders in D-dimensional cellular automata could be quantitatively analyzed in rigorously mathematical sense. In this paper, by introducing the D-dimensional symbolic space, some fundamental dynamical properties of D-dimensional shift map are explored in a subtle way. The purpose of this article is to present an accurate characterization of complex symbolic dynamics of gliders in Conway’s game of life. A series of dynamical properties of gliders on their concrete subsystems are investigated by means of the directed graph representation and transition matrix. More specifically, the gliders here are topologically mixing and possess the positive topological entropy on their subsystems. Finally, it is worth mentioning that the method presented in this paper is also applicable to other gliders in different D dimensions.

Magnetic field topology and chemical abundance distributions of the young, rapidly rotating, chemically peculiar star HR 5624

NASA Astrophysics Data System (ADS)

Kochukhov, O.; Silvester, J.; Bailey, J. D.; Landstreet, J. D.; Wade, G. A.

2017-09-01

Context. The young, rapidly rotating Bp star HR 5624 (HD 133880) shows an unusually strong non-sinusoidal variability of its longitudinal magnetic field. This behaviour was previously interpreted as the signature of an exceptionally strong, quadrupole-dominated surface magnetic field geometry. Aims: We studied the magnetic field structure and chemical abundance distributions of HR 5624 with the aim to verify the unusual quadrupolar nature of its magnetic field and to investigate correlations between the field topology and chemical spots. Methods: We analysed high-resolution, time series Stokes parameter spectra of HR 5624 with the help of a magnetic Doppler imaging inversion code based on detailed polarised radiative transfer modelling of the line profiles. Results: We refined the stellar parameters, revised the rotational period, and obtained new longitudinal magnetic field measurements. Our magnetic Doppler inversions reveal that the field structure of HR 5624 is considerably simpler and the field strength is much lower than proposed by previous studies. We find a maximum local field strength of 12 kG and a mean field strength of 4 kG, which is about a factor of three weaker than predicted by quadrupolar field models. Our model implies that overall large-scale field topology of HR 5624 is better described as a distorted, asymmetric dipole rather than an axisymmetric quadrupole. The chemical abundance maps of Mg, Si, Ti, Cr, Fe, and Nd obtained in our study are characterised by large-scale, high-contrast abundance patterns. These structures correlate weakly with the magnetic field geometry and, in particular, show no distinct element concentrations in the horizontal field regions predicted by theoretical atomic diffusion calculations. Conclusions: We conclude that the surface magnetic field topology of HR 5624 is not as unusual as previously proposed. Considering these results together with other recent magnetic mapping analyses of early-type stars suggests that predominantly quadrupolar magnetic field topologies, invoked to be present in a significant number of stars, probably do not exist in real stars. This finding agrees with an outcome of the MHD simulations of fossil field evolution in stably stratified stellar interiors. Based on observations collected at the European Southern Observatory, Chile (ESO programs 085.D-0296, 089.D-0383, 095.D-0194) and on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

Dynamic Analysis of the Carotid-Kundalini Map

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Liang, Qingyong; Meng, Juan

The nature of the fixed points of the Carotid-Kundalini (C-K) map was studied and the boundary equation of the first bifurcation of the C-K map in the parameter plane is presented. Using the quantitative criterion and rule of chaotic system, the paper reveals the general features of the C-K Map transforming from regularity to chaos. The following conclusions are obtained: (i) chaotic patterns of the C-K map may emerge out of double-periodic bifurcation; (ii) the chaotic crisis phenomena are found. At the same time, the authors analyzed the orbit of critical point of the complex C-K Map and put forward the definition of Mandelbrot-Julia set of the complex C-K Map. The authors generalized the Welstead and Cromer's periodic scanning technique and using this technology constructed a series of the Mandelbrot-Julia sets of the complex C-K Map. Based on the experimental mathematics method of combining the theory of analytic function of one complex variable with computer aided drawing, we investigated the symmetry of the Mandelbrot-Julia set and studied the topological inflexibility of distribution of the periodic region in the Mandelbrot set, and found that the Mandelbrot set contains abundant information of the structure of Julia sets by finding the whole portray of Julia sets based on Mandelbrot set qualitatively.

Faciotopy—A face-feature map with face-like topology in the human occipital face area

PubMed Central

Henriksson, Linda; Mur, Marieke; Kriegeskorte, Nikolaus

2015-01-01

The occipital face area (OFA) and fusiform face area (FFA) are brain regions thought to be specialized for face perception. However, their intrinsic functional organization and status as cortical areas with well-defined boundaries remains unclear. Here we test these regions for “faciotopy”, a particular hypothesis about their intrinsic functional organisation. A faciotopic area would contain a face-feature map on the cortical surface, where cortical patches represent face features and neighbouring patches represent features that are physically neighbouring in a face. The faciotopy hypothesis is motivated by the idea that face regions might develop from a retinotopic protomap and acquire their selectivity for face features through natural visual experience. Faces have a prototypical configuration of features, are usually perceived in a canonical upright orientation, and are frequently fixated in particular locations. To test the faciotopy hypothesis, we presented images of isolated face features at fixation to subjects during functional magnetic resonance imaging. The responses in V1 were best explained by low-level image properties of the stimuli. OFA, and to a lesser degree FFA, showed evidence for faciotopic organization. When a single patch of cortex was estimated for each face feature, the cortical distances between the feature patches reflected the physical distance between the features in a face. Faciotopy would be the first example, to our knowledge, of a cortical map reflecting the topology, not of a part of the organism itself (its retina in retinotopy, its body in somatotopy), but of an external object of particular perceptual significance. PMID:26235800

Faciotopy-A face-feature map with face-like topology in the human occipital face area.

PubMed

Henriksson, Linda; Mur, Marieke; Kriegeskorte, Nikolaus

2015-11-01

The occipital face area (OFA) and fusiform face area (FFA) are brain regions thought to be specialized for face perception. However, their intrinsic functional organization and status as cortical areas with well-defined boundaries remains unclear. Here we test these regions for "faciotopy", a particular hypothesis about their intrinsic functional organisation. A faciotopic area would contain a face-feature map on the cortical surface, where cortical patches represent face features and neighbouring patches represent features that are physically neighbouring in a face. The faciotopy hypothesis is motivated by the idea that face regions might develop from a retinotopic protomap and acquire their selectivity for face features through natural visual experience. Faces have a prototypical configuration of features, are usually perceived in a canonical upright orientation, and are frequently fixated in particular locations. To test the faciotopy hypothesis, we presented images of isolated face features at fixation to subjects during functional magnetic resonance imaging. The responses in V1 were best explained by low-level image properties of the stimuli. OFA, and to a lesser degree FFA, showed evidence for faciotopic organization. When a single patch of cortex was estimated for each face feature, the cortical distances between the feature patches reflected the physical distance between the features in a face. Faciotopy would be the first example, to our knowledge, of a cortical map reflecting the topology, not of a part of the organism itself (its retina in retinotopy, its body in somatotopy), but of an external object of particular perceptual significance. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Efficient discretization in finite difference method

NASA Astrophysics Data System (ADS)

Rozos, Evangelos; Koussis, Antonis; Koutsoyiannis, Demetris

2015-04-01

Finite difference method (FDM) is a plausible and simple method for solving partial differential equations. The standard practice is to use an orthogonal discretization to form algebraic approximate formulations of the derivatives of the unknown function and a grid, much like raster maps, to represent the properties of the function domain. For example, for the solution of the groundwater flow equation, a raster map is required for the characterization of the discretization cells (flow cell, no-flow cell, boundary cell, etc.), and two raster maps are required for the hydraulic conductivity and the storage coefficient. Unfortunately, this simple approach to describe the topology comes along with the known disadvantages of the FDM (rough representation of the geometry of the boundaries, wasted computational resources in the unavoidable expansion of the grid refinement in all cells of the same column and row, etc.). To overcome these disadvantages, Hunt has suggested an alternative approach to describe the topology, the use of an array of neighbours. This limits the need for discretization nodes only for the representation of the boundary conditions and the flow domain. Furthermore, the geometry of the boundaries is described more accurately using a vector representation. Most importantly, graded meshes can be employed, which are capable of restricting grid refinement only in the areas of interest (e.g. regions where hydraulic head varies rapidly, locations of pumping wells, etc.). In this study, we test the Hunt approach against MODFLOW, a well established finite difference model, and the Finite Volume Method with Simplified Integration (FVMSI). The results of this comparison are examined and critically discussed.

Flow topologies and turbulence scales in a jet-in-cross-flow

DOE PAGES

Oefelein, Joseph C.; Ruiz, Anthony M.; Lacaze, Guilhem

2015-04-03

This study presents a detailed analysis of the flow topologies and turbulence scales in the jet-in-cross-flow experiment of [Su and Mungal JFM 2004]. The analysis is performed using the Large Eddy Simulation (LES) technique with a highly resolved grid and time-step and well controlled boundary conditions. This enables quantitative agreement with the first and second moments of turbulence statistics measured in the experiment. LES is used to perform the analysis since experimental measurements of time-resolved 3D fields are still in their infancy and because sampling periods are generally limited with direct numerical simulation. A major focal point is the comprehensivemore » characterization of the turbulence scales and their evolution. Time-resolved probes are used with long sampling periods to obtain maps of the integral scales, Taylor microscales, and turbulent kinetic energy spectra. Scalar-fluctuation scales are also quantified. In the near-field, coherent structures are clearly identified, both in physical and spectral space. Along the jet centerline, turbulence scales grow according to a classical one-third power law. However, the derived maps of turbulence scales reveal strong inhomogeneities in the flow. From the modeling perspective, these insights are useful to design optimized grids and improve numerical predictions in similar configurations.« less

On the Relationship between Variational Level Set-Based and SOM-Based Active Contours

PubMed Central

Abdelsamea, Mohammed M.; Gnecco, Giorgio; Gaber, Mohamed Medhat; Elyan, Eyad

2015-01-01

Most Active Contour Models (ACMs) deal with the image segmentation problem as a functional optimization problem, as they work on dividing an image into several regions by optimizing a suitable functional. Among ACMs, variational level set methods have been used to build an active contour with the aim of modeling arbitrarily complex shapes. Moreover, they can handle also topological changes of the contours. Self-Organizing Maps (SOMs) have attracted the attention of many computer vision scientists, particularly in modeling an active contour based on the idea of utilizing the prototypes (weights) of a SOM to control the evolution of the contour. SOM-based models have been proposed in general with the aim of exploiting the specific ability of SOMs to learn the edge-map information via their topology preservation property and overcoming some drawbacks of other ACMs, such as trapping into local minima of the image energy functional to be minimized in such models. In this survey, we illustrate the main concepts of variational level set-based ACMs, SOM-based ACMs, and their relationship and review in a comprehensive fashion the development of their state-of-the-art models from a machine learning perspective, with a focus on their strengths and weaknesses. PMID:25960736

Nonlinear microrheology and molecular imaging to map microscale deformations of entangled DNA networks

NASA Astrophysics Data System (ADS)

Wu, Tsai-Chin; Anderson, Rae

We use active microrheology coupled to single-molecule fluorescence imaging to elucidate the microscale dynamics of entangled DNA. DNA naturally exists in a wide range of lengths and topologies, and is often confined in cell nucleui, forming highly concentrated and entangled biopolymer networks. Thus, DNA is the model polymer for understanding entangled polymer dynamics as well as the crowded environment of cells. These networks display complex viscoelastic properties that are not well understood, especially at the molecular-level and in response to nonlinear perturbations. Specifically, how microscopic stresses and strains propagate through entangled networks, and what molecular deformations lead to the network stress responses are unknown. To answer these important questions, we optically drive a microsphere through entangled DNA, perturbing the system far from equilibrium, while measuring the resistive force the DNA exerts on the bead during and after bead motion. We simultaneously image single fluorescent-labeled DNA molecules throughout the network to directly link the microscale stress response to molecular deformations. We characterize the deformation of the network from the molecular-level to the mesoscale, and map the stress propagation throughout the network. We further study the impact of DNA length (11 - 115 kbp) and topology (linear vs ring DNA) on deformation and propagation dynamics, exploring key nonlinear features such as tube dilation and power-law relaxation.

Topological Schemas of Memory Spaces

PubMed Central

Babichev, Andrey; Dabaghian, Yuri A.

2018-01-01

Hippocampal cognitive map—a neuronal representation of the spatial environment—is widely discussed in the computational neuroscience literature for decades. However, more recent studies point out that hippocampus plays a major role in producing yet another cognitive framework—the memory space—that incorporates not only spatial, but also non-spatial memories. Unlike the cognitive maps, the memory spaces, broadly understood as “networks of interconnections among the representations of events,” have not yet been studied from a theoretical perspective. Here we propose a mathematical approach that allows modeling memory spaces constructively, as epiphenomena of neuronal spiking activity and thus to interlink several important notions of cognitive neurophysiology. First, we suggest that memory spaces have a topological nature—a hypothesis that allows treating both spatial and non-spatial aspects of hippocampal function on equal footing. We then model the hippocampal memory spaces in different environments and demonstrate that the resulting constructions naturally incorporate the corresponding cognitive maps and provide a wider context for interpreting spatial information. Lastly, we propose a formal description of the memory consolidation process that connects memory spaces to the Morris' cognitive schemas-heuristic representations of the acquired memories, used to explain the dynamics of learning and memory consolidation in a given environment. The proposed approach allows evaluating these constructs as the most compact representations of the memory space's structure. PMID:29740306

ICD-10 procedure codes produce transition challenges

PubMed Central

Boyd, Andrew D.; Li, Jianrong ‘John’; Kenost, Colleen; Zaim, Samir Rachid; Krive, Jacob; Mittal, Manish; Satava, Richard A.; Burton, Michael; Smith, Jacob; Lussier, Yves A.

2018-01-01

The transition of procedure coding from ICD-9-CM-Vol-3 to ICD-10-PCS has generated problems for the medical community at large resulting from the lack of clarity required to integrate two non-congruent coding systems. We hypothesized that quantifying these issues with network topology analyses offers a better understanding of the issues, and therefore we developed solutions (online tools) to empower hospital administrators and researchers to address these challenges. Five topologies were identified: “identity”(I), “class-to-subclass”(C2S), “subclass-toclass”(S2C), “convoluted(C)”, and “no mapping”(NM). The procedure codes in the 2010 Illinois Medicaid dataset (3,290 patients, 116 institutions) were categorized as C=55%, C2S=40%, I=3%, NM=2%, and S2C=1%. Majority of the problematic and ambiguous mappings (convoluted) pertained to operations in ophthalmology cardiology, urology, gyneco-obstetrics, and dermatology. Finally, the algorithms were expanded into a user-friendly tool to identify problematic topologies and specify lists of procedural codes utilized by medical professionals and researchers for mitigating error-prone translations, simplifying research, and improving quality.http://www.lussiergroup.org/transition-to-ICD10PCS PMID:29888037

Design Optimization of Irregular Cellular Structure for Additive Manufacturing

NASA Astrophysics Data System (ADS)

Song, Guo-Hua; Jing, Shi-Kai; Zhao, Fang-Lei; Wang, Ye-Dong; Xing, Hao; Zhou, Jing-Tao

2017-09-01

Irregularcellular structurehas great potential to be considered in light-weight design field. However, the research on optimizing irregular cellular structures has not yet been reporteddue to the difficulties in their modeling technology. Based on the variable density topology optimization theory, an efficient method for optimizing the topology of irregular cellular structures fabricated through additive manufacturing processes is proposed. The proposed method utilizes tangent circles to automatically generate the main outline of irregular cellular structure. The topological layoutof each cellstructure is optimized using the relative density informationobtained from the proposed modified SIMP method. A mapping relationship between cell structure and relative densityelement is builtto determine the diameter of each cell structure. The results show that the irregular cellular structure can be optimized with the proposed method. The results of simulation and experimental test are similar for irregular cellular structure, which indicate that the maximum deformation value obtained using the modified Solid Isotropic Microstructures with Penalization (SIMP) approach is lower 5.4×10-5 mm than that using the SIMP approach under the same under the same external load. The proposed research provides the instruction to design the other irregular cellular structure.

Topological superconductivity in the extended Kitaev-Heisenberg model

NASA Astrophysics Data System (ADS)

Schmidt, Johann; Scherer, Daniel D.; Black-Schaffer, Annica M.

2018-01-01

We study superconducting pairing in the doped Kitaev-Heisenberg model by taking into account the recently proposed symmetric off-diagonal exchange Γ . By performing a mean-field analysis, we classify all possible superconducting phases in terms of symmetry, explicitly taking into account effects of spin-orbit coupling. Solving the resulting gap equations self-consistently, we map out a phase diagram that involves several topologically nontrivial states. For Γ <0 , we find a competition between a time-reversal symmetry-breaking chiral phase with Chern number ±1 and a time-reversal symmetric nematic phase that breaks the rotational symmetry of the lattice. On the other hand, for Γ ≥0 we find a time-reversal symmetric phase that preserves all the lattice symmetries, thus yielding clearly distinguishable experimental signatures for all superconducting phases. Both of the time-reversal symmetric phases display a transition to a Z2 nontrivial phase at high doping levels. Finally, we also include a symmetry-allowed spin-orbit coupling kinetic energy and show that it destroys a tentative symmetry-protected topological order at lower doping levels. However, it can be used to tune the time-reversal symmetric phases into a Z2 nontrivial phase even at lower doping.

SModelS v1.1 user manual: Improving simplified model constraints with efficiency maps

NASA Astrophysics Data System (ADS)

Ambrogi, Federico; Kraml, Sabine; Kulkarni, Suchita; Laa, Ursula; Lessa, Andre; Magerl, Veronika; Sonneveld, Jory; Traub, Michael; Waltenberger, Wolfgang

2018-06-01

SModelS is an automatized tool for the interpretation of simplified model results from the LHC. It allows to decompose models of new physics obeying a Z2 symmetry into simplified model components, and to compare these against a large database of experimental results. The first release of SModelS, v1.0, used only cross section upper limit maps provided by the experimental collaborations. In this new release, v1.1, we extend the functionality of SModelS to efficiency maps. This increases the constraining power of the software, as efficiency maps allow to combine contributions to the same signal region from different simplified models. Other new features of version 1.1 include likelihood and χ2 calculations, extended information on the topology coverage, an extended database of experimental results as well as major speed upgrades for both the code and the database. We describe in detail the concepts and procedures used in SModelS v1.1, explaining in particular how upper limits and efficiency map results are dealt with in parallel. Detailed instructions for code usage are also provided.

Simulating Electron Cyclotron Maser Emission for Low Mass Stars

NASA Astrophysics Data System (ADS)

Llama, Joe; Jardine, Moira

2018-01-01

Zeeman-Doppler Imaging (ZDI) is a powerful technique that enables us to map the large-scale magnetic fields of stars spanning the pre- and main-sequence. Coupling these magnetic maps with field extrapolation methods allow us to investigate the topology of the closed, X-ray bright corona, and the cooler, open stellar wind.Using ZDI maps of young M dwarfs with simultaneous radio light curves obtained from the VLA, we present the results of modeling the Electron-Cyclotron Maser (ECM) emission from these systems. We determine the X-ray luminosity and ECM emission that is produced using the ZDI maps and our field extrapolation model. We compare these findings with the observed radio light curves of these stars. This allows us to predict the relative phasing and amplitude of the stellar X-ray and radio light curves.This benchmarking of our model using these systems allows us to predict the ECM emission for all stars that have a ZDI map and an observed X-ray luminosity. Our model allows us to understand the origin of transient radio emission observations and is crucial for disentangling stellar and exoplanetary radio signals.

Destruction of the Last Good Magnetic Surface in Diii-D Usn with Elms and C-Coils Shot 115467 due to Generalized Asymmetries Using Maps

NASA Astrophysics Data System (ADS)

Herrera, A.; Ali, H.; Punjabi, A.

2004-11-01

The unperturbed magnetic topology of DIII-D USN shot 115467 in the absence of ELMs and C-coils is described by the symmetric simple map (SSM) with the map parameter k=0.2623. For this k, the last good surface passes through x=0 and y=0.9995, q_edge=6.48 if six iterations of the SSM are taken to be equivalent to a single toroidal circuit of DIII-D, and the q_edge equals the q_edge in the DIII-D for shot 115467 [1]. The map parameter k represents the effects of the toroidal asymmetries. We study the changes in the last good surface and its destruction as the map parameter k is increased. This work is supported by NASA SHARP program and DE-FG02-02ER54673. [1] H. Ali, A. Punjabi, A. Boozer, and T. Evans, presented at the 31st European Physical Society Plasma Physics Meeting, London, UK, June 29, 2004, paper P2-172.

Mapping the band structure of a surface phononic crystal

NASA Astrophysics Data System (ADS)

Maznev, A. A.; Wright, O. B.; Matsuda, O.

2011-01-01

We map the band structure of surface acoustic modes of a periodic array of copper lines embedded in a SiO2 film on a silicon substrate by means of the laser-induced transient grating technique. A detailed map of the lowest sheet of the ω(k) surface and partial maps of two higher-order sheets are obtained. We discuss the topology of the ω(k) surface and explain how it arises from the Rayleigh and Sezawa modes of the film/substrate system. In the vicinity of the bandgap formed at the Brillouin zone boundary, the first and second dispersion sheets take the form of a saddle and a bowl, respectively, in agreement with a weak perturbation model. The shape of the third dispersion sheet, however, appears to defy expectations based on the perturbation approach. In particular, it contains minima located off the symmetry directions, which implies the existence of zero group velocity modes with an obliquely directed wavevector.

Cross-entropy embedding of high-dimensional data using the neural gas model.

PubMed

Estévez, Pablo A; Figueroa, Cristián J; Saito, Kazumi

2005-01-01

A cross-entropy approach to mapping high-dimensional data into a low-dimensional space embedding is presented. The method allows to project simultaneously the input data and the codebook vectors, obtained with the Neural Gas (NG) quantizer algorithm, into a low-dimensional output space. The aim of this approach is to preserve the relationship defined by the NG neighborhood function for each pair of input and codebook vectors. A cost function based on the cross-entropy between input and output probabilities is minimized by using a Newton-Raphson method. The new approach is compared with Sammon's non-linear mapping (NLM) and the hierarchical approach of combining a vector quantizer such as the self-organizing feature map (SOM) or NG with the NLM recall algorithm. In comparison with these techniques, our method delivers a clear visualization of both data points and codebooks, and it achieves a better mapping quality in terms of the topology preservation measure q(m).

T-duality simplifies bulk-boundary correspondence: the noncommutative case

NASA Astrophysics Data System (ADS)

Hannabuss, Keith C.; Mathai, Varghese; Thiang, Guo Chuan

2018-05-01

We state and prove a general result establishing that T-duality, or the Connes-Thom isomorphism, simplifies the bulk-boundary correspondence, given by a boundary map in K-theory, in the sense of converting it to a simple geometric restriction map. This settles in the affirmative several earlier conjectures of the authors and provides a clear geometric picture of the correspondence. In particular, our result holds in arbitrary spatial dimension, in both the real and complex cases, and also in the presence of disorder, magnetic fields, and H-flux. These special cases are relevant both to string theory and to the study of the quantum Hall effect and topological insulators with defects in condensed matter physics.

Singlet oxygen Triplet Energy Transfer based imaging technology for mapping protein-protein proximity in intact cells

PubMed Central

To, Tsz-Leung; Fadul, Michael J.; Shu, Xiaokun

2014-01-01

Many cellular processes are carried out by large protein complexes that can span several tens of nanometers. Whereas Forster resonance energy transfer has a detection range of <10 nm, here we report the theoretical development and experimental demonstration of a new fluorescence imaging technology with a detection range of up to several tens of nanometers: singlet oxygen triplet energy transfer. We demonstrate that our method confirms the topology of a large protein complex in intact cells, which spans from the endoplasmic reticulum to the outer mitochondrial membrane and the matrix. This new method is thus suited for mapping protein proximity in large protein complexes. PMID:24905026

Inverse Problems for Semilinear Wave Equations on Lorentzian Manifolds

NASA Astrophysics Data System (ADS)

Lassas, Matti; Uhlmann, Gunther; Wang, Yiran

2018-06-01

We consider inverse problems in space-time ( M, g), a 4-dimensional Lorentzian manifold. For semilinear wave equations {\\square_g u + H(x, u) = f}, where {\\square_g} denotes the usual Laplace-Beltrami operator, we prove that the source-to-solution map {L: f → u|_V}, where V is a neighborhood of a time-like geodesic {μ}, determines the topological, differentiable structure and the conformal class of the metric of the space-time in the maximal set, where waves can propagate from {μ} and return back. Moreover, on a given space-time ( M, g), the source-to-solution map determines some coefficients of the Taylor expansion of H in u.

Terrain following of arbitrary surfaces using a high intensity LED proximity sensor

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

Baker, J.E.

1992-01-01

Many robotic operations, e.g., mapping, scanning, feature following, etc., require accurate surface following of arbitrary targets. This paper presents a versatile surface following and mapping system designed to promote hardware, software and application independence, modular development, and upward expandability. These goals are met by: a full, a priori specification of the hardware and software interfaces; a modular system architecture; and a hierarchical surface-data analysis method, permitting application specific tuning at each conceptual level of topological abstraction. This surface following system was fully designed and independently of any specific robotic host, then successfully integrated with and demonstrated on a completely amore » priori unknown, real-time robotic system. 7 refs.« less

2D massless Dirac Fermi gas model of superconductivity in the surface state of a topological insulator at high magnetic fields

NASA Astrophysics Data System (ADS)

Zhuravlev, Vladimir; Duan, Wenye; Maniv, Tsofar

2017-10-01

The Nambu-Gorkov Green's function approach is applied to strongly type-II superconductivity in a 2D spin-momentum-locked (Weyl) Fermi gas model at high perpendicular magnetic fields. The resulting phase diagram can be mapped onto that derived for the standard, parabolic band-structure model, having the same Fermi surface parameters, E F and v, but with cyclotron effective mass m\\ast=EF/2v2 . Significant deviations from the predicted mapping are found only for very small E F , when the Landau-Level filling factors are smaller than unity, and E F shrinks below the cutoff energy.

An ab initio investigation of Bi2Se3 topological insulator deposited on amorphous SiO2.

PubMed

de Oliveira, I S S; Scopel, W L; Miwa, R H

2017-02-01

We use first-principles simulations to investigate the topological properties of Bi 2 Se 3 thin films deposited on amorphous SiO 2 , Bi 2 Se 3 /a-SiO 2 , which is a promising substrate for topological insulator (TI) based device applications. The Bi 2 Se 3 films are bonded to a-SiO 2 mediated by van der Waals interactions. Upon interaction with the substrate, the Bi 2 Se 3 topological surface and interface states remain present, however the degeneracy between the Dirac-like cones is broken. The energy separation between the two Dirac-like cones increases with the number of Bi 2 Se 3 quintuple layers (QLs) deposited on the substrate. Such a degeneracy breaking is caused by (i) charge transfer from the TI to the substrate and charge redistribution along the Bi 2 Se 3 QLs, and (ii) by deformation of the QL in contact with the a-SiO 2 substrate. We also investigate the role played by oxygen vacancies ([Formula: see text]) on the a-SiO 2 , which increases the energy splitting between the two Dirac-like cones. Finally, by mapping the electronic structure of Bi 2 Se 3 /a-SiO 2 , we found that the a-SiO 2 surface states, even upon the presence of [Formula: see text], play a minor role on gating the electronic transport properties of Bi 2 Se 3 .

Cognitive Mapping Based on Conjunctive Representations of Space and Movement

PubMed Central

Zeng, Taiping; Si, Bailu

2017-01-01

It is a challenge to build robust simultaneous localization and mapping (SLAM) system in dynamical large-scale environments. Inspired by recent findings in the entorhinal–hippocampal neuronal circuits, we propose a cognitive mapping model that includes continuous attractor networks of head-direction cells and conjunctive grid cells to integrate velocity information by conjunctive encodings of space and movement. Visual inputs from the local view cells in the model provide feedback cues to correct drifting errors of the attractors caused by the noisy velocity inputs. We demonstrate the mapping performance of the proposed cognitive mapping model on an open-source dataset of 66 km car journey in a 3 km × 1.6 km urban area. Experimental results show that the proposed model is robust in building a coherent semi-metric topological map of the entire urban area using a monocular camera, even though the image inputs contain various changes caused by different light conditions and terrains. The results in this study could inspire both neuroscience and robotic research to better understand the neural computational mechanisms of spatial cognition and to build robust robotic navigation systems in large-scale environments. PMID:29213234

Open quantum maps from complex scaling of kicked scattering systems

NASA Astrophysics Data System (ADS)

Mertig, Normann; Shudo, Akira

2018-04-01

We derive open quantum maps from periodically kicked scattering systems and discuss the computation of their resonance spectra in terms of theoretically grounded methods, such as complex scaling and sufficiently weak absorbing potentials. In contrast, we also show that current implementations of open quantum maps, based on strong absorptive or even projective openings, fail to produce the resonance spectra of kicked scattering systems. This comparison pinpoints flaws in current implementations of open quantum maps, namely, the inability to separate resonance eigenvalues from the continuum as well as the presence of diffraction effects due to strong absorption. The reported deviations from the true resonance spectra appear, even if the openings do not affect the classical trapped set, and become appreciable for shorter-lived resonances, e.g., those associated with chaotic orbits. This makes the open quantum maps, which we derive in this paper, a valuable alternative for future explorations of quantum-chaotic scattering systems, for example, in the context of the fractal Weyl law. The results are illustrated for a quantum map model whose classical dynamics exhibits key features of ionization and a trapped set which is organized by a topological horseshoe.

Preliminary Results on the Heat Deposition on Divertor Plate using Low MN Map

NASA Astrophysics Data System (ADS)

Ali, Halima; Punjabi, Alkesh; Boozer, Allen

2003-10-01

The study of magnetic field line behavior and the closely related plasma behavior are important not only for their tokamak application but also for their application to other Hamiltonian, or near-Hamiltonian, systems. The behavior of field lines near a tokamak separatrix has been studied extensively using various approaches. Our approach is called method of maps. In this paper, we introduce an area-preserving map called Low MN map. We first derive the map from the general theory of maps /1/, and then use it to calculate the effects of m = 1, n = 1 perturbations on the stochastic layer and magnetic footprint in single-null divertor tokamaks. We show that there are self-similarities, singularities, and topological equivalences in the pattern of physical parameters that characterize the stochastic layer and the magnetic footprint. Preliminary results in the investigation on the heat distribution on the divertor plate indicate multiple peaked in heat flux profile distributed radially across the divertor target when the amplitude is 10-3. This, and other features, are in good agreement with experimental observations. This work is done under the DOE grant number DE-FG02-01ER54624. 1. A. Punjabi et al, J. Plasma Phys. 52, 91 (1994).

Extracting Lane Geometry and Topology Information from Vehicle Fleet Trajectories in Complex Urban Scenarios Using a Reversible Jump Mcmc Method

NASA Astrophysics Data System (ADS)

Roeth, O.; Zaum, D.; Brenner, C.

2017-05-01

Highly automated driving (HAD) requires maps not only of high spatial precision but also of yet unprecedented actuality. Traditionally small highly specialized fleets of measurement vehicles are used to generate such maps. Nevertheless, for achieving city-wide or even nation-wide coverage, automated map update mechanisms based on very large vehicle fleet data gain importance since highly frequent measurements are only to be obtained using such an approach. Furthermore, the processing of imprecise mass data in contrast to few dedicated highly accurate measurements calls for a high degree of automation. We present a method for the generation of lane-accurate road network maps from vehicle trajectory data (GPS or better). Our approach therefore allows for exploiting today's connected vehicle fleets for the generation of HAD maps. The presented algorithm is based on elementary building blocks which guarantees useful lane models and uses a Reversible Jump Markov chain Monte Carlo method to explore the models parameters in order to reconstruct the one most likely emitting the input data. The approach is applied to a challenging urban real-world scenario of different trajectory accuracy levels and is evaluated against a LIDAR-based ground truth map.

The binary protein-protein interaction landscape of Escherichia coli

PubMed Central

Rajagopala, Seesandra V.; Vlasblom, James; Arnold, Roland; Franca-Koh, Jonathan; Pakala, Suman B.; Phanse, Sadhna; Ceol, Arnaud; Häuser, Roman; Siszler, Gabriella; Wuchty, Stefan; Emili, Andrew; Babu, Mohan; Aloy, Patrick; Pieper, Rembert; Uetz, Peter

2014-01-01

Efforts to map the Escherichia coli interactome have identified several hundred macromolecular complexes, but direct binary protein-protein interactions (PPIs) have not been surveyed on a large scale. Here we performed yeast two-hybrid screens of 3,305 baits against 3,606 preys (~70% of the E. coli proteome) in duplicate to generate a map of 2,234 interactions, approximately doubling the number of known binary PPIs in E. coli. Integration of binary PPIs and genetic interactions revealed functional dependencies among components involved in cellular processes, including envelope integrity, flagellum assembly and protein quality control. Many of the binary interactions that could be mapped within multi-protein complexes were informative regarding internal topology and indicated that interactions within complexes are significantly more conserved than those interactions connecting different complexes. This resource will be useful for inferring bacterial gene function and provides a draft reference of the basic physical wiring network of this evolutionarily significant model microbe. PMID:24561554

Elastic models: a comparative study applied to retinal images.

PubMed

Karali, E; Lambropoulou, S; Koutsouris, D

2011-01-01

In this work various methods of parametric elastic models are compared, namely the classical snake, the gradient vector field snake (GVF snake) and the topology-adaptive snake (t-snake), as well as the method of self-affine mapping system as an alternative to elastic models. We also give a brief overview of the methods used. The self-affine mapping system is implemented using an adapting scheme and minimum distance as optimization criterion, which is more suitable for weak edges detection. All methods are applied to glaucomatic retinal images with the purpose of segmenting the optical disk. The methods are compared in terms of segmentation accuracy and speed, as these are derived from cross-correlation coefficients between real and algorithm extracted contours and segmentation time, respectively. As a result, the method of self-affine mapping system presents adequate segmentation time and segmentation accuracy, and significant independence from initialization.

Complex Networks in Psychological Models

NASA Astrophysics Data System (ADS)

Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.

We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.

Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

PubMed

Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

2007-08-20

In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

(Semi-)Automated landform mapping of the alpine valley Gradental (Austria) based on LiDAR data

NASA Astrophysics Data System (ADS)

Strasser, T.; Eisank, C.

2012-04-01

Alpine valleys are typically characterised as complex, hierarchical structured systems with rapid landform changes. Detection of landform changes can be supported by automated geomorphological mapping. Especially, the analysis over short time scales require a method for standardised, unbiased geomorphological map reproduction, which is delivered by automated mapping techniques. In general, digital geomorphological mapping is a challenging task, since knowledge about landforms with respect to their natural boundaries as well as their hierarchical and scaling relationships, has to be integrated in an objective way. A combination of very-high spatial resolution data (VHSR) such as LiDAR and new methods like object based image analysis (OBIA) allow for a more standardised production of geomorphological maps. In OBIA the processing units are spatially configured objects that are created by multi-scale segmentation. Therefore, not only spectral information can be used for assigning the objects to geomorphological classes, but also spatial and topological properties can be exploited. In this study we focus on the detection of landforms, especially bedrock sediment deposits (alluvion, debris cone, talus, moraine, rockglacier), as well as glaciers. The study site Gradental [N 46°58'29.1"/ E 12°48'53.8"] is located in the Schobergruppe (Austria, Carinthia) and is characterised by heterogenic geology conditions and high process activity. The area is difficult to access and dominated by steep slopes, thus hindering a fast and detailed geomorphological field mapping. Landforms are identified using aerial and terrestrial LiDAR data (1 m spatial resolution). These DEMs are analysed by an object based hierarchical approach, which is structured in three main steps. The first step is to define occurring landforms by basic land surface parameters (LSPs), topology and hierarchy relations. Based on those definitions a semantic model is created. Secondly, a multi-scale segmentation is performed on a three-band LSP that integrates slope, aspect and plan curvature, which expresses the driving forces of geomorphological processes. In the third step, the generated multi-level object structures are classified in order to produce the geomorphological map. The classification rules are derived from the semantic model. Due to landform type-specific scale dependencies of LSPs, the values of LSPs used in the classification are calculated in a multi-scale manner by constantly enlarging the size of the moving window. In addition, object form properties (density, compactness, rectangular fit) are utilised as additional information for landform characterisation. Validation of classification is performed by intersecting a visually interpreted reference map with the classification output map and calculating accuracy matrices. Validation shows an overall accuracy of 78.25 % and a Kappa of 0.65. The natural borders of landforms can be easily detected by the use of slope, aspect and plan curvature. This study illustrates the potential of OBIA for a more standardised and automated mapping of surface units (landforms, landcover). Therefore, the presented methodology features a prospective automated geomorphological mapping approach for alpine regions.

KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms

PubMed Central

Chiu, Yi-Yuan; Lin, Chih-Ta; Huang, Jhang-Wei; Hsu, Kai-Cheng; Tseng, Jen-Hu; You, Syuan-Ren; Yang, Jinn-Moon

2013-01-01

Kinases play central roles in signaling pathways and are promising therapeutic targets for many diseases. Designing selective kinase inhibitors is an emergent and challenging task, because kinases share an evolutionary conserved ATP-binding site. KIDFamMap (http://gemdock.life.nctu.edu.tw/KIDFamMap/) is the first database to explore kinase-inhibitor families (KIFs) and kinase-inhibitor-disease (KID) relationships for kinase inhibitor selectivity and mechanisms. This database includes 1208 KIFs, 962 KIDs, 55 603 kinase-inhibitor interactions (KIIs), 35 788 kinase inhibitors, 399 human protein kinases, 339 diseases and 638 disease allelic variants. Here, a KIF can be defined as follows: (i) the kinases in the KIF with significant sequence similarity, (ii) the inhibitors in the KIF with significant topology similarity and (iii) the KIIs in the KIF with significant interaction similarity. The KIIs within a KIF are often conserved on some consensus KIDFamMap anchors, which represent conserved interactions between the kinase subsites and consensus moieties of their inhibitors. Our experimental results reveal that the members of a KIF often possess similar inhibition profiles. The KIDFamMap anchors can reflect kinase conformations types, kinase functions and kinase inhibitor selectivity. We believe that KIDFamMap provides biological insights into kinase inhibitor selectivity and binding mechanisms. PMID:23193279

Calculation of stochastic broadening due to low mn magnetic perturbation in the simple map in action-angle coordinates

NASA Astrophysics Data System (ADS)

Hinton, Courtney; Punjabi, Alkesh; Ali, Halima

2009-11-01

The simple map is the simplest map that has topology of divertor tokamaks [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Let. A 364, 140--145 (2007)]. Recently, the action-angle coordinates for simple map are analytically calculated, and simple map is constructed in action-angle coordinates [O. Kerwin, A. Punjabi, and H. Ali, Phys. Plasmas 15, 072504 (2008)]. Action-angle coordinates for simple map cannot be inverted to real space coordinates (R,Z). Because there is logarithmic singularity on the ideal separatrix, trajectories cannot cross separatrix [op cit]. Simple map in action-angle coordinates is applied to calculate stochastic broadening due to the low mn magnetic perturbation with mode numbers m=1, and n=±1. The width of stochastic layer near the X-point scales as 0.63 power of the amplitude δ of low mn perturbation, toroidal flux loss scales as 1.16 power of δ, and poloidal flux loss scales as 1.26 power of δ. Scaling of width deviates from Boozer-Rechester scaling by 26% [A. Boozer, and A. Rechester, Phys. Fluids 21, 682 (1978)]. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

Design and experimental observation of valley-Hall edge states in diatomic-graphene-like elastic waveguides

NASA Astrophysics Data System (ADS)

Zhu, Hongfei; Liu, Ting-Wei; Semperlotti, Fabio

2018-05-01

We report on the design and experimental validation of a two-dimensional phononic elastic waveguide exhibiting topological valley-Hall edge states. The lattice structure of the waveguide is inspired by diatomic graphene, and it is imprinted in an initially flat plate by means of geometric indentations. The indentations are distributed according to a hexagonal lattice structure which guarantees the existence of Dirac dispersion at the boundary of the Brillouin zone. Starting from this basic material, domain walls capable of supporting edge states can be obtained by contrasting waveguides having broken space-inversion symmetry (SIS) achieved by using local resonant elements. Our theoretical study shows that such material maps into the acoustic analog of the quantum valley-Hall effect, while numerical and experimental results confirm the existence of protected edge states traveling along the walls of topologically distinct domains.

A topology of mineralization and its meaning for prospecting

USGS Publications Warehouse

Neuerburg, G.J.

1982-01-01

Epigenetic mineral deposits are universal members of an orderly spatial and temporal arrangement of igneous rocks, endomorphic rocks, and hydrothermally altered rocks. The association and sequence of these rocks is invariant whereas the metric relations and configurations of the properties of these rocks are unlimited in variety. This characterization satisfies the doctrines of topology. Metric relations are statistical, and their modes are among the better guides to optimal areas for exploration. Metric configurations are graphically irregular and unpredictable mathematical surfaces like mountain topography. Each mineral edifice must be mapped to locate its mineral deposits. All measurements and observations are only positive or neutral for the occurrence of a mineral deposit. Effective prospecting is based on an increasing density of positive data with proximity to the mineral deposit. This means sampling for maximal numbers of positive data, pragmatically the highest ore-element assays at each site, by selecting rock showing maximal development of lode attributes.

Spatial and layer-controlled variability in fracture networks

NASA Astrophysics Data System (ADS)

Procter, Andrew; Sanderson, David J.

2018-03-01

Topological sampling, based on 1) node counting and 2) circular sampling areas, is used to measure fracture intensity in surface exposures of a layered limestone/shale sequence in north Somerset, UK. This method provides similar levels of precision as more traditional line samples, but is about 10 times quicker and allows characterization of the network topology. Georeferencing of photographs of the sample sites allows later analysis of trace lengths and orientations, and identification of joint set development. ANOVA tests support a complex interaction of within-layer, between-layer and between-location variability in fracture intensity, with the different layers showing anomalous intensity at different locations. This variation is not simply due to bed thickness, nor can it be related to any obvious compositional or textural variation between the limestone beds. These results are used to assess approaches to the spatial mapping of fracture intensity.

Topological semimetals carrying arbitrary Hopf numbers: Fermi surface topologies of a Hopf link, Solomon's knot, trefoil knot, and other linked nodal varieties

NASA Astrophysics Data System (ADS)

Ezawa, Motohiko

2017-07-01

We propose a type of Hopf semimetal indexed by a pair of numbers (p ,q ) , where the Hopf number is given by p q . The Fermi surface is given by a preimage of the Hopf map, which consists of loops nontrivially linked for a nonzero Hopf number. The Fermi surface forms a torus link, whose examples are a Hopf link indexed by (1 ,1 ) , Solomon's knot (2 ,1 ) , a double Hopf link (2 ,2 ) , and a double trefoil knot (3 ,2 ) . We may choose p or q to be a half integer, where the Fermi surface is a torus knot, such as a trefoil knot (3 /2 ,1 ) . It is even possible to make the Hopf number an arbitrary rational number, where a semimetal whose Fermi surface forms open strings is generated.

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

PubMed

Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

2017-07-01

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

Topological properties of the limited penetrable horizontal visibility graph family

NASA Astrophysics Data System (ADS)

Wang, Minggang; Vilela, André L. M.; Du, Ruijin; Zhao, Longfeng; Dong, Gaogao; Tian, Lixin; Stanley, H. Eugene

2018-05-01

The limited penetrable horizontal visibility graph algorithm was recently introduced to map time series in complex networks. In this work, we extend this algorithm to create a directed-limited penetrable horizontal visibility graph and an image-limited penetrable horizontal visibility graph. We define two algorithms and provide theoretical results on the topological properties of these graphs associated with different types of real-value series. We perform several numerical simulations to check the accuracy of our theoretical results. Finally, we present an application of the directed-limited penetrable horizontal visibility graph to measure real-value time series irreversibility and an application of the image-limited penetrable horizontal visibility graph that discriminates noise from chaos. We also propose a method to measure the systematic risk using the image-limited penetrable horizontal visibility graph, and the empirical results show the effectiveness of our proposed algorithms.

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

PubMed Central

Naughton, Catherine; Avlonitis, Nicolaos; Corless, Samuel; Prendergast, James G.; Mati, Ioulia K.; Eijk, Paul P.; Cockroft, Scott L.; Bradley, Mark; Ylstra, Bauke; Gilbert, Nick

2013-01-01

DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. PMID:23416946

On building a memory evolutive system for application to learning and cognition modeling.

PubMed

de Lima do Rego Monteiro, Julio; Kogler, Joao Eduardo; Ribeiro, Joao Henrique Ranhel; Netto, Marcio Lobo

2010-01-01

We address here aspects of the implementation of a memory evolutive system (MES), based on the model proposed by A. Ehresmann and J. Vanbremeersch (2007), by means of a simulated network of spiking neurons with time dependent plasticity. We point out the advantages and challenges of applying category theory for the representation of cognition, by using the MES architecture. Then we discuss the issues concerning the minimum requirements that an artificial neural network (ANN) should fulfill in order that it would be capable of expressing the categories and mappings between them, underlying the MES. We conclude that a pulsed ANN based on Izhikevich's formal neuron with STDP (spike time-dependent plasticity) has sufficient dynamical properties to achieve these requirements, provided it can cope with the topological requirements. Finally, we present some perspectives of future research concerning the proposed ANN topology.

On load paths and load bearing topology from finite element analysis

NASA Astrophysics Data System (ADS)

Kelly, D.; Reidsema, C.; Lee, M.

2010-06-01

Load paths can be mapped from vector plots of 'pointing stress vectors'. They define a path along which a component of load remains constant as it traverses the solution domain. In this paper the theory for the paths is first defined. Properties of the plots that enable a designer to interpret the structural behavior from the contours are then identified. Because stress is a second order tensor defined on an orthogonal set of axes, the vector plots define separate paths for load transfer in each direction of the set of axes. An algorithm is therefore presented that combines the vectors to define a topology to carry the loads. The algorithm is shown to straighten the paths reducing bending moments and removing stress concentration. Application to a bolted joint, a racing car body and a yacht hull demonstrate the usefulness of the plots.

Evolution of the social network of scientific collaborations

NASA Astrophysics Data System (ADS)

Barabasi, Albert-Laszlo; Jeong, Hawoong; Neda, Zoltan; Ravasz, Erzsebet; Schubert, Andras; Vicsek, Tamas

2002-03-01

The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer the dynamic and the structural mechanisms that govern the evolution and topology of this complex system. First, empirical measurements allow us to uncover the topological measures that characterize the network at a given moment, as well as the time evolution of these quantities. The results indicate that the network is scale-free, and that the network evolution is governed by preferential attachment, affecting both internal and external links. However, in contrast with most model predictions the average degree increases in time, and the node separation decreases. Second, we propose a simple model that captures the network's time evolution. Third, numerical simulations are used to uncover the behavior of quantities that could not be predicted analytically.

Holographic free-electron light source

PubMed Central

Li, Guanhai; Clarke, Brendan P.; So, Jin-Kyu; MacDonald, Kevin F.; Zheludev, Nikolay I.

2016-01-01

Recent advances in the physics and technology of light generation via free-electron proximity and impact interactions with nanostructures (gratings, photonic crystals, nano-undulators, metamaterials and antenna arrays) have enabled the development of nanoscale-resolution techniques for such applications as mapping plasmons, studying nanoparticle structural transformations and characterizing luminescent materials (including time-resolved measurements). Here, we introduce a universal approach allowing generation of light with prescribed wavelength, direction, divergence and topological charge via point-excitation of holographic plasmonic metasurfaces. It is illustrated using medium-energy free-electron injection to generate highly-directional visible to near-infrared light beams, at selected wavelengths in prescribed azimuthal and polar directions, with brightness two orders of magnitude higher than that from an unstructured surface, and vortex beams with topological charge up to ten. Such emitters, with micron-scale dimensions and the freedom to fully control radiation parameters, offer novel applications in nano-spectroscopy, nano-chemistry and sensing. PMID:27910853

Analysis of Discontinuity Induced Bifurcations in a Dual Input DC-DC Converter

NASA Astrophysics Data System (ADS)

Giaouris, Damian; Banerjee, Soumitro; Mandal, Kuntal; Al-Hindawi, Mohammed M.; Abusorrah, Abdullah; Al-Turki, Yusuf; El Aroudi, Abdelali

DC-DC power converters with multiple inputs and a single output are used in numerous applications where multiple sources, e.g. two or more renewable energy sources and/or a battery, feed a single load. In this work, a classical boost converter topology with two input branches connected to two different sources is chosen, with each branch independently being controlled by a separate peak current mode controller. We demonstrate for the first time that even though this converter is similar to other well known topologies that have been studied before, it exhibits many complex nonlinear behaviors that are not found in any other standard PWM controlled power converter. The system undergoes period incrementing cascade as a parameter is varied, with discontinuous hard transitions between consecutive periodicities. We show that the system can be described by a discontinuous map, which explains the observed bifurcation phenomena. The results have been experimentally validated.

Geologic map of the Haji-Gak iron deposit, Bamyan Province, Afghanistan, modified from the 1965 original map compilation of M.S. Smirnov and I.K. Kusov

USGS Publications Warehouse

Renaud, Karine M.; Tucker, Robert D.; Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geological-structural map of Hajigak iron-ore deposit, scale 1:10,000, which was compiled by M.S. Smirnov and I.K. Kusov in 1965. (Refer to the References Cited section in the Map PDF for complete citations of the original map and a related report.) USGS scientists, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original documents and also visited the field area in November 2009. This modified map illustrates the geological structure of the Haji-Gak iron deposit and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of these documents. Elevations on the cross sections are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

An accurate symplectic calculation of the inboard magnetic footprint from statistical topological noise and field errors in the DIII-D

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

Punjabi, Alkesh; Ali, Halima

2011-02-15

Any canonical transformation of Hamiltonian equations is symplectic, and any area-preserving transformation in 2D is a symplectomorphism. Based on these, a discrete symplectic map and its continuous symplectic analog are derived for forward magnetic field line trajectories in natural canonical coordinates. The unperturbed axisymmetric Hamiltonian for magnetic field lines is constructed from the experimental data in the DIII-D [J. L. Luxon and L. E. Davis, Fusion Technol. 8, 441 (1985)]. The equilibrium Hamiltonian is a highly accurate, analytic, and realistic representation of the magnetic geometry of the DIII-D. These symplectic mathematical maps are used to calculate the magnetic footprint onmore » the inboard collector plate in the DIII-D. Internal statistical topological noise and field errors are irreducible and ubiquitous in magnetic confinement schemes for fusion. It is important to know the stochasticity and magnetic footprint from noise and error fields. The estimates of the spectrum and mode amplitudes of the spatial topological noise and magnetic errors in the DIII-D are used as magnetic perturbation. The discrete and continuous symplectic maps are used to calculate the magnetic footprint on the inboard collector plate of the DIII-D by inverting the natural coordinates to physical coordinates. The combination of highly accurate equilibrium generating function, natural canonical coordinates, symplecticity, and small step-size together gives a very accurate calculation of magnetic footprint. Radial variation of magnetic perturbation and the response of plasma to perturbation are not included. The inboard footprint from noise and errors are dominated by m=3, n=1 mode. The footprint is in the form of a toroidally winding helical strip. The width of stochastic layer scales as (1/2) power of amplitude. The area of footprint scales as first power of amplitude. The physical parameters such as toroidal angle, length, and poloidal angle covered before striking, and the safety factor all have fractal structure. The average field diffusion near the X-point for lines that strike and that do not strike differs by about three to four orders of magnitude. The magnetic footprint gives the maximal bounds on size and heat flux density on collector plate.« less

Innovating Big Data Computing Geoprocessing for Analysis of Engineered-Natural Systems

NASA Astrophysics Data System (ADS)

Rose, K.; Baker, V.; Bauer, J. R.; Vasylkivska, V.

2016-12-01

Big data computing and analytical techniques offer opportunities to improve predictions about subsurface systems while quantifying and characterizing associated uncertainties from these analyses. Spatial analysis, big data and otherwise, of subsurface natural and engineered systems are based on variable resolution, discontinuous, and often point-driven data to represent continuous phenomena. We will present examples from two spatio-temporal methods that have been adapted for use with big datasets and big data geo-processing capabilities. The first approach uses regional earthquake data to evaluate spatio-temporal trends associated with natural and induced seismicity. The second algorithm, the Variable Grid Method (VGM), is a flexible approach that presents spatial trends and patterns, such as those resulting from interpolation methods, while simultaneously visualizing and quantifying uncertainty in the underlying spatial datasets. In this presentation we will show how we are utilizing Hadoop to store and perform spatial analyses to efficiently consume and utilize large geospatial data in these custom analytical algorithms through the development of custom Spark and MapReduce applications that incorporate ESRI Hadoop libraries. The team will present custom `Big Data' geospatial applications that run on the Hadoop cluster and integrate with ESRI ArcMap with the team's probabilistic VGM approach. The VGM-Hadoop tool has been specially built as a multi-step MapReduce application running on the Hadoop cluster for the purpose of data reduction. This reduction is accomplished by generating multi-resolution, non-overlapping, attributed topology that is then further processed using ESRI's geostatistical analyst to convey a probabilistic model of a chosen study region. Finally, we will share our approach for implementation of data reduction and topology generation via custom multi-step Hadoop applications, performance benchmarking comparisons, and Hadoop-centric opportunities for greater parallelization of geospatial operations.

Special Issue on a Fault Tolerant Network on Chip Architecture

NASA Astrophysics Data System (ADS)

Janidarmian, Majid; Tinati, Melika; Khademzadeh, Ahmad; Ghavibazou, Maryam; Fekr, Atena Roshan

2010-06-01

In this paper a fast and efficient spare switch selection algorithm is presented in a reliable NoC architecture based on specific application mapped onto mesh topology called FERNA. Based on ring concept used in FERNA, this algorithm achieves best results equivalent to exhaustive algorithm with much less run time improving two parameters. Inputs of FERNA algorithm for response time of the system and extra communication cost minimization are derived from simulation of high transaction level using SystemC TLM and mathematical formulation, respectively. The results demonstrate that improvement of above mentioned parameters lead to advance whole system reliability that is analytically calculated. Mapping algorithm has been also investigated as an effective issue on extra bandwidth requirement and system reliability.

Geologic map of the Khanneshin carbonatite complex, Helmand Province, Afghanistan, modified from the 1976 original map compilation of V.G. Cheremytsin

USGS Publications Warehouse

Tucker, Robert D.; Peters, Stephen G.; Schulz, Klaus J.; Renaud, Karine M.; Stettner, Will R.; Masonic, Linda M.; Packard, Patricia H.

2011-01-01

This map is a modified version of the Geological map of the Khanneshin carbonatite complex, scale 1:10,000, which was compiled by V.G. Cheremytsin in 1976. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original map and also visited the field area in September 2009, August 2010, and February 2011. This modified map, which includes cross sections, illustrates the geologic structure of the Khanneshin carbonatite complex. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of that map and a related report, and based on observations made during our field visits. (Refer to the References section in the Map PDF for complete citations of the original map and related report.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

Building blocks of topological quantum chemistry: Elementary band representations

NASA Astrophysics Data System (ADS)

Cano, Jennifer; Bradlyn, Barry; Wang, Zhijun; Elcoro, L.; Vergniory, M. G.; Felser, C.; Aroyo, M. I.; Bernevig, B. Andrei

2018-01-01

The link between chemical orbitals described by local degrees of freedom and band theory, which is defined in momentum space, was proposed by Zak several decades ago for spinless systems with and without time reversal in his theory of "elementary" band representations. In a recent paper [Bradlyn et al., Nature (London) 547, 298 (2017), 10.1038/nature23268] we introduced the generalization of this theory to the experimentally relevant situation of spin-orbit coupled systems with time-reversal symmetry and proved that all bands that do not transform as band representations are topological. Here we give the full details of this construction. We prove that elementary band representations are either connected as bands in the Brillouin zone and are described by localized Wannier orbitals respecting the symmetries of the lattice (including time reversal when applicable), or, if disconnected, describe topological insulators. We then show how to generate a band representation from a particular Wyckoff position and determine which Wyckoff positions generate elementary band representations for all space groups. This theory applies to spinful and spinless systems, in all dimensions, with and without time reversal. We introduce a homotopic notion of equivalence and show that it results in a finer classification of topological phases than approaches based only on the symmetry of wave functions at special points in the Brillouin zone. Utilizing a mapping of the band connectivity into a graph theory problem, we show in companion papers which Wyckoff positions can generate disconnected elementary band representations, furnishing a natural avenue for a systematic materials search.

Analysis of Resting-State fMRI Topological Graph Theory Properties in Methamphetamine Drug Users Applying Box-Counting Fractal Dimension.

PubMed

Siyah Mansoory, Meysam; Oghabian, Mohammad Ali; Jafari, Amir Homayoun; Shahbabaie, Alireza

2017-01-01

Graph theoretical analysis of functional Magnetic Resonance Imaging (fMRI) data has provided new measures of mapping human brain in vivo. Of all methods to measure the functional connectivity between regions, Linear Correlation (LC) calculation of activity time series of the brain regions as a linear measure is considered the most ubiquitous one. The strength of the dependence obligatory for graph construction and analysis is consistently underestimated by LC, because not all the bivariate distributions, but only the marginals are Gaussian. In a number of studies, Mutual Information (MI) has been employed, as a similarity measure between each two time series of the brain regions, a pure nonlinear measure. Owing to the complex fractal organization of the brain indicating self-similarity, more information on the brain can be revealed by fMRI Fractal Dimension (FD) analysis. In the present paper, Box-Counting Fractal Dimension (BCFD) is introduced for graph theoretical analysis of fMRI data in 17 methamphetamine drug users and 18 normal controls. Then, BCFD performance was evaluated compared to those of LC and MI methods. Moreover, the global topological graph properties of the brain networks inclusive of global efficiency, clustering coefficient and characteristic path length in addict subjects were investigated too. Compared to normal subjects by using statistical tests (P<0.05), topological graph properties were postulated to be disrupted significantly during the resting-state fMRI. Based on the results, analyzing the graph topological properties (representing the brain networks) based on BCFD is a more reliable method than LC and MI.

Mapping Autonomous System’s Router Level Topology in IPv6

DTIC Science & Technology

2007-06-01

useful and is called rate limiting. Rate limiting sends enough probes to one of the alias addresses to cause the router to begin rate limiting the...network. The second key capability required was alias and anonymous resolution: if there was no method of making these functions happen then any graph...command, then port unreachable responses were received by probes through d5 to interface d13 or d5. Again, it is believed that this happened

TIGER 2010 Boundaries

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This web service includes the State and County boundaries from the TIGER shapefiles compiled into a single national coverage for each layer. The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB).

Exact determination of asymptotic CMB temperature-redshift relation

NASA Astrophysics Data System (ADS)

Hahn, Steffen; Hofmann, Ralf

2018-02-01

Based on energy conservation in a Friedmann-Lemaître-Robertson-Walker (FLRW) Universe, on the Legendre transformation between energy density and pressure, and on nonperturbative asymptotic freedom at high temperatures, we derive the coefficient νCMB in the high-temperature (T) — redshift (z) relation, T/T0 = νCMB(z + 1), of the Cosmic Microwave Background (CMB). Theoretically, our calculation relies on a deconfining SU(2) rather than a U(1) photon gas. We prove that νCMB = (1/4)1/3 = 0.629960(5), representing a topological invariant. Interestingly, the relative deviation of νCMB from the critical exponent associated with the correlation length l of the 3D Ising model, νIsing = 0.629971(4), is less than 2 × 10-5. We are not in a position to establish a direct theoretical link between νCMB and νIsing as suggested by the topological nature of νCMB and the fact that both theories are members of the same universality class. We do, however, spell out a somewhat speculative, strictly monotonic map from the physical Ising temperature 𝜃 to a fictitious SU(2) Yang-Mills temperature T, the latter continuing the asymptotic dependence of the scale factor a on T/T0 for T/T0 ≫ 1 down to T = 0, and we identify an exponential map from a to l to reproduce critical Ising behavior.

Properties of Interstellar Turbulence from Gradients of Linear Polarization Maps

NASA Astrophysics Data System (ADS)

Burkhart, Blakesley; Lazarian, A.; Gaensler, B. M.

2012-04-01

Faraday rotation of linearly polarized radio signals provides a very sensitive probe of fluctuations in the interstellar magnetic field and ionized gas density resulting from magnetohydrodynamic (MHD) turbulence. We used a set of statistical tools to analyze images of the spatial gradient of linearly polarized radio emission (|∇P|) for both observational data from a test image of the Southern Galactic Plane Survey (SGPS) and isothermal three-dimensional simulations of MHD turbulence. Visually, in both observations and simulations, a complex network of filamentary structures is seen. Our analysis shows that the filaments in |∇P| can be produced both by interacting shocks and random fluctuations characterizing the non-differentiable field of MHD turbulence. The latter dominates for subsonic turbulence, while the former is only present in supersonic turbulence. We show that supersonic and subsonic turbulence exhibit different distributions as well as different morphologies in the maps of |∇P|. Particularly, filaments produced by shocks show a characteristic "double jump" profile at the sites of shock fronts resulting from delta function-like increases in the density and/or magnetic field, while those produced by subsonic turbulence show a single jump profile. In order to quantitatively characterize these differences, we use the topology tool known as the genus curve as well as the probability distribution function moments of the image distribution. We find that higher values for the moments correspond to cases of |∇P| with larger sonic Mach numbers. The genus analysis of the supersonic simulations of |∇P| reveals a "swiss cheese" topology, while the subsonic cases have characteristics of a "clump" topology. Based on the analysis of the genus and the higher order moments, the SGPS test region data have a distribution and morphology that match subsonic- to transonic-type turbulence, which confirms what is now expected for the warm ionized medium.

An Intelligent Pinger Network for Solid Glacier Environments

NASA Astrophysics Data System (ADS)

Schönitz, S.; Reuter, S.; Henke, C.; Jeschke, S.; Ewert, D.; Eliseev, D.; Heinen, D.; Linder, P.; Scholz, F.; Weinstock, L.; Wickmann, S.; Wiebusch, C.; Zierke, S.

2016-12-01

This talk presents a novel approach for an intelligent, agent-based pinger network in an extraterrestrial glacier environment. Because of recent findings of the Cassini spacecraft, a mission to Saturn's moon Enceladus is planned in order search for extraterrestrial life within the ocean beneath Enceladus' ice crust. Therefore, a maneuverable melting probe, the EnEx probe, was developed to melt into Enceladus' ice and take liquid samples from water-filled crevasses. Hence, the probe collecting the samples has to be able to navigate in ice which is a hard problem, because neither visual nor gravitational methods can be used. To enhance the navigability of the probe, a network of autonomous pinger units (APU) is in development that is able to extract a map of the ice environment via ultrasonic soundwaves. A network of these APUs will be deployed on the surface of Enceladus, melt into the ice and form a network to help guide the probe safely to its destination. The APU network is able to form itself fully autonomously and to compensate system failures of individual APUs. The agents controlling the single APU are realized by rule-based expert systems implemented in CLIPS. The rule-based expert system evaluates available information of the environment, decides for actions to take to achieve the desired goal (e.g. a specific network topology), and executes and monitors such actions. In general, it encodes certain situations that are evaluated whenever an APU is currently idle, and then decides for a next action to take. It bases this decision on its internal world model that is shared with the other APUs. The optimal network topology that defines each agents position is iteratively determined by mixed-integer nonlinear programming. Extensive simulations studies show that the proposed agent design enables the APUs to form a robust network topology that is suited to create a reliable 3D map of the ice environment.

Imaging of electrical response of NiO x under controlled environment with sub-25-nm resolution

DOE PAGES

Jacobs, Christopher B.; Ievlev, Anton V.; Collins, Liam F.; ...

2016-07-19

The spatially resolved electrical response of rf-sputtered polycrystalline NiO x films composed of 40 nm crystallites was investigated under different relative humidity levels (RH). The topological and electrical properties (surface potential and resistance) were characterized using Kelvin probe force microscopy (KPFM) and conductive scanning probe microscopy at 0%, 50%, and 80% relative humidity with sub 25nm resolution. The surface potential of NiO x decreased by about 180 mV and resistance decreased in a nonlinear fashion by about 2 G when relative humidity was increased from 0% to 80%. The dimensionality of surface features obtained through autocorrelation analysis of topological, surfacemore » potential and resistance maps increased linearly with increased relative humidity as water was adsorbed onto the film surface. Spatially resolved surface potential and resistance of the NiO x films were found to be heterogeneous, with distinct features that grew in size from about 60 nm to 175 nm between 0% and 80% RH levels, respectively. Here, we find that the changes in the heterogeneous character of the NiO films are consistent through the topological, surface potential, and resistance measurements, suggesting that the nanoscale surface potential and resistance properties converge with the mesoscale properties as water is adsorbed onto the NiO x film.« less

Revealing the global map of protein folding space by large-scale simulations

NASA Astrophysics Data System (ADS)

Sinner, Claude; Lutz, Benjamin; Verma, Abhinav; Schug, Alexander

2015-12-01

The full characterization of protein folding is a remarkable long-standing challenge both for experiment and simulation. Working towards a complete understanding of this process, one needs to cover the full diversity of existing folds and identify the general principles driving the process. Here, we want to understand and quantify the diversity in folding routes for a large and representative set of protein topologies covering the full range from all alpha helical topologies towards beta barrels guided by the key question: Does the majority of the observed routes contribute to the folding process or only a particular route? We identified a set of two-state folders among non-homologous proteins with a sequence length of 40-120 residues. For each of these proteins, we ran native-structure based simulations both with homogeneous and heterogeneous contact potentials. For each protein, we simulated dozens of folding transitions in continuous uninterrupted simulations and constructed a large database of kinetic parameters. We investigate folding routes by tracking the formation of tertiary structure interfaces and discuss whether a single specific route exists for a topology or if all routes are equiprobable. These results permit us to characterize the complete folding space for small proteins in terms of folding barrier ΔG‡, number of routes, and the route specificity RT.

An improved spatial contour tree constructed method

NASA Astrophysics Data System (ADS)

Zheng, Yi; Zhang, Ling; Guilbert, Eric; Long, Yi

2018-05-01

Contours are important data to delineate the landform on a map. A contour tree provides an object-oriented description of landforms and can be used to enrich the topological information. The traditional contour tree is used to store topological relationships between contours in a hierarchical structure and allows for the identification of eminences and depressions as sets of nested contours. This research proposes an improved contour tree so-called spatial contour tree that contains not only the topological but also the geometric information. It can be regarded as a terrain skeleton in 3-dimention, and it is established based on the spatial nodes of contours which have the latitude, longitude and elevation information. The spatial contour tree is built by connecting spatial nodes from low to high elevation for a positive landform, and from high to low elevation for a negative landform to form a hierarchical structure. The connection between two spatial nodes can provide the real distance and direction as a Euclidean vector in 3-dimention. In this paper, the construction method is tested in the experiment, and the results are discussed. The proposed hierarchical structure is in 3-demintion and can show the skeleton inside a terrain. The structure, where all nodes have geo-information, can be used to distinguish different landforms and applied for contour generalization with consideration of geographic characteristics.

The shape of strings to come: How topological defects twist, bend, and wrinkle filament bundles

NASA Astrophysics Data System (ADS)

Bruss, Isaac; Grason, Gregory

2015-03-01

Topological defects are crucial to the thermodynamics and structure of condensed matter systems. For instance, when incorporated into crystalline membranes like graphene, 5- and 7-fold disclinations produce conical- and saddle-like geometries respectively. A recently discovered mapping between the inter-filament spacing within a deformed bundle and the metric properties of curved surfaces, suggests previously unexplored parallels between the two, specifically in regards to how 2D patterning promotes 3D shape transitions. This discovery is poised to describe the structure of a host of filamentous materials-both biological and microfabricated-that exhibit distinctive shapes and packings. Motivated by the filamentous analogs to the conical and saddles shapes found in thin membranes, we investigate for the first time the interplay between defects in the cross section of a bundle and its global structure, using a combination of continuum elasticity theory and numerical simulation of cohesive bundles with a fixed packing topology. Focusing primarily on the instability response to disclinations, we predict a host of new equilibria structures, some of which are without direct parallel to the analogous membrane, including torsional wrinkling, radial kinking, and helical winding. Center for Hierarchical Manufacturing-CMMI 10-25020, NSF CAREER Award-DMR 09-55760, & UMass MRSEC.

Quantifying chaos for ecological stoichiometry.

PubMed

Duarte, Jorge; Januário, Cristina; Martins, Nuno; Sardanyés, Josep

2010-09-01

The theory of ecological stoichiometry considers ecological interactions among species with different chemical compositions. Both experimental and theoretical investigations have shown the importance of species composition in the outcome of the population dynamics. A recent study of a theoretical three-species food chain model considering stoichiometry [B. Deng and I. Loladze, Chaos 17, 033108 (2007)] shows that coexistence between two consumers predating on the same prey is possible via chaos. In this work we study the topological and dynamical measures of the chaotic attractors found in such a model under ecological relevant parameters. By using the theory of symbolic dynamics, we first compute the topological entropy associated with unimodal Poincaré return maps obtained by Deng and Loladze from a dimension reduction. With this measure we numerically prove chaotic competitive coexistence, which is characterized by positive topological entropy and positive Lyapunov exponents, achieved when the first predator reduces its maximum growth rate, as happens at increasing δ1. However, for higher values of δ1 the dynamics become again stable due to an asymmetric bubble-like bifurcation scenario. We also show that a decrease in the efficiency of the predator sensitive to prey's quality (increasing parameter ζ) stabilizes the dynamics. Finally, we estimate the fractal dimension of the chaotic attractors for the stoichiometric ecological model.

Majorana spin liquids, topology, and superconductivity in ladders

NASA Astrophysics Data System (ADS)

Le Hur, Karyn; Soret, Ariane; Yang, Fan

2017-11-01

We theoretically address spin chain analogs of the Kitaev quantum spin model on the honeycomb lattice. The emergent quantum spin-liquid phases or Anderson resonating valence-bond (RVB) states can be understood, as an effective model, in terms of p -wave superconductivity and Majorana fermions. We derive a generalized phase diagram for the two-leg ladder system with tunable interaction strengths between chains allowing us to vary the shape of the lattice (from square to honeycomb ribbon or brickwall ladder). We evaluate the winding number associated with possible emergent (topological) gapless modes at the edges. In the Az phase, as a result of the emergent Z2 gauge fields and π -flux ground state, one may build spin-1/2 (loop) qubit operators by analogy to the toric code. In addition, we show how the intermediate gapless B phase evolves in the generalized ladder model. For the brick-wall ladder, the B phase is reduced to one line, which is analyzed through perturbation theory in a rung tensor product states representation and bosonization. Finally, we show that doping with a few holes can result in the formation of hole pairs and leads to a mapping with the Su-Schrieffer-Heeger model in polyacetylene; a superconducting-insulating quantum phase transition for these hole pairs is accessible, as well as related topological properties.

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.

The GIS Weasel: An interface for the development of geographic information used in environmental simulation modeling

USGS Publications Warehouse

Viger, R.J.

2008-01-01

The GIS Weasel is a freely available, open-source software package built on top of ArcInfo Workstation?? [ESRI, Inc., 2001, ArcInfo Workstation (8.1 ed.), Redlands, CA] for creating maps and parameters of geographic features used in environmental simulation models. The software has been designed to minimize the need for GIS expertise and automate the preparation of the geographic information as much as possible. Although many kinds of data can be exploited with the GIS Weasel, the only information required is a raster dataset of elevation for the user's area of interest (AOI). The user-defined AOI serves as a starting point from which to create maps of many different types of geographic features, including sub-watersheds, streams, elevation bands, land cover patches, land parcels, or anything else that can be discerned from the available data. The GIS Weasel has a library of over 200 routines that can be applied to any raster map of geographic features to generate information about shape, area, or topological association with other features of the same or different maps. In addition, a wide variety of parameters can be derived using ancillary data layers such as soil and vegetation maps.

Destruction of the Last Good Magnetic Surface in Diii-D Usn with Elms and C-Coils Shot 115467 due to C-Coils Using Maps

NASA Astrophysics Data System (ADS)

McCray, A.; Punjabi, A.; Ali, H.

2004-11-01

Unperturbed magnetic topology of DIII-D shot 115467 is described by the symmetric simple map (SSM) with map parameter k=0.2623 [1], then last good surface passes through x=0 and y=0.9995, q_edge=6.48 (same as in shot 115467) if six iterations of SSM are taken to be equivalent to single toroidal circuit of DIII-D. The dipole map (DM) calculates the effects of localized, external high mode numbers magnetic perturbations on motion of field lines. We use dipole map to describe effects of C-coils on field line trajectories in DIII-D. We apply DM after each iteration of SSM, with s=1.0021, x_dipole=1.5617, y_dipole= 0 [1] for shot 115467. We study the changes in the last good surface and its destruction as a function of I_C-coil. This work is supported by NASA SHARP program and DE-FG02-02ER54673. [1] H. Ali, A. Punjabi, A. Boozer, and T. Evans, presented at the 31st European Physical Society Plasma Physics Meeting, London, UK, June 29, 2004, paper P2-172.

A quantitative analysis of IRAS maps of molecular clouds

NASA Technical Reports Server (NTRS)

Wiseman, Jennifer J.; Adams, Fred C.

1994-01-01

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Destruction of the Last Good Magnetic Surface in Diii-D Usn with Elms and C-Coils Shot 115467 due to ELMs Using Maps

NASA Astrophysics Data System (ADS)

Butcher, L.; Ali, H.; Punjabi, A.

2004-11-01

The unperturbed magnetic topology of DIII-D USN shot 115467 in the absence of ELMs and C-coils is described by the symmetric simple map (SSM) with the map parameter k=0.2623 [1]. For this k, the last good surface passes through x=0 and y=0.9995, q_edge=6.48 if six iterations of the SSM are taken to be equivalent to a single toroidal circuit of DIII-D, and the q_edge equals the q_edge in the DIII-D for shot 115467. The low mn map calculates the effects of the m=1, n=+1,-1 internal magnetic perturbation on the trajectories of field lines. We use the low mn map to represent the effects of the ELMs in the DIII-D. We study the changes in the last good surface and its destruction as the amplitude ɛ in the low mn map is increased. This work is supported by NASA SHARP program and DE-FG02-02ER54673. [1] H. Ali, A. Punjabi, A. Boozer, and T. Evans, presented at the 31st European Physical Society Plasma Physics Meeting, London, UK, June 29, 2004, paper P2-172.

Probabilistic self-localisation on a qualitative map based on occlusions

NASA Astrophysics Data System (ADS)

Santos, Paulo E.; Martins, Murilo F.; Fenelon, Valquiria; Cozman, Fabio G.; Dee, Hannah M.

2016-09-01

Spatial knowledge plays an essential role in human reasoning, permitting tasks such as locating objects in the world (including oneself), reasoning about everyday actions and describing perceptual information. This is also the case in the field of mobile robotics, where one of the most basic (and essential) tasks is the autonomous determination of the pose of a robot with respect to a map, given its perception of the environment. This is the problem of robot self-localisation (or simply the localisation problem). This paper presents a probabilistic algorithm for robot self-localisation that is based on a topological map constructed from the observation of spatial occlusion. Distinct locations on the map are defined by means of a classical formalism for qualitative spatial reasoning, whose base definitions are closer to the human categorisation of space than traditional, numerical, localisation procedures. The approach herein proposed was systematically evaluated through experiments using a mobile robot equipped with a RGB-D sensor. The results obtained show that the localisation algorithm is successful in locating the robot in qualitatively distinct regions.

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

A first theoretical realization of honeycomb topological magnon insulator.

PubMed

Owerre, S A

2016-09-28

It has been recently shown that in the Heisenberg (anti)ferromagnet on the honeycomb lattice, the magnons (spin wave quasipacticles) realize a massless two-dimensional (2D) Dirac-like Hamiltonian. It was shown that the Dirac magnon Hamiltonian preserves time-reversal symmetry defined with the sublattice pseudo spins and the Dirac points are robust against magnon-magnon interactions. The Dirac points also occur at nonzero energy. In this paper, we propose a simple realization of nontrivial topology (magnon edge states) in this system. We show that the Dirac points are gapped when the inversion symmetry of the lattice is broken by introducing a next-nearest neighbour Dzyaloshinskii-Moriya (DM) interaction. Thus, the system realizes magnon edge states similar to the Haldane model for quantum anomalous Hall effect in electronic systems. However, in contrast to electronic spin current where dissipation can be very large due to Ohmic heating, noninteracting topological magnons can propagate for a long time without dissipation as magnons are uncharged particles. We observe the same magnon edge states for the XY model on the honeycomb lattice. Remarkably, in this case the model maps to interacting hardcore bosons on the honeycomb lattice. Quantum magnetic systems with nontrivial magnon edge states are called topological magnon insulators. They have been studied theoretically on the kagome lattice and recently observed experimentally on the kagome magnet Cu(1-3, bdc) with three magnon bulk bands. Our results for the honeycomb lattice suggests an experimental procedure to search for honeycomb topological magnon insulators within a class of 2D quantum magnets and ultracold atoms trapped in honeycomb optical lattices. In 3D lattices, Dirac and Weyl points were recently studied theoretically, however, the criteria that give rise to them were not well-understood. We argue that the low-energy Hamiltonian near the Weyl points should break time-reversal symmetry of the pseudo spins. Thus, recovering the same criteria in electronic systems.

Investigations of surface structural, dynamical, and magnetic properties of systems exhibiting multiferroicity, and topological phases by helium scattering spectroscopies

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

El-Batanouny, Maged

2015-08-03

We propose to investigate the surface structural, dynamics and magnetic properties of the novel class of topological insulator crystals, as well as crystals that exhibit multiferroicity, magnetoelectricity and thermoelectricity. Topological insulators (TIs) are a new class of insulators in which a bulk gap for electronic excitations is generated because of the strong spin-orbit coupling inherent to these systems. These materials are distinguished from ordinary insulators by the presence of gapless metallic surface states, resembling chiral edge modes in quantum Hall systems, but with unconventional spin textures. These exotic metallic states are formed by topological conditions that also render the electrons travelling on such surfaces insensitive to scattering by impurities. The electronic quasi-particles populating the topological surface state are Dirac fermions; they have a linear dispersion and thus are massless just like photons. We propose to investigate the interaction of these massless Dirac fermions with the massive lattice in the newly discovered crystals, Bi2Se3, Bi2Te3 and Sb2Te3. We shall use inelastic helium beam scattering from surfaces to search for related signatures in surface phonon dispersions mappings that cover the entire surface Brillouin zone of these materials. Our recent investigations of the (001) surface of the multiferroic crystals (Li/Na)Cu2O2 revealed an anomalous surface structural behavior where surface Cumore » $$^{2+}$$ row rise above the surface plane as the crystal was cooled. Subsequent worming revealed the onset of a thermally activated incommensurate surface phase, driven by the elevated rows. We are currently investigating the structure of the magnetic phases in these quasi-one-dimensional magnetic rows. Multiferroics are excellent candidates for large magnetoelectric response. We propose to extend this investigation to the class of delafossites which are also multiferroics and have been investigated as good candidates for thermoelectric power devices. They are also typical triangular lattice antiferromagnets with geometric magnetic frustration that leads to helimagnetic structures.« less

GRASS GIS: The first Open Source Temporal GIS

NASA Astrophysics Data System (ADS)

Gebbert, Sören; Leppelt, Thomas

2015-04-01

GRASS GIS is a full featured, general purpose Open Source geographic information system (GIS) with raster, 3D raster and vector processing support[1]. Recently, time was introduced as a new dimension that transformed GRASS GIS into the first Open Source temporal GIS with comprehensive spatio-temporal analysis, processing and visualization capabilities[2]. New spatio-temporal data types were introduced in GRASS GIS version 7, to manage raster, 3D raster and vector time series. These new data types are called space time datasets. They are designed to efficiently handle hundreds of thousands of time stamped raster, 3D raster and vector map layers of any size. Time stamps can be defined as time intervals or time instances in Gregorian calendar time or relative time. Space time datasets are simplifying the processing and analysis of large time series in GRASS GIS, since these new data types are used as input and output parameter in temporal modules. The handling of space time datasets is therefore equal to the handling of raster, 3D raster and vector map layers in GRASS GIS. A new dedicated Python library, the GRASS GIS Temporal Framework, was designed to implement the spatio-temporal data types and their management. The framework provides the functionality to efficiently handle hundreds of thousands of time stamped map layers and their spatio-temporal topological relations. The framework supports reasoning based on the temporal granularity of space time datasets as well as their temporal topology. It was designed in conjunction with the PyGRASS [3] library to support parallel processing of large datasets, that has a long tradition in GRASS GIS [4,5]. We will present a subset of more than 40 temporal modules that were implemented based on the GRASS GIS Temporal Framework, PyGRASS and the GRASS GIS Python scripting library. These modules provide a comprehensive temporal GIS tool set. The functionality range from space time dataset and time stamped map layer management over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

Geologic map of the western Haji-Gak iron deposit, Bamyan Province, Afghanistan, modified from the 1965 original map compilation of V.V. Reshetniak and I.K. Kusov

USGS Publications Warehouse

Renaud, Karine M.; Tucker, Robert D.; Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geologic-prospecting plan of western area of Hajigak iron-ore deposit, scale 1:2,000, which was compiled by V.V. Reshetniak and I.K. Kusov in 1965. (Refer to the References Cited section in the Map PDF for complete citations of the original map and related reports.) USGS scientists, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original documents and also visited the field area in November 2009. This modified map illustrates the geological structure of the western Haji-Gak iron deposit and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and includes modifications based on our examination of that document. We constructed the cross sections from data derived from the original map. Elevations on the cross sections are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

PDES Logical Layer Initiation Task.

DTIC Science & Technology

1986-04-28

surface. We have heard such expressions as "topology sits on tcp of geometry." We choose to avoid subordinating one to the other by bringing them together...a mapping from Discipline model to Global model. 38 A~A g d ip . t ~ P A1 / /oaefZ - - 6jOM#AL Mat&mft9 We have attempted to group basqd on the...FIGURE PHASE 2: Conceptualization and Integration. In this phase conceptual entities and relationships are discovered. An integrated conceptual modelO

Hexahedral Mesh Untangling

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

KNUPP,PATRICK

2000-12-13

We investigate a well-motivated mesh untangling objective function whose optimization automatically produces non-inverted elements when possible. Examples show the procedure is highly effective on simplicial meshes and on non-simplicial (e.g., hexahedral) meshes constructed via mapping or sweeping algorithms. The current whisker-weaving (WW) algorithm in CUBIT usually produces hexahedral meshes that are unsuitable for analyses due to inverted elements. The majority of these meshes cannot be untangled using the new objective function. The most likely source of the difficulty is poor mesh topology.

On the structure of the set of coincidence points

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

Arutyunov, A V; Gel'man, B D

2015-03-31

We consider the set of coincidence points for two maps between metric spaces. Cardinality, metric and topological properties of the coincidence set are studied. We obtain conditions which guarantee that this set (a) consists of at least two points; (b) consists of at least n points; (c) contains a countable subset; (d) is uncountable. The results are applied to study the structure of the double point set and the fixed point set for multivalued contractions. Bibliography: 12 titles.

The invariant of the stiffness filter function with the weight filter function of the power function form

NASA Astrophysics Data System (ADS)

Shang, Zhen; Sui, Yun-Kang

2012-12-01

Based on the independent, continuous and mapping (ICM) method and homogenization method, a research model is constructed to propose and deduce a theorem and corollary from the invariant between the weight filter function and the corresponding stiffness filter function of the form of power function. The efficiency in searching for optimum solution will be raised via the choice of rational filter functions, so the above mentioned results are very important to the further study of structural topology optimization.

Uncountably many maximizing measures for a dense subset of continuous functions

NASA Astrophysics Data System (ADS)

Shinoda, Mao

2018-05-01

Ergodic optimization aims to single out dynamically invariant Borel probability measures which maximize the integral of a given ‘performance’ function. For a continuous self-map of a compact metric space and a dense set of continuous functions, we show the existence of uncountably many ergodic maximizing measures. We also show that, for a topologically mixing subshift of finite type and a dense set of continuous functions there exist uncountably many ergodic maximizing measures with full support and positive entropy.

TIGER 2010 Boundaries

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This web service includes the State, County, and Census Block Groups boundaries from the TIGER shapefiles compiled into a single national coverage for each layer. The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB).

Geologic map of the Shaida deposit and Misgaran prospect, Herat Province, Afghanistan, modified from the 1973 original map compilation of V.I. Tarasenko and others

USGS Publications Warehouse

Tucker, Robert D.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2014-01-01

This map is a modified version of Geological map and map of useful minerals, Shaida area, scale 1:50,000, which was compiled by V.I. Tarasenko, N.I. Borozenets, and others in 1973. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original document and related reports and also visited the field area in August 2010.This modified map illustrates the geological structure of the Shaida copper-lead-zinc deposit and Misgaran copper-lead-zinc prospect in western Afghanistan and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of these documents and on observations made during our field visit. Elevations on the cross sections are derived from the original Soviet topography and might not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map.The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

NeatMap--non-clustering heat map alternatives in R.

PubMed

Rajaram, Satwik; Oono, Yoshi

2010-01-22

The clustered heat map is the most popular means of visualizing genomic data. It compactly displays a large amount of data in an intuitive format that facilitates the detection of hidden structures and relations in the data. However, it is hampered by its use of cluster analysis which does not always respect the intrinsic relations in the data, often requiring non-standardized reordering of rows/columns to be performed post-clustering. This sometimes leads to uninformative and/or misleading conclusions. Often it is more informative to use dimension-reduction algorithms (such as Principal Component Analysis and Multi-Dimensional Scaling) which respect the topology inherent in the data. Yet, despite their proven utility in the analysis of biological data, they are not as widely used. This is at least partially due to the lack of user-friendly visualization methods with the visceral impact of the heat map. NeatMap is an R package designed to meet this need. NeatMap offers a variety of novel plots (in 2 and 3 dimensions) to be used in conjunction with these dimension-reduction techniques. Like the heat map, but unlike traditional displays of such results, it allows the entire dataset to be displayed while visualizing relations between elements. It also allows superimposition of cluster analysis results for mutual validation. NeatMap is shown to be more informative than the traditional heat map with the help of two well-known microarray datasets. NeatMap thus preserves many of the strengths of the clustered heat map while addressing some of its deficiencies. It is hoped that NeatMap will spur the adoption of non-clustering dimension-reduction algorithms.

Calculation of stochastic broadening due to noise and field errors in the simple map in action-angle coordinates

NASA Astrophysics Data System (ADS)

Hinton, Courtney; Punjabi, Alkesh; Ali, Halima

2008-11-01

The simple map is the simplest map that has topology of divertor tokamaks [1]. Recently, the action-angle coordinates for simple map are analytically calculated, and simple map is constructed in action-angle coordinates [2]. Action-angle coordinates for simple map can not be inverted to real space coordinates (R,Z). Because there is logarithmic singularity on the ideal separatrix, trajectories can not cross separatrix [2]. Simple map in action-angle coordinates is applied to calculate stochastic broadening due to magnetic noise and field errors. Mode numbers for noise + field errors from the DIII-D tokamak are used. Mode numbers are (m,n)=(3,1), (4,1), (6,2), (7,2), (8,2), (9,3), (10,3), (11,3), (12,3) [3]. The common amplitude δ is varied from 0.8X10-5 to 2.0X10-5. For this noise and field errors, the width of stochastic layer in simple map is calculated. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793 1. A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Let. A 364, 140--145 (2007). 2. O. Kerwin, A. Punjabi, and H. Ali, to appear in Physics of Plasmas. 3. A. Punjabi and H. Ali, P1.012, 35^th EPS Conference on Plasma Physics, June 9-13, 2008, Hersonissos, Crete, Greece.

Vectoring of parallel synthetic jets: A parametric study

NASA Astrophysics Data System (ADS)

Berk, Tim; Gomit, Guillaume; Ganapathisubramani, Bharathram

2016-11-01

The vectoring of a pair of parallel synthetic jets can be described using five dimensionless parameters: the aspect ratio of the slots, the Strouhal number, the Reynolds number, the phase difference between the jets and the spacing between the slots. In the present study, the influence of the latter four on the vectoring behaviour of the jets is examined experimentally using particle image velocimetry. Time-averaged velocity maps are used to study the variations in vectoring behaviour for a parametric sweep of each of the four parameters independently. A topological map is constructed for the full four-dimensional parameter space. The vectoring behaviour is described both qualitatively and quantitatively. A vectoring mechanism is proposed, based on measured vortex positions. We acknowledge the financial support from the European Research Council (ERC Grant Agreement No. 277472).

One-dimensional statistical parametric mapping in Python.

PubMed

Pataky, Todd C

2012-01-01

Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.

Universal recovery map for approximate Markov chains.

PubMed

Sutter, David; Fawzi, Omar; Renner, Renato

2016-02-01

A central question in quantum information theory is to determine how well lost information can be reconstructed. Crucially, the corresponding recovery operation should perform well without knowing the information to be reconstructed. In this work, we show that the quantum conditional mutual information measures the performance of such recovery operations. More precisely, we prove that the conditional mutual information I ( A : C | B ) of a tripartite quantum state ρ ABC can be bounded from below by its distance to the closest recovered state [Formula: see text], where the C -part is reconstructed from the B -part only and the recovery map [Formula: see text] merely depends on ρ BC . One particular application of this result implies the equivalence between two different approaches to define topological order in quantum systems.

Universal recovery map for approximate Markov chains

PubMed Central

Sutter, David; Fawzi, Omar; Renner, Renato

2016-01-01

A central question in quantum information theory is to determine how well lost information can be reconstructed. Crucially, the corresponding recovery operation should perform well without knowing the information to be reconstructed. In this work, we show that the quantum conditional mutual information measures the performance of such recovery operations. More precisely, we prove that the conditional mutual information I(A:C|B) of a tripartite quantum state ρABC can be bounded from below by its distance to the closest recovered state RB→BC(ρAB), where the C-part is reconstructed from the B-part only and the recovery map RB→BC merely depends on ρBC. One particular application of this result implies the equivalence between two different approaches to define topological order in quantum systems. PMID:27118889

Induction Mapping of the 3D-Modulated Spin Texture of Skyrmions in Thin Helimagnets

NASA Astrophysics Data System (ADS)

Schneider, S.; Wolf, D.; Stolt, M. J.; Jin, S.; Pohl, D.; Rellinghaus, B.; Schmidt, M.; Büchner, B.; Goennenwein, S. T. B.; Nielsch, K.; Lubk, A.

2018-05-01

Envisaged applications of Skyrmions in magnetic memory and logic devices crucially depend on the stability and mobility of these topologically nontrivial magnetic textures in thin films. We present for the first time quantitative maps of the magnetic induction that provide evidence for a 3D modulation of the Skyrmionic spin texture. The projected in-plane magnetic induction maps as determined from in-line and off-axis electron holography carry the clear signature of Bloch Skyrmions. However, the magnitude of this induction is much smaller than the values expected for homogeneous Bloch Skyrmions that extend throughout the thickness of the film. This finding can only be understood if the underlying spin textures are modulated along the out-of-plane z direction. The projection of (the in-plane magnetic induction of) helices is further found to exhibit thickness-dependent lateral shifts, which show that this z modulation is accompanied by an (in-plane) modulation along the x and y directions.

Multiple site receptor modeling with a minimal spanning tree combined with a Kohonen neural network

NASA Astrophysics Data System (ADS)

Hopke, Philip K.

1999-12-01

A combination of two pattern recognition methods has been developed that allows the generation of geographical emission maps form multivariate environmental data. In such a projection into a visually interpretable subspace by a Kohonen Self-Organizing Feature Map, the topology of the higher dimensional variables space can be preserved, but parts of the information about the correct neighborhood among the sample vectors will be lost. This can partly be compensated for by an additional projection of Prim's Minimal Spanning Tree into the trained neural network. This new environmental receptor modeling technique has been adapted for multiple sampling sites. The behavior of the method has been studied using simulated data. Subsequently, the method has been applied to mapping data sets from the Southern California Air Quality Study. The projection of a 17 chemical variables measured at up to 8 sampling sites provided a 2D, visually interpretable, geometrically reasonable arrangement of air pollution source sin the South Coast Air Basin.

Age-related changes in brain structural covariance networks.

PubMed

Li, Xinwei; Pu, Fang; Fan, Yubo; Niu, Haijun; Li, Shuyu; Li, Deyu

2013-01-01

Previous neuroimaging studies have suggested that cerebral changes over normal aging are not simply characterized by regional alterations, but rather by the reorganization of cortical connectivity patterns. The investigation of structural covariance networks (SCNs) using voxel-based morphometry is an advanced approach to examining the pattern of covariance in gray matter (GM) volumes among different regions of the human cortex. To date, how the organization of critical SCNs change during normal aging remains largely unknown. In this study, we used an SCN mapping approach to investigate eight large-scale networks in 240 healthy participants aged 18-89 years. These participants were subdivided into young (18-23 years), middle aged (30-58 years), and older (61-89 years) subjects. Eight seed regions were chosen from widely reported functional intrinsic connectivity networks. The voxels showing significant positive associations with these seed regions were used to describe the topological organization of an SCN. All of these networks exhibited non-linear patterns in their spatial extent that were associated with normal aging. These networks, except the primary motor network, had a distributed topology in young participants, a sharply localized topology in middle aged participants, and were relatively stable in older participants. The structural covariance derived using the primary motor cortex was limited to the ipsilateral motor regions in the young and older participants, but included contralateral homologous regions in the middle aged participants. In addition, there were significant between-group differences in the structural networks associated with language-related speech and semantics processing, executive control, and the default-mode network (DMN). Taken together, the results of this study demonstrate age-related changes in the topological organization of SCNs, and provide insights into normal aging of the human brain.

Influence of semisynthetic modification of the scaffold of a contact domain of HbS on polymerization: role of flexible surface topology in polymerization inhibition.

PubMed

Sonati, Srinivasulu; Bhutoria, Savita; Prabhakaran, Muthuchidambaran; Acharya, Seetharama A

2018-02-01

A new variant of HbS, HbS-Einstein with a deletion of segment α 23-26 in the B-helix, has been assembled by semisynthetic approach. B-helix of the α chain of cis αβ-dimer of HbS plays dominant role in the quinary interactions of deoxy HbS dimer. This B-helix is the primary scaffold that provides the orientation for the side chains of contact residues of this intermolecular contact domain. The design of HbS-Einstein has been undertaken to map the influence of perturbation of molecular surface topology and the flexibility of surface residues in the polymerization. The internal deletion exerts a strong inhibitory influence on Val-6 (β)-dependent polymerization, comparable to single contact site mutations and not for complete neutralization of Val-6(β)-dependent polymerization. The scaffold modification in cis-dimer is inhibitory, and is without any effect when present on the trans dimer. The flexibility changes in the surface topology in the region of scaffold modification apparently counteracts the intrinsic polymerization potential of the molecule. The inhibition is close to that of Le Lamentin mutation [His-20 (α) → Gln] wherein a mutation engineered without much change in flexibility of the contact domain. Interestingly, the chimeric HbS with swine-human chimeric α chain with multiple non-conservative mutations completely inhibits the Val-6(β)-dependent polymerization. The deformabilities of surface topology of chimeric HbS are comparable to HbS in spite of the multiple contact site mutations in the α-chain. We conclude that the design of antisickling Hbs for gene therapy of sickle cell disease should involve multiple mutations of intermolecular contact sites.

Stability of whole brain and regional network topology within and between resting and cognitive states.

PubMed

Rzucidlo, Justyna K; Roseman, Paige L; Laurienti, Paul J; Dagenbach, Dale

2013-01-01

Graph-theory based analyses of resting state functional Magnetic Resonance Imaging (fMRI) data have been used to map the network organization of the brain. While numerous analyses of resting state brain organization exist, many questions remain unexplored. The present study examines the stability of findings based on this approach over repeated resting state and working memory state sessions within the same individuals. This allows assessment of stability of network topology within the same state for both rest and working memory, and between rest and working memory as well. fMRI scans were performed on five participants while at rest and while performing the 2-back working memory task five times each, with task state alternating while they were in the scanner. Voxel-based whole brain network analyses were performed on the resulting data along with analyses of functional connectivity in regions associated with resting state and working memory. Network topology was fairly stable across repeated sessions of the same task, but varied significantly between rest and working memory. In the whole brain analysis, local efficiency, Eloc, differed significantly between rest and working memory. Analyses of network statistics for the precuneus and dorsolateral prefrontal cortex revealed significant differences in degree as a function of task state for both regions and in local efficiency for the precuneus. Conversely, no significant differences were observed across repeated sessions of the same state. These findings suggest that network topology is fairly stable within individuals across time for the same state, but also fluid between states. Whole brain voxel-based network analyses may prove to be a valuable tool for exploring how functional connectivity changes in response to task demands.

Global surface pressure measurements of static and dynamic stall on a wind turbine airfoil at low Reynolds number

NASA Astrophysics Data System (ADS)

Disotell, Kevin J.; Nikoueeyan, Pourya; Naughton, Jonathan W.; Gregory, James W.

2016-05-01

Recognizing the need for global surface measurement techniques to characterize the time-varying, three-dimensional loading encountered on rotating wind turbine blades, fast-responding pressure-sensitive paint (PSP) has been evaluated for resolving unsteady aerodynamic effects in incompressible flow. Results of a study aimed at demonstrating the laser-based, single-shot PSP technique on a low Reynolds number wind turbine airfoil in static and dynamic stall are reported. PSP was applied to the suction side of a Delft DU97-W-300 airfoil (maximum thickness-to-chord ratio of 30 %) at a chord Reynolds number of 225,000 in the University of Wyoming open-return wind tunnel. Static and dynamic stall behaviors are presented using instantaneous and phase-averaged global pressure maps. In particular, a three-dimensional pressure topology driven by a stall cell pattern is detected near the maximum lift condition on the steady airfoil. Trends in the PSP-measured pressure topology on the steady airfoil were confirmed using surface oil visualization. The dynamic stall case was characterized by a sinusoidal pitching motion with mean angle of 15.7°, amplitude of 11.2°, and reduced frequency of 0.106 based on semichord. PSP images were acquired at selected phase positions, capturing the breakdown of nominally two-dimensional flow near lift stall, development of post-stall suction near the trailing edge, and a highly three-dimensional topology as the flow reattaches. Structural patterns in the surface pressure topologies are considered from the analysis of the individual PSP snapshots, enabled by a laser-based excitation system that achieves sufficient signal-to-noise ratio in the single-shot images. The PSP results are found to be in general agreement with observations about the steady and unsteady stall characteristics expected for the airfoil.

Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

PubMed

Sun, Yunxiang; Ming, Dengming

2014-01-01

Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

Spatial potential ripples of azimuthal surface modes in topological insulator Bi2Te3 nanowires

PubMed Central

Muñoz Rojo, Miguel; Zhang, Yingjie; Manzano, Cristina V.; Alvaro, Raquel; Gooth, Johannes; Salmeron, Miquel; Martin-Gonzalez, Marisol

2016-01-01

Topological insulators (TI) nanowires (NW) are an emerging class of structures, promising both novel quantum effects and potential applications in low-power electronics, thermoelectrics and spintronics. However, investigating the electronic states of TI NWs is complicated, due to their small lateral size, especially at room temperature. Here, we perform scanning probe based nanoscale imaging to resolve the local surface potential landscapes of Bi2Te3 nanowires (NWs) at 300 K. We found equipotential rings around the NWs perimeter that we attribute to azimuthal 1D modes. Along the NW axis, these modes are altered, forming potential ripples in the local density of states, due to intrinsic disturbances. Potential mapping of electrically biased NWs enabled us to accurately determine their conductivity which was found to increase with the decrease of NW diameter, consistent with surface dominated transport. Our results demonstrate that TI NWs can pave the way to both exotic quantum states and novel electronic devices. PMID:26751282

Spatial potential ripples of azimuthal surface modes in topological insulator Bi2Te3 nanowires.

PubMed

Muñoz Rojo, Miguel; Zhang, Yingjie; Manzano, Cristina V; Alvaro, Raquel; Gooth, Johannes; Salmeron, Miquel; Martin-Gonzalez, Marisol

2016-01-11

Topological insulators (TI) nanowires (NW) are an emerging class of structures, promising both novel quantum effects and potential applications in low-power electronics, thermoelectrics and spintronics. However, investigating the electronic states of TI NWs is complicated, due to their small lateral size, especially at room temperature. Here, we perform scanning probe based nanoscale imaging to resolve the local surface potential landscapes of Bi2Te3 nanowires (NWs) at 300 K. We found equipotential rings around the NWs perimeter that we attribute to azimuthal 1D modes. Along the NW axis, these modes are altered, forming potential ripples in the local density of states, due to intrinsic disturbances. Potential mapping of electrically biased NWs enabled us to accurately determine their conductivity which was found to increase with the decrease of NW diameter, consistent with surface dominated transport. Our results demonstrate that TI NWs can pave the way to both exotic quantum states and novel electronic devices.

Holographic Symmetries and Generalized Order Parameters for Topological Matter

NASA Astrophysics Data System (ADS)

Cobanera, Emilio; Ortiz, Gerardo; Nussinov, Zohar

2013-03-01

We introduce a universally applicable method, based on the bond-algebraic theory of dualities, to search for generalized order parameters in a wide variety of non-Landau systems, including topologically ordered matter. To this end we introduce the key notion of holographic symmetry. It reflects situations in which global symmetries become exact boundary symmetries under a duality mapping. Holographic symmetries are naturally related to edge modes and localization. The utility of our approach is illustrated by presenting a systematic derivation of generalized order parameters for pure and matter-coupled Abelian gauge theories and (extended) toric codes. Also we introduce a many-body extension of the Kitaev wire, the gauged Kitaev wire, and exploit holographic symmetries and dualities to describe its phase diagram, generalized order parameter, and edge states. [arXiv:1211.0564] This work was supported by the Dutch Science Foundation NWO/FOM and an ERC Advanced Investigator grant, and, in part, under grants No. NSF PHY11-25915 and CMMT 1106293.

Design of crystal-like aperiodic solids with selective disorder–phonon coupling

PubMed Central

Overy, Alistair R.; Cairns, Andrew B.; Cliffe, Matthew J.; Simonov, Arkadiy; Tucker, Matthew G.; Goodwin, Andrew L.

2016-01-01

Functional materials design normally focuses on structurally ordered systems because disorder is considered detrimental to many functional properties. Here we challenge this paradigm by showing that particular types of strongly correlated disorder can give rise to useful characteristics that are inaccessible to ordered states. A judicious combination of low-symmetry building unit and high-symmetry topological template leads to aperiodic ‘procrystalline' solids that harbour this type of disorder. We identify key classes of procrystalline states together with their characteristic diffraction behaviour, and establish mappings onto known and target materials. The strongly correlated disorder found in these systems is associated with specific sets of modulation periodicities distributed throughout the Brillouin zone. Lattice dynamical calculations reveal selective disorder-driven phonon broadening that resembles the poorly understood ‘waterfall' effect observed in relaxor ferroelectrics. This property of procrystalline solids suggests a mechanism by which strongly correlated topological disorder might allow independently optimized thermal and electronic transport behaviour, such as required for high-performance thermoelectrics. PMID:26842772

Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

PubMed Central

Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I.; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan; Dekker, Job; Taylor, James; Corces, Victor G.

2013-01-01

Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. PMID:23706625

Antiholomorphic perturbations of Weierstrass Zeta functions and Green’s function on tori

NASA Astrophysics Data System (ADS)

Bogdanov, Konstantin; Mamayusupov, Khudoyor; Mukherjee, Sabyasachi; Schleicher, Dierk

2017-08-01

In Bergweiler and Eremenko (2016 Proc. Am. Math. Soc. 144 2911-22), Bergweiler and Eremenko computed the number of critical points of the Green’s function on a torus by investigating the dynamics of a certain family of antiholomorphic meromorphic functions on tori. They also observed that hyperbolic maps are dense in this family of meromorphic functions in a rather trivial way. In this paper, we study the parameter space of this family of meromorphic functions, which can be written as antiholomorphic perturbations of Weierstrass Zeta functions. On the one hand, we give a complete topological description of the hyperbolic components and their boundaries, and on the other hand, we show that these sets admit natural parametrizations by associated dynamical invariants. This settles a conjecture, made in Lin and Wang (2010 Ann. Math. 172 911-54), on the topology of the regions in the upper half plane {H} where the number of critical points of the Green’s function remains constant.

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.

PubMed

Luo, Jie; Cimermancic, Peter; Viswanath, Shruthi; Ebmeier, Christopher C; Kim, Bong; Dehecq, Marine; Raman, Vishnu; Greenberg, Charles H; Pellarin, Riccardo; Sali, Andrej; Taatjes, Dylan J; Hahn, Steven; Ranish, Jeff

2015-09-03

TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved "topological regions" that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with xeroderma pigmentosum and trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit. Copyright © 2015 Elsevier Inc. All rights reserved.

Predicting catastrophes of non-autonomous networks with visibility graphs and horizontal visibility

NASA Astrophysics Data System (ADS)

Zhang, Haicheng; Xu, Daolin; Wu, Yousheng

2018-05-01

Prediction of potential catastrophes in engineering systems is a challenging problem. We first attempt to construct a complex network to predict catastrophes of a multi-modular floating system in advance of their occurrences. Response time series of the system can be mapped into an virtual network by using visibility graph or horizontal visibility algorithm. The topology characteristics of the networks can be used to forecast catastrophes of the system. Numerical results show that there is an obvious corresponding relationship between the variation of topology characteristics and the onset of catastrophes. A Catastrophe Index (CI) is proposed as a numerical indicator to measure a qualitative change from a stable state to a catastrophic state. The two approaches, the visibility graph and horizontal visibility algorithms, are compared by using the index in the reliability analysis with different data lengths and sampling frequencies. The technique of virtual network method is potentially extendable to catastrophe predictions of other engineering systems.

Modular networks with delayed coupling: Synchronization and frequency control

NASA Astrophysics Data System (ADS)

Maslennikov, Oleg V.; Nekorkin, Vladimir I.

2014-07-01

We study the collective dynamics of modular networks consisting of map-based neurons which generate irregular spike sequences. Three types of intramodule topology are considered: a random Erdös-Rényi network, a small-world Watts-Strogatz network, and a scale-free Barabási-Albert network. The interaction between the neurons of different modules is organized by relatively sparse connections with time delay. For all the types of the network topology considered, we found that with increasing delay two regimes of module synchronization alternate with each other: inphase and antiphase. At the same time, the average rate of collective oscillations decreases within each of the time-delay intervals corresponding to a particular synchronization regime. A dual role of the time delay is thus established: controlling a synchronization mode and degree and controlling an average network frequency. Furthermore, we investigate the influence on the modular synchronization by other parameters: the strength of intermodule coupling and the individual firing rate.

Non-Functional Property Driven Service Governance: Performance Implications

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

Liu, Yan; Zhu, Liming; Bass, Len

2007-09-17

Service governance is a set of businesses processes, policies and technical solutions that support enterprises in their implementation and management of their SOA. The decisions of service governance, especially concerning service boundaries at the enterprise level, influence the deployment topology of business services across or within business organizations. Deployment topologies are realized by integration technologies such as Enterprise Service Bus (ESB). Service governance and technical solutions interact in a subtle way including through communication patterns and protocols between services and ESBs, as well as the deployment and configuration of ESB. These factors have a strong influence on the Non- Functionalmore » Properties (NFP) of a SOA solution. A systematic approach is essential to understand alternative technical solutions for a specific service governance decision. This paper proposes a modeling approach to evaluate the performance-related NFP impacts when mapping service governance to technical solutions using an ESB. This approach is illustrated by the quantitative performance analysis of a real« less

High-resolution mapping reveals topologically distinct cellular pools of phosphatidylserine

PubMed Central

Fairn, Gregory D.; Schieber, Nicole L.; Ariotti, Nicholas; Murphy, Samantha; Kuerschner, Lars; Webb, Richard I.; Grinstein, Sergio

2011-01-01

Phosphatidylserine (PS) plays a central role in cell signaling and in the biosynthesis of other lipids. To date, however, the subcellular distribution and transmembrane topology of this crucial phospholipid remain ill-defined. We transfected cells with a GFP-tagged C2 domain of lactadherin to detect by light and electron microscopy PS exposed on the cytosolic leaflet of the plasmalemma and organellar membranes. Cytoplasmically exposed PS was found to be clustered on the plasma membrane, and to be associated with caveolae, the trans-Golgi network, and endocytic organelles including intraluminal vesicles of multivesicular endosomes. This labeling pattern was compared with the total cellular distribution of PS as visualized using a novel on-section technique. These complementary methods revealed PS in the interior of the ER, Golgi complex, and mitochondria. These results indicate that PS in the lumenal monolayer of the ER and Golgi complex becomes exposed cytosolically at the trans-Golgi network. Transmembrane flipping of PS may contribute to the exit of cargo from the Golgi complex. PMID:21788369

Interarrival times of message propagation on directed networks.

PubMed

Mihaljev, Tamara; de Arcangelis, Lucilla; Herrmann, Hans J

2011-08-01

One of the challenges in fighting cybercrime is to understand the dynamics of message propagation on botnets, networks of infected computers used to send viruses, unsolicited commercial emails (SPAM) or denial of service attacks. We map this problem to the propagation of multiple random walkers on directed networks and we evaluate the interarrival time distribution between successive walkers arriving at a target. We show that the temporal organization of this process, which models information propagation on unstructured peer to peer networks, has the same features as SPAM reaching a single user. We study the behavior of the message interarrival time distribution on three different network topologies using two different rules for sending messages. In all networks the propagation is not a pure Poisson process. It shows universal features on Poissonian networks and a more complex behavior on scale free networks. Results open the possibility to indirectly learn about the process of sending messages on networks with unknown topologies, by studying interarrival times at any node of the network.

Interarrival times of message propagation on directed networks

NASA Astrophysics Data System (ADS)

Mihaljev, Tamara; de Arcangelis, Lucilla; Herrmann, Hans J.

2011-08-01

One of the challenges in fighting cybercrime is to understand the dynamics of message propagation on botnets, networks of infected computers used to send viruses, unsolicited commercial emails (SPAM) or denial of service attacks. We map this problem to the propagation of multiple random walkers on directed networks and we evaluate the interarrival time distribution between successive walkers arriving at a target. We show that the temporal organization of this process, which models information propagation on unstructured peer to peer networks, has the same features as SPAM reaching a single user. We study the behavior of the message interarrival time distribution on three different network topologies using two different rules for sending messages. In all networks the propagation is not a pure Poisson process. It shows universal features on Poissonian networks and a more complex behavior on scale free networks. Results open the possibility to indirectly learn about the process of sending messages on networks with unknown topologies, by studying interarrival times at any node of the network.

Stochastic Stability of Nonlinear Sampled Data Systems with a Jump Linear Controller

NASA Technical Reports Server (NTRS)

Gonzalez, Oscar R.; Herencia-Zapana, Heber; Gray, W. Steven

2004-01-01

This paper analyzes the stability of a sampled- data system consisting of a deterministic, nonlinear, time- invariant, continuous-time plant and a stochastic, discrete- time, jump linear controller. The jump linear controller mod- els, for example, computer systems and communication net- works that are subject to stochastic upsets or disruptions. This sampled-data model has been used in the analysis and design of fault-tolerant systems and computer-control systems with random communication delays without taking into account the inter-sample response. To analyze stability, appropriate topologies are introduced for the signal spaces of the sampled- data system. With these topologies, the ideal sampling and zero-order-hold operators are shown to be measurable maps. This paper shows that the known equivalence between the stability of a deterministic, linear sampled-data system and its associated discrete-time representation as well as between a nonlinear sampled-data system and a linearized representation holds even in a stochastic framework.

Exploring the Electronic Structure and Chemical Homogeneity of Individual Bi2Te3 Nanowires by Nano-Angle-Resolved Photoemission Spectroscopy.

PubMed

Krieg, Janina; Chen, Chaoyu; Avila, José; Zhang, Zeying; Sigle, Wilfried; Zhang, Hongbin; Trautmann, Christina; Asensio, Maria Carmen; Toimil-Molares, Maria Eugenia

2016-07-13

Due to their high surface-to-volume ratio, cylindrical Bi2Te3 nanowires are employed as model systems to investigate the chemistry and the unique conductive surface states of topological insulator nanomaterials. We report on nanoangle-resolved photoemission spectroscopy (nano-ARPES) characterization of individual cylindrical Bi2Te3 nanowires with a diameter of 100 nm. The nanowires are synthesized by electrochemical deposition inside channels of ion-track etched polymer membranes. Core level spectra recorded with submicron resolution indicate a homogeneous chemical composition along individual nanowires, while nano-ARPES intensity maps reveal the valence band structure at the single nanowire level. First-principles electronic structure calculations for chosen crystallographic orientations are in good agreement with those revealed by nano-ARPES. The successful application of nano-ARPES on single one-dimensional nanostructures constitutes a new avenue to achieve a better understanding of the electronic structure of topological insulator nanomaterials.

Gauge field entanglement in Kitaev's honeycomb model

NASA Astrophysics Data System (ADS)

Dóra, Balázs; Moessner, Roderich

2018-01-01

A spin fractionalizes into matter and gauge fermions in Kitaev's spin liquid on the honeycomb lattice. This follows from a Jordan-Wigner mapping to fermions, allowing for the construction of a minimal entropy ground-state wave function on the cylinder. We use this to calculate the entanglement entropy by choosing several distinct partitionings. First, by partitioning an infinite cylinder into two, the -ln2 topological entanglement entropy is reconfirmed. Second, the reduced density matrix of the gauge sector on the full cylinder is obtained after tracing out the matter degrees of freedom. This allows for evaluating the gauge entanglement Hamiltonian, which contains infinitely long-range correlations along the symmetry axis of the cylinder. The matter-gauge entanglement entropy is (Ny-1 )ln2 , with Ny the circumference of the cylinder. Third, the rules for calculating the gauge sector entanglement of any partition are determined. Rather small correctly chosen gauge partitions can still account for the topological entanglement entropy in spite of long-range correlations in the gauge entanglement Hamiltonian.

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

PubMed

Ron, Gil; Globerson, Yuval; Moran, Dror; Kaplan, Tommy

2017-12-21

Proximity-ligation methods such as Hi-C allow us to map physical DNA-DNA interactions along the genome, and reveal its organization into topologically associating domains (TADs). As the Hi-C data accumulate, computational methods were developed for identifying domain borders in multiple cell types and organisms. Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter-enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify over-represented DNA-DNA interactions across the genome. By analyzing the published Hi-C data sets in human and mouse, we identify hundreds of thousands of putative enhancers and their target genes, and compile an extensive genome-wide catalog of gene regulation in human and mouse. As we show, our predictions are highly enriched for ChIP-seq and DNA accessibility data, evolutionary conservation, eQTLs and other DNA-DNA interaction data.

Coarse-grained sequences for protein folding and design.

PubMed

Brown, Scott; Fawzi, Nicolas J; Head-Gordon, Teresa

2003-09-16

We present the results of sequence design on our off-lattice minimalist model in which no specification of native-state tertiary contacts is needed. We start with a sequence that adopts a target topology and build on it through sequence mutation to produce new sequences that comprise distinct members within a target fold class. In this work, we use the alpha/beta ubiquitin fold class and design two new sequences that, when characterized through folding simulations, reproduce the differences in folding mechanism seen experimentally for proteins L and G. The primary implication of this work is that patterning of hydrophobic and hydrophilic residues is the physical origin for the success of relative contact-order descriptions of folding, and that these physics-based potentials provide a predictive connection between free energy landscapes and amino acid sequence (the original protein folding problem). We present results of the sequence mapping from a 20- to the three-letter code for determining a sequence that folds into the WW domain topology to illustrate future extensions to protein design.

Learning disordered topological phases by statistical recovery of symmetry

NASA Astrophysics Data System (ADS)

Yoshioka, Nobuyuki; Akagi, Yutaka; Katsura, Hosho

2018-05-01

We apply the artificial neural network in a supervised manner to map out the quantum phase diagram of disordered topological superconductors in class DIII. Given the disorder that keeps the discrete symmetries of the ensemble as a whole, translational symmetry which is broken in the quasiparticle distribution individually is recovered statistically by taking an ensemble average. By using this, we classify the phases by the artificial neural network that learned the quasiparticle distribution in the clean limit and show that the result is totally consistent with the calculation by the transfer matrix method or noncommutative geometry approach. If all three phases, namely the Z2, trivial, and thermal metal phases, appear in the clean limit, the machine can classify them with high confidence over the entire phase diagram. If only the former two phases are present, we find that the machine remains confused in a certain region, leading us to conclude the detection of the unknown phase which is eventually identified as the thermal metal phase.

Learning directed acyclic graphs from large-scale genomics data.

PubMed

Nikolay, Fabio; Pesavento, Marius; Kritikos, George; Typas, Nassos

2017-09-20

In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactions-Detector (GENIE) to identify the complex biological dependencies among genes and to compute the DAG topology that matches the DK measurements best. Furthermore, we extend the GENIE program by incorporating genetic interaction profile (GI-profile) data to further enhance the detection performance. In addition, we propose a sequential scalability technique for large sets of genes under study, in order to provide statistically significant results for real measurement data. Finally, we show via numeric simulations that the GENIE program and the GI-profile data extended GENIE (GI-GENIE) program clearly outperform the conventional techniques and present real data results for our proposed sequential scalability technique.

Spatial potential ripples of azimuthal surface modes in topological insulator Bi 2Te 3 nanowires

DOE PAGES

Muñoz Rojo, Miguel; Zhang, Yingjie; Manzano, Cristina V.; ...

2016-01-11

Topological insulators (TI) nanowires (NW) are an emerging class of structures, promising both novel quantum effects and potential applications in low-power electronics, thermoelectrics and spintronics. However, investigating the electronic states of TI NWs is complicated, due to their small lateral size, especially at room temperature. Here, we perform scanning probe based nanoscale imaging to resolve the local surface potential landscapes of Bi 2Te 3 nanowires (NWs) at 300 K. We found equipotential rings around the NWs perimeter that we attribute to azimuthal 1D modes. Along the NW axis, these modes are altered, forming potential ripples in the local density ofmore » states, due to intrinsic disturbances. Potential mapping of electrically biased NWs enabled us to accurately determine their conductivity which was found to increase with the decrease of NW diameter, consistent with surface dominated transport. Finally, our results demonstrate that TI NWs can pave the way to both exotic quantum states and novel electronic devices.« less