Topological order following a quantum quench

NASA Astrophysics Data System (ADS)

Tsomokos, Dimitris I.; Hamma, Alioscia; Zhang, Wen; Haas, Stephan; Fazio, Rosario

2009-12-01

We determine the conditions under which topological order survives a rapid quantum quench. Specifically, we consider the case where a quantum spin system is prepared in the ground state of the toric code model and, after the quench, it evolves with a Hamiltonian that does not support topological order. We provide analytical results supported by numerical evidence for a variety of quench Hamiltonians. The robustness of topological order under nonequilibrium situations is tested by studying the topological entropy and a dynamical measure, which makes use of the similarity between partial density matrices obtained from different topological sectors.

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

PubMed

Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun

2015-12-17

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Manipulating topological-insulator properties using quantum confinement

NASA Astrophysics Data System (ADS)

Kotulla, M.; Zülicke, U.

2017-07-01

Recent discoveries have spurred the theoretical prediction and experimental realization of novel materials that have topological properties arising from band inversion. Such topological insulators are insulating in the bulk but have conductive surface or edge states. Topological materials show various unusual physical properties and are surmised to enable the creation of exotic Majorana-fermion quasiparticles. How the signatures of topological behavior evolve when the system size is reduced is interesting from both a fundamental and an application-oriented point of view, as such understanding may form the basis for tailoring systems to be in specific topological phases. This work considers the specific case of quantum-well confinement defining two-dimensional layers. Based on the effective-Hamiltonian description of bulk topological insulators, and using a harmonic-oscillator potential as an example for a softer-than-hard-wall confinement, we have studied the interplay of band inversion and size quantization. Our model system provides a useful platform for systematic study of the transition between the normal and topological phases, including the development of band inversion and the formation of massless-Dirac-fermion surface states. The effects of bare size quantization, two-dimensional-subband mixing, and electron-hole asymmetry are disentangled and their respective physical consequences elucidated.

A contribution to the design specification of single-cell multi-resonant converters

NASA Astrophysics Data System (ADS)

Franck, F.; Schroeder, D.

The state plane technique is used to develop a design-specification procedure that enables the designer to directly calculate the stresses on all elements of the different topologies for quasi-resonant converters. If parasitic elements are considered, multiresonant topologies are obtained. These topologies can be calculated for the design specification if the procedure for quasi-resonant topologies is adapted to this situation. A novel theoretical approach for describing the internal behavior of multiresonant converters and for visualizing the switching conditions and the points of maximum component stresses is proposed. The multiresonant switching technique combines two advantages: the lossless snubbing of both the transistor and the diode is achieved by only three reactive elements, and a controllable no-load operation is possible. This analysis procedure is well suited for calculating dc-dc converter with an output power up to several hundred watts.

The Medieval Kingdom Topology: Peer Relations in Kindergarten Children.

ERIC Educational Resources Information Center

Bennett, Andrew; Derervensky, Jeffrey

1995-01-01

Examines the applicability of the medieval kingdom social role topology with kindergarten children and assesses the association between the social roles children assume and seven nonbehavioral variables. Confirmed hypotheses that the topology could be distilled from a sample of kindergarten children (n=173) and that specific nonbehavioral…

Global topological dominance in the left hemisphere.

PubMed

Wang, Bo; Zhou, Tian Gang; Zhuo, Yan; Chen, Lin

2007-12-26

A series of experiments with right-handers demonstrated that the left hemisphere (LH) is reliably and consistently superior to the right hemisphere (RH) for global topological perception. These experiments generalized the topological account of lateralization to different kinds of topological properties (including holes, inside/outside relation, and "presence vs. absence") in comparison with a broad spectrum of geometric properties, including orientation, distance, size, mirror-symmetry, parallelism, collinearity, etc. The stimuli and paradigms used were also designed to prevent subjects from using various nontopological properties in performing the tasks of topological discrimination. Furthermore, task factors commonly considered in the study of hemispheric asymmetry, such as response latency vs. accuracy, vertical vs. horizontal presentation, detection vs. recognition, and simultaneous vs. sequential judgment, were manipulated to not be confounding factors. Moreover, left-handed subjects were tested and showed the right lateralization of topological perception, in the opposite direction of lateralization compared with right-handers. In addition, the functional magnetic resonance imaging measure revealed that only a region in the left temporal gyrus was consistently more activated across subjects in the task of topological discrimination, consistent with the behavioral results. In summary, the global topological dominance in the LH is well supported by the converging evidence from the variety of paradigms and techniques, and it suggests a unified solution to the current major controversies on visual lateralization.

Thermoelectric properties of an ultra-thin topological insulator.

PubMed

Islam, S K Firoz; Ghosh, T K

2014-04-23

Thermoelectric coefficients of an ultra-thin topological insulator are presented here. The hybridization between top and bottom surface states of a topological insulator plays a significant role. In the absence of a magnetic field, the thermopower increases and thermal conductivity decreases with an increase in the hybridization energy. In the presence of a magnetic field perpendicular to the ultra-thin topological insulator, thermoelectric coefficients exhibit quantum oscillations with inverse magnetic field, whose frequency is strongly modified by the Zeeman energy and whose phase factor is governed by the product of the Landé g-factor and the hybridization energy. In addition to the numerical results, the low-temperature approximate analytical results for the thermoelectric coefficients are also provided. It is also observed that for a given magnetic field these transport coefficients oscillate with hybridization energy, at a frequency that depends on the Landé g-factor.

Tracking the Topological: The Effects of Standardised Data upon Teachers' Practice

ERIC Educational Resources Information Center

Lewis, Steven; Hardy, Ian

2017-01-01

This article draws upon recent theorising of the "becoming topological" of space--specifically, how new social spaces are constituted through relations rather than physical locations--to explore how standardised data, and specifically test data, have influenced teachers' work and learning. We outline the varied ways in which teacher…

Topological Quantum Buses: Coherent Quantum Information Transfer between Topological and Conventional Qubits

NASA Astrophysics Data System (ADS)

Bonderson, Parsa; Lutchyn, Roman M.

2011-04-01

We propose computing bus devices that enable quantum information to be coherently transferred between topological and conventional qubits. We describe a concrete realization of such a topological quantum bus acting between a topological qubit in a Majorana wire network and a conventional semiconductor double quantum dot qubit. Specifically, this device measures the joint (fermion) parity of these two different qubits by using the Aharonov-Casher effect in conjunction with an ancilliary superconducting flux qubit that facilitates the measurement. Such a parity measurement, together with the ability to apply Hadamard gates to the two qubits, allows one to produce states in which the topological and conventional qubits are maximally entangled and to teleport quantum states between the topological and conventional quantum systems.

The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology

PubMed Central

Hsiao, Hao-Ching; Gonzalez, Kim L.; Catanese, Daniel J.; Jordy, Kristopher E.; Matthews, Kathleen S.; Bondos, Sarah E.

2014-01-01

Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues. PMID:25286318

Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovar-specific teichoic acids

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

Bielmann, Regula; Habann, Matthias; Eugster, Marcel R.

Adsorption of a bacteriophage to the host requires recognition of a cell wall-associated receptor by a receptor binding protein (RBP). This recognition is specific, and high affinity binding is essential for efficient virus attachment. The molecular details of phage adsorption to the Gram-positive cell are poorly understood. We present the first description of receptor binding proteins and a tail tip structure for the siphovirus group infecting Listeria monocytogenes. The host-range determining factors in two phages, A118 and P35 specific for L. monocytogenes serovar 1/2 have been determined. Two proteins were identified as RBPs in phage A118. Rhamnose residues in wallmore » teichoic acids represent the binding ligands for both proteins. In phage P35, protein gp16 could be identified as RBP and the role of both rhamnose and N-acetylglucosamine in phage adsorption was confirmed. Immunogold-labeling and transmission electron microscopy allowed the creation of a topological model of the A118 phage tail. - Highlights: • We present the first description of receptor binding proteins and a tail tip structure for the Siphovirus group infecting Listeria monocytogenes. • The host-range determining factors in two phages, A118 and P35 specific for L. monocytogenes serovar 1/2 have been determined. • Rhamnose residues in wall teichoic acids represent the binding ligands for both receptor binding proteins in phage A118. • Rhamnose and N-acetylglucosamine are required for adsorption of phage P35. • We preset a topological model of the A118 phage tail.« less

The Dynamic Interplay Between DNA Topoisomerases and DNA Topology.

PubMed

Seol, Yeonee; Neuman, Keir C

2016-09-01

Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo . Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

The dynamic interplay between DNA topoisomerases and DNA topology.

PubMed

Seol, Yeonee; Neuman, Keir C

2016-11-01

Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

PubMed

Amaral, Paulo P; Leonardi, Tommaso; Han, Namshik; Viré, Emmanuelle; Gascoigne, Dennis K; Arias-Carrasco, Raúl; Büscher, Magdalena; Pandolfini, Luca; Zhang, Anda; Pluchino, Stefano; Maracaja-Coutinho, Vinicius; Nakaya, Helder I; Hemberg, Martin; Shiekhattar, Ramin; Enright, Anton J; Kouzarides, Tony

2018-03-15

The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes. These positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are coexpressed in a tissue-specific manner. Over half of positionally conserved RNAs in this set are linked to chromatin organization structures, overlapping binding sites for the CTCF chromatin organiser and located at chromatin loop anchor points and borders of topologically associating domains (TADs). We define these RNAs as topological anchor point RNAs (tapRNAs). Characterization of these noncoding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other's expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Furthermore, we find that tapRNAs contain conserved sequence domains that are enriched in motifs for zinc finger domain-containing RNA-binding proteins and transcription factors, whose binding sites are found mutated in cancers. This work leverages positional conservation to identify lncRNAs with potential importance in genome organization, development and disease. The evidence that many developmental transcription factors are physically and functionally connected to lncRNAs represents an exciting stepping-stone to further our understanding of genome regulation.

Topological quantum buses: coherent quantum information transfer between topological and conventional qubits.

PubMed

Bonderson, Parsa; Lutchyn, Roman M

2011-04-01

We propose computing bus devices that enable quantum information to be coherently transferred between topological and conventional qubits. We describe a concrete realization of such a topological quantum bus acting between a topological qubit in a Majorana wire network and a conventional semiconductor double quantum dot qubit. Specifically, this device measures the joint (fermion) parity of these two different qubits by using the Aharonov-Casher effect in conjunction with an ancilliary superconducting flux qubit that facilitates the measurement. Such a parity measurement, together with the ability to apply Hadamard gates to the two qubits, allows one to produce states in which the topological and conventional qubits are maximally entangled and to teleport quantum states between the topological and conventional quantum systems. © 2011 American Physical Society

Current transport properties and phase diagram of a Kitaev chain with long-range pairing

NASA Astrophysics Data System (ADS)

Giuliano, Domenico; Paganelli, Simone; Lepori, Luca

2018-04-01

We describe a method to probe the quantum phase transition between the short-range topological phase and the long-range topological phase in the superconducting Kitaev chain with long-range pairing, both exhibiting subgap modes localized at the edges. The method relies on the effects of the finite mass of the subgap edge modes in the long-range regime (which survives in the thermodynamic limit) on the single-particle scattering coefficients through the chain connected to two normal leads. Specifically, we show that, when the leads are biased at a voltage V with respect to the superconducting chain, the Fano factor is either zero (in the short-range correlated phase) or 2 e (in the long-range correlated phase). As a result, we find that the Fano factor works as a directly measurable quantity to probe the quantum phase transition between the two phases. In addition, we note a remarkable "critical fractionalization effect" in the Fano factor, which is exactly equal to e along the quantum critical line. Finally, we note that a dual implementation of our proposed device makes it suitable as a generator of large-distance entangled two-particle states.

Simulating quantum spin Hall effect in the topological Lieb lattice of a linear circuit network

NASA Astrophysics Data System (ADS)

Zhu, Weiwei; Hou, Shanshan; Long, Yang; Chen, Hong; Ren, Jie

2018-02-01

Inspired by the topological insulator circuit experimentally proposed by Jia Ningyuan et al. [Phys. Rev. X 5, 021031 (2015), 10.1103/PhysRevX.5.021031], we theoretically realize the topological Lieb lattice, a line-centered square lattice with rich topological properties, in a radio-frequency circuit. We design a specific capacitor-inductor connection to resemble the intrinsic spin-orbit coupling and construct the analog spin by mixing degrees of freedom of voltages. As such, we are able to simulate the quantum spin Hall effect in the topological Lieb lattice of linear circuits. We then investigate the spin-resolved topological edge mode and the topological phase transition of the band structure varied with capacitances. Finally, we discuss the extension of the π /2 phase change of hopping between sites to arbitrary phase values. Our results may find implications in engineering microwave topological metamaterials for signal transmission and energy harvesting.

Data Fusion of Geographically Dispersed Information: Experience With the Scalable Data Grid

DTIC Science & Technology

2011-03-01

framework that exposes calls to this HLA interface to registered plug-ins (Figure 2). The SDG exploits this plug-in to intercept and log messages and...implementation and use of the SDG and Hadoop Figure 4. Schematic meshrouter topology. Figure 5. Factored Meshrouter implementation, with application-specific...communications primitives. Yao, Ward, & Davis 92 ITEA Journal show promise for the T&E environments. It reported on experiments implementing the SDG and on

Negative Magnetoresistance without Chiral Anomaly in Topological Insulators.

PubMed

Dai, Xin; Du, Z Z; Lu, Hai-Zhou

2017-10-20

An intriguing phenomenon in topological semimetals and topological insulators is the negative magnetoresistance (MR) observed when a magnetic field is applied along the current direction. A prevailing understanding to the negative MR in topological semimetals is the chiral anomaly, which, however, is not well defined in topological insulators. We calculate the MR of a three-dimensional topological insulator, by using the semiclassical equations of motion, in which the Berry curvature explicitly induces an anomalous velocity and orbital moment. Our theoretical results are in quantitative agreement with the experiments. The negative MR is not sensitive to temperature and increases as the Fermi energy approaches the band edge. The orbital moment and g factors also play important roles in the negative MR. Our results give a reasonable explanation to the negative MR in 3D topological insulators and will be helpful in understanding the anomalous quantum transport in topological states of matter.

Effective field theories for topological insulators by functional bosonization

NASA Astrophysics Data System (ADS)

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

2013-02-01

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

Topological image texture analysis for quality assessment

NASA Astrophysics Data System (ADS)

Asaad, Aras T.; Rashid, Rasber Dh.; Jassim, Sabah A.

2017-05-01

Image quality is a major factor influencing pattern recognition accuracy and help detect image tampering for forensics. We are concerned with investigating topological image texture analysis techniques to assess different type of degradation. We use Local Binary Pattern (LBP) as a texture feature descriptor. For any image construct simplicial complexes for selected groups of uniform LBP bins and calculate persistent homology invariants (e.g. number of connected components). We investigated image quality discriminating characteristics of these simplicial complexes by computing these models for a large dataset of face images that are affected by the presence of shadows as a result of variation in illumination conditions. Our tests demonstrate that for specific uniform LBP patterns, the number of connected component not only distinguish between different levels of shadow effects but also help detect the infected regions as well.

Local characterization of one-dimensional topologically ordered states

NASA Astrophysics Data System (ADS)

Cui, Jian; Amico, Luigi; Fan, Heng; Gu, Mile; Hamma, Alioscia; Vedral, Vlatko

2013-09-01

We consider one-dimensional Hamiltonian systems whose ground states display symmetry-protected topological order. We show that ground states within the topological phase cannot be connected with each other through local operations and classical communication between a bipartition of the system. Our claim is demonstrated by analyzing the entanglement spectrum and Rényi entropies of different physical systems that provide examples for symmetry-protected topological phases. Specifically, we consider the spin-1/2 cluster-Ising model and a class of spin-1 models undergoing quantum phase transitions to the Haldane phase. Our results provide a probe for symmetry-protected topological order. Since the picture holds even at the system's local scale, our analysis can serve as a local experimental test for topological order.

Analysis of stationary availability factor of two-level backbone computer networks with arbitrary topology

NASA Astrophysics Data System (ADS)

Rahman, P. A.

2018-05-01

This scientific paper deals with the two-level backbone computer networks with arbitrary topology. A specialized method, offered by the author for calculation of the stationary availability factor of the two-level backbone computer networks, based on the Markov reliability models for the set of the independent repairable elements with the given failure and repair rates and the methods of the discrete mathematics, is also discussed. A specialized algorithm, offered by the author for analysis of the network connectivity, taking into account different kinds of the network equipment failures, is also observed. Finally, this paper presents an example of calculation of the stationary availability factor for the backbone computer network with the given topology.

Propagation of optical vortices with fractional topological charge in free space

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles.

PubMed

Liu, Juan; Postupalenko, Viktoriia; Lörcher, Samuel; Wu, Dalin; Chami, Mohamed; Meier, Wolfgang; Palivan, Cornelia G

2016-11-09

Self-organization of nanocomponents was mainly focused on solid nanoparticles, quantum dots, or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nanocompartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine-tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes, and no aggregation. Unexpected, extended DNA bridges that result from migration of the DNA strands inside the thick polymer membrane (about 12 nm) represent a key stability and control factor, not yet exploited for other synthetic nano-object networks. The replacement of the empty polymersomes with artificial organelles, already reported for single polymersome architecture, will provide an excellent platform for the development of artificial systems mimicking natural organelles or cells and represents a fundamental step in the engineering of molecular factories.

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)

The Optimizer Topology Characteristics in Seismic Hazards

NASA Astrophysics Data System (ADS)

Sengor, T.

2015-12-01

The characteristic data of the natural phenomena are questioned in a topological space approach to illuminate whether there is an algorithm behind them bringing the situation of physics of phenomena to optimized states even if they are hazards. The optimized code designing the hazard on a topological structure mashes the metric of the phenomena. The deviations in the metric of different phenomena push and/or pull the fold of the other suitable phenomena. For example if the metric of a specific phenomenon A fits to the metric of another specific phenomenon B after variation processes generated with the deviation of the metric of previous phenomenon A. Defining manifold processes covering the metric characteristics of each of every phenomenon is possible for all the physical events; i.e., natural hazards. There are suitable folds in those manifold groups so that each subfold fits to the metric characteristics of one of the natural hazard category at least. Some variation algorithms on those metric structures prepare a gauge effect bringing the long time stability of Earth for largely scaled periods. The realization of that stability depends on some specific conditions. These specific conditions are called optimized codes. The analytical basics of processes in topological structures are developed in [1]. The codes are generated according to the structures in [2]. Some optimized codes are derived related to the seismicity of NAF beginning from the quakes of the year 1999. References1. Taner SENGOR, "Topological theory and analytical configuration for a universal community model," Procedia- Social and Behavioral Sciences, Vol. 81, pp. 188-194, 28 June 2013, 2. Taner SENGOR, "Seismic-Climatic-Hazardous Events Estimation Processes via the Coupling Structures in Conserving Energy Topologies of the Earth," The 2014 AGU Fall Meeting, Abstract no.: 31374, ABD.

Cross-talk between topological defects in different fields revealed by nematic microfluidics

PubMed Central

Giomi, Luca; Kos, Žiga; Ravnik, Miha

2017-01-01

Topological defects are singularities in material fields that play a vital role across a range of systems: from cosmic microwave background polarization to superconductors and biological materials. Although topological defects and their mutual interactions have been extensively studied, little is known about the interplay between defects in different fields—especially when they coevolve—within the same physical system. Here, using nematic microfluidics, we study the cross-talk of topological defects in two different material fields—the velocity field and the molecular orientational field. Specifically, we generate hydrodynamic stagnation points of different topological charges at the center of star-shaped microfluidic junctions, which then interact with emergent topological defects in the orientational field of the nematic director. We combine experiments and analytical and numerical calculations to show that a hydrodynamic singularity of a given topological charge can nucleate a nematic defect of equal topological charge and corroborate this by creating −1, −2, and −3 topological defects in four-, six-, and eight-arm junctions. Our work is an attempt toward understanding materials that are governed by distinctly multifield topology, where disparate topology-carrying fields are coupled and concertedly determine the material properties and response. PMID:28674012

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma

PubMed Central

Liu, Li; Dinu, Valentin

2018-01-01

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway’s topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher’s exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level. PMID:29666752

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma.

PubMed

Li, Chaoxing; Liu, Li; Dinu, Valentin

2018-01-01

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level.

Topology optimized and 3D printed polymer-bonded permanent magnets for a predefined external field

NASA Astrophysics Data System (ADS)

Huber, C.; Abert, C.; Bruckner, F.; Pfaff, C.; Kriwet, J.; Groenefeld, M.; Teliban, I.; Vogler, C.; Suess, D.

2017-08-01

Topology optimization offers great opportunities to design permanent magnetic systems that have specific external field characteristics. Additive manufacturing of polymer-bonded magnets with an end-user 3D printer can be used to manufacture permanent magnets with structures that had been difficult or impossible to manufacture previously. This work combines these two powerful methods to design and manufacture permanent magnetic systems with specific properties. The topology optimization framework is simple, fast, and accurate. It can also be used for the reverse engineering of permanent magnets in order to find the topology from field measurements. Furthermore, a magnetic system that generates a linear external field above the magnet is presented. With a volume constraint, the amount of magnetic material can be minimized without losing performance. Simulations and measurements of the printed systems show very good agreement.

Optical and Casimir effects in topological materials

NASA Astrophysics Data System (ADS)

Wilson, Justin H.

Two major electromagnetic phenomena, magneto-optical effects and the Casimir effect, have seen much theoretical and experimental use for many years. On the other hand, recently there has been an explosion of theoretical and experimental work on so-called topological materials, and a natural question to ask is how such electromagnetic phenomena change with these novel materials. Specifically, we will consider are topological insulators and Weyl semimetals. When Dirac electrons on the surface of a topological insulator are gapped or Weyl fermions in the bulk of a Weyl semimetal appear due to time-reversal symmetry breaking, there is a resulting quantum anomalous Hall effect (2D in one case and bulk 3D in the other, respectively). For topological insulators, we investigate the role of localized in-gap states which can leave their own fingerprints on the magneto-optics and can therefore be probed. We have shown that these states resonantly contribute to the Hall conductivity and are magneto-optically active. For Weyl semimetals we investigate the Casimir force and show that with thickness, chemical potential, and magnetic field, a repulsive and tunable Casimir force can be obtained. Additionally, various values of the parameters can give various combinations of traps and antitraps. We additionally probe the topological transition called a Lifshitz transition in the band structure of a material and show that in a Casimir experiment, one can observe a non-analytic "kink'' in the Casimir force across such a transition. The material we propose is a spin-orbit coupled semiconductor with large g-factor that can be magnetically tuned through such a transition. Additionally, we propose an experiment with a two-dimensional metal where weak localization is tuned with an applied field in order to definitively test the effect of diffusive electrons on the Casimir force---an issue that is surprisingly unresolved to this day. Lastly, we show how the time-continuous coherent state path integral breaks down for both the single-site Bose-Hubbard model and the spin path integral. Specifically, when the Hamiltonian is quadratic in a generator of the algebra used to construct coherent states, the path integral fails to produce correct results following from an operator approach. We note that the problems do not arise in the time-discretized version of the path integral, as expected.

Topology search of 3-DOF translational parallel manipulators with three identical limbs for leg mechanisms

NASA Astrophysics Data System (ADS)

Wang, Mingfeng; Ceccarelli, Marco

2015-07-01

Three-degree of freedom(3-DOF) translational parallel manipulators(TPMs) have been widely studied both in industry and academia in the past decades. However, most architectures of 3-DOF TPMs are created mainly on designers' intuition, empirical knowledge, or associative reasoning and the topology synthesis researches of 3-DOF TPMs are still limited. In order to find out the atlas of designs for 3-DOF TPMs, a topology search is presented for enumeration of 3-DOF TPMs whose limbs can be modeled as 5-DOF serial chains. The proposed topology search of 3-DOF TPMs is aimed to overcome the sensitivities of the design solution of a 3-DOF TPM for a LARM leg mechanism in a biped robot. The topology search, which is based on the concept of generation and specialization in graph theory, is reported as a step-by-step procedure with desired specifications, principle and rules of generalization, design requirements and constraints, and algorithm of number synthesis. In order to obtain new feasible designs for a chosen example and to limit the search domain under general considerations, one topological generalized kinematic chain is chosen to be specialized. An atlas of new feasible designs is obtained and analyzed for a specific solution as leg mechanisms. The proposed methodology provides a topology search for 3-DOF TPMs for leg mechanisms, but it can be also expanded for other applications and tasks.

Anomalous Z2 antiferromagnetic topological phase in pressurized SmB6

NASA Astrophysics Data System (ADS)

Chang, Kai-Wei; Chen, Peng-Jen

2018-05-01

Antiferromagnetic materials, whose time-reversal symmetry is broken, can be classified into the Z2 topology if they respect some specific symmetry. Since the theoretical proposal, however, no materials have been found to host such Z2 antiferromagnetic topological (Z2-AFT ) phase to date. Here we demonstrate that the topological Kondo insulator SmB6 can be a Z2-AFT system when pressurized to undergo an antiferromagnetic phase transition. In addition to proposing the possible candidate for a Z2-AFT material, in this work we also illustrate the anomalous topological surface states of the Z2-AFT phase which have not been discussed before. Originating from the interplay between the topological properties and the antiferromagnetic surface magnetization, the topological surface states of the Z2-AFT phase behave differently as compared with those of a topological insulator. Besides, the Z2-AFT insulators are also found promising in the generation of tunable spin currents, which is an important application in spintronics.

Charmless B_{(s)}→ VV decays in factorization-assisted topological-amplitude approach

NASA Astrophysics Data System (ADS)

Wang, Chao; Zhang, Qi-An; Li, Ying; Lü, Cai-Dian

2017-05-01

Within the factorization-assisted topological-amplitude approach, we studied the 33 charmless B_{(s)} → VV decays, where V stands for a light vector meson. According to the flavor flows, the amplitude of each process can be decomposed into eight different topologies. In contrast to the conventional flavor diagrammatic approach, we further factorize each topological amplitude into decay constant, form factors and unknown universal parameters. By χ ^2 fitting 46 experimental observables, we extracted 10 theoretical parameters with χ ^2 per degree of freedom around 2. Using the fitted parameters, we calculated the branching fractions, polarization fractions, CP asymmetries and relative phases between polarization amplitudes of each decay mode. The decay channels dominated by tree diagram have large branching fractions and large longitudinal polarization fraction. The branching fractions and longitudinal polarization fractions of color-suppressed decays become smaller. Current experimental data of large transverse polarization fractions in the penguin dominant decay channels can be explained by only one transverse amplitude of penguin annihilation diagram. Our predictions of the not yet measured channels can be tested in the ongoing LHCb experiment and the Belle-II experiment in the future.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Analytical description of optical vortices generated by discretized vortex-producing lenses

NASA Astrophysics Data System (ADS)

Rumi, Gonzalo; Actis, Daniel; Amaya, Dafne; Gómez, Jorge A.; Rueda, Edgar; Lencina, Alberto

2018-06-01

In this article, a general analytical treatment (any topological charge—any number of discretization levels) for the diffraction of a Gaussian beam through a discretized vortex-producing lens is presented. In the proposal, the field is expressed as a sum of Kummer beams with different amplitudes and topological charges, which are focalized at different planes on the propagation axis. Likewise, it is demonstrated that characteristics of diffracted light can be modified by tuning the parameters of the setup. Vortex lines are analyzed to understand the internal mechanism of measurable topological charges that appear in specific planes, apparently violating topological charge conservation. Conservation of the topological charge is verified and theoretical predictions are supported by experiments.

Graph Theory-Based Analysis of the Lymph Node Fibroblastic Reticular Cell Network.

PubMed

Novkovic, Mario; Onder, Lucas; Bocharov, Gennady; Ludewig, Burkhard

2017-01-01

Secondary lymphoid organs have developed segregated niches that are able to initiate and maintain effective immune responses. Such global organization requires tight control of diverse cellular components, specifically those that regulate lymphocyte trafficking. Fibroblastic reticular cells (FRCs) form a densely interconnected network in lymph nodes and provide key factors necessary for T cell migration and retention, and foster subsequent interactions between T cells and dendritic cells. Development of integrative systems biology approaches has made it possible to elucidate this multilevel complexity of the immune system. Here, we present a graph theory-based analysis of the FRC network in murine lymph nodes, where generation of the network topology is performed using high-resolution confocal microscopy and 3D reconstruction. This approach facilitates the analysis of physical cell-to-cell connectivity, and estimation of topological robustness and global behavior of the network when it is subjected to perturbation in silico.

Tilt Grain Boundary Topology Induced by Substrate Topography.

PubMed

Yu, Henry; Gupta, Nitant; Hu, Zhili; Wang, Kai; Srijanto, Bernadeta R; Xiao, Kai; Geohegan, David B; Yakobson, Boris I

2017-09-26

Synthesis of two-dimensional (2D) crystals is a topic of great current interest, since their chemical makeup, electronic, mechanical, catalytic, and optical properties are so diverse. A universal challenge, however, is the generally random formation of defects caused by various growth factors on flat surfaces. Here we show through theoretical analysis and experimental demonstration that nonplanar, curved-topography substrates permit the intentional and controllable creation of topological defects within 2D materials. We augment a common phase-field method by adding a geometric phase to track the crystal misorientation on a curved surface and to detect the formation of grain boundaries, especially when a growing monocrystal "catches its own tail" on a nontrivial topographical feature. It is specifically illustrated by simulated growth of a trigonal symmetry crystal on a conical-planar substrate, to match the experimental synthesis of WS 2 on silicon template, with satisfactory and in some cases remarkable agreement of theory predictions and experimental evidence.

Making connections: Insulators organize eukaryotic chromosomes into independent cis-regulatory networks

PubMed Central

Chetverina, Darya; Aoki, Tsutomu; Erokhin, Maksim; Georgiev, Pavel; Schedl, Paul

2015-01-01

Summary Insulators play a central role in subdividing the chromosome into a series of discrete topologically independent domains and in ensuring that enhancers and silencers contact their appropriate target genes. In this review we first discuss the general characteristics of insulator elements and their associated protein factors. A growing collection of insulator proteins have been identified including a family of proteins whose expression is developmental regulator. We next consider several unexpected discoveries that require us to completely rethink both how insulators function (and how they can best be assayed). These discoveries also require a reevaluation of how insulators might restrict or orchestrate (by preventing or promoting) interactions between regulatory elements and their target genes. We conclude by connecting these new insights into the mechanisms of insulator action to dynamic changes in the 3-dimensional topology of the chromatin fiber and the generation of specific patterns of gene activity during development and differentiation. PMID:24277632

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

PubMed

Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Michał; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz

2016-12-01

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures. © 2016 Szałaj et al.; Published by Cold Spring Harbor Laboratory Press.

Two-component quantum Hall effects in topological flat bands

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

Zeng, Tian-Sheng; Zhu, Wei; Sheng, D. N.

2017-03-27

Here in this paper, we study quantum Hall states for two-component particles (hardcore bosons and fermions) loading in topological lattice models. By tuning the interplay of interspecies and intraspecies interactions, we demonstrate that two-component fractional quantum Hall states emerge at certain fractional filling factors ν = 1/2 for fermions (ν = 2/3 for bosons) in the lowest Chern band, classified by features from ground states including the unique Chern number matrix (inverse of the K matrix), the fractional charge and spin pumpings, and two parallel propagating edge modes. Moreover, we also apply our strategy to two-component fermions at integer fillingmore » factor ν = 2 , where a possible topological Neel antiferromagnetic phase is under intense debate very recently. For the typical π -flux checkerboard lattice, by tuning the onsite Hubbard repulsion, we establish a first-order phase transition directly from a two-component fermionic ν = 2 quantum Hall state at weak interaction to a topologically trivial antiferromagnetic insulator at strong interaction, and therefore exclude the possibility of an intermediate topological phase for our system.« less

How cells explore shape space: a quantitative statistical perspective of cellular morphogenesis.

PubMed

Yin, Zheng; Sailem, Heba; Sero, Julia; Ardy, Rico; Wong, Stephen T C; Bakal, Chris

2014-12-01

Through statistical analysis of datasets describing single cell shape following systematic gene depletion, we have found that the morphological landscapes explored by cells are composed of a small number of attractor states. We propose that the topology of these landscapes is in large part determined by cell-intrinsic factors, such as biophysical constraints on cytoskeletal organization, and reflects different stable signaling and/or transcriptional states. Cell-extrinsic factors act to determine how cells explore these landscapes, and the topology of the landscapes themselves. Informational stimuli primarily drive transitions between stable states by engaging signaling networks, while mechanical stimuli tune, or even radically alter, the topology of these landscapes. As environments fluctuate, the topology of morphological landscapes explored by cells dynamically adapts to these fluctuations. Finally we hypothesize how complex cellular and tissue morphologies can be generated from a limited number of simple cell shapes. © 2014 WILEY Periodicals, Inc.

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

PubMed

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

2015-07-01

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

Quasi-topological Ricci polynomial gravities

NASA Astrophysics Data System (ADS)

Li, Yue-Zhou; Liu, Hai-Shan; Lü, H.

2018-02-01

Quasi-topological terms in gravity can be viewed as those that give no contribution to the equations of motion for a special subclass of metric ansätze. They therefore play no rôle in constructing these solutions, but can affect the general perturbations. We consider Einstein gravity extended with Ricci tensor polynomial invariants, which admits Einstein metrics with appropriate effective cosmological constants as its vacuum solutions. We construct three types of quasi-topological gravities. The first type is for the most general static metrics with spherical, toroidal or hyperbolic isometries. The second type is for the special static metrics where g tt g rr is constant. The third type is the linearized quasitopological gravities on the Einstein metrics. We construct and classify results that are either dependent on or independent of dimensions, up to the tenth order. We then consider a subset of these three types and obtain Lovelock-like quasi-topological gravities, that are independent of the dimensions. The linearized gravities on Einstein metrics on all dimensions are simply Einstein and hence ghost free. The theories become quasi-topological on static metrics in one specific dimension, but non-trivial in others. We also focus on the quasi-topological Ricci cubic invariant in four dimensions as a specific example to study its effect on holography, including shear viscosity, thermoelectric DC conductivities and butterfly velocity. In particular, we find that the holographic diffusivity bounds can be violated by the quasi-topological terms, which can induce an extra massive mode that yields a butterfly velocity unbound above.

The topological basis realization and the corresponding XXX spin chain

NASA Astrophysics Data System (ADS)

Sun, C. F.; Xue, K.; Wang, G. C.; Zhou, C. C.; Du, G. J.

2011-06-01

In this paper, it is shown that the XXX model can be constructed from the Temperley-Lieb algebra (TLA) generator. We find that the topological basis states are the two eigenstaes of a closed four-qubit Heisenberg XXX spin chain. Specifically, the spin single states and the energy single state of the system all fall on the topological basis states. It is worth mentioning that for the closed 2N-qubit (N=2, 3, 4, ...) Heisenberg XXX spin chain, all the topological basis states for 2N particles are the spin single states of the system. And the number of the topological basis states is equal to the number of the spin single states of the system, which is \\frac{(2N)!}{N!(N+1)!} .

Single Phase Passive Rectification Versus Active Rectification Applied to High Power Stirling Engines

NASA Technical Reports Server (NTRS)

Santiago, Walter; Birchenough, Arthur G.

2006-01-01

Stirling engine converters are being considered as potential candidates for high power energy conversion systems required by future NASA explorations missions. These types of engines typically contain two major moving parts, the displacer and the piston, in which a linear alternator is attached to the piston to produce a single phase sinusoidal waveform at a specific electric frequency. Since all Stirling engines perform at low electrical frequencies (less or equal to 100 Hz), space explorations missions that will employ these engines will be required to use DC power management and distribution (PMAD) system instead of an AC PMAD system to save on space and weight. Therefore, to supply such DC power an AC to DC converter is connected to the Stirling engine. There are two types of AC to DC converters that can be employed, a passive full bridge diode rectifier and an active switching full bridge rectifier. Due to the inherent line inductance of the Stirling Engine-Linear Alternator (SE-LA), their sinusoidal voltage and current will be phase shifted producing a power factor below 1. In order to keep power the factor close to unity, both AC to DC converters topologies will implement power factor correction. This paper discusses these power factor correction methods as well as their impact on overall mass for exploration applications. Simulation results on both AC to DC converters topologies with power factor correction as a function of output power and SE-LA line inductance impedance are presented and compared.

Tuning thermoelectricity in a Bi 2Se 3 topological insulator via varied film thickness

DOE PAGES

Guo, Minghua; Wang, Zhenyu; Xu, Yong; ...

2016-01-12

We report thermoelectric transport studies on Bi 2Se 3 topological insulator thin films with varied thickness grown by molecular beam epitaxy. We find that the Seebeck coefficient and thermoelectric power factor decrease systematically with the reduction of film thickness. These experimental observations can be explained quantitatively by theoretical calculations based on realistic electronic band structure of the Bi 2Se 3 thin films. Lastly, this work illustrates the crucial role played by the topological surface states on the thermoelectric transport of topological insulators, and sheds new light on further improvement of their thermoelectric performance.

Scaling of the flow-stiffness relationship in weakly correlated single fractures

NASA Astrophysics Data System (ADS)

Petrovitch, Christopher L.

The remote characterization of the hydraulic properties of fractures in rocks is important in many subsurface projects. Fractures create uncertainty in the hydraulic properties of the subsurface in that their topology controls the amount of flow that can occur in addition to that from the matrix. In turn, the fracture topology is also affected by stress which alters the topology as the stress changes directly. This alteration of fracture topology with stress is captured by fracture specific stiffness. The specific stiffness of a single fracture can be remotely probed from the attenuation and velocity of seismic waves. The hydromechanical coupling of single fractures, i.e. the relationship between flow and stiffness, holds the key to finding a method to remotely characterize a fractures hydraulic properties. This thesis is separated into two parts: (1) a description of the hydromechanical coupling of fractures based on numerical models used to generate synthetic fractures, compute the flow through a fracture, and deform fracture topologies to unravel the scaling function that is fundamental to the hydromechanical coupling of single fractures; (2) a Discontinuous Galerkin (DG) method was developed to accurately simulate the scattered seismic waves from realistic fracture topologies. The scaling regimes of fluid flow and specific stiffness in weakly correlated fractures are identified by using techniques from Percolation Theory and initially treating the two processes separately. The fixed points associated with fluid flow were found to display critical scaling while the fixed points for specific stiffness were trivial. The two processes could be indirectly related because the trivial scaling of the mechanical properties allowed the specific stiffness to be used as surrogate to the void area fraction. The dynamic transport exponent was extracted at threshold by deforming fracture geometries within the effective medium regime (near the ``cubic law'' regime) to the critical regime. From this, a scaling function was defined for the hydromechanical coupling. This scaling function provides the link between fluid flow and fracture specific stiffness so that seismic waves may be used to remotely probe the hydraulic properties of fractures. Then, the DG method is shown to be capable of measuring such fracture specific stiffnesses by numerically measuring the velocity of interface waves when propagated across laboratory measured fracture geometries of Austin Chalk.

Controlled Visual Sensing and Exploration

DTIC Science & Technology

2015-09-16

point cloud. This is clearly insufficient for most other tasks that require at least the topology of the scene to determine what surfaces or “objects...or whether it is empty space, as in the latter case it is traversable, in the former it is not. To this end, we have developed methods for topology ...Specific achievements include: • We have shown that surface topology and geometry can be computed without minimal surface bias, yielding water-tight

The phase transitions between Z n × Z n bosonic topological phases in 1 + 1D, and a constraint on the central charge for the critical points between bosonic symmetry protected topological phases

DOE PAGES

Tsui, Lokman; Huang, Yen-Ta; Jiang, Hong-Chen; ...

2017-03-27

The study of continuous phase transitions triggered by spontaneous symmetry breaking has brought revolutionary ideas to physics. Recently, through the discovery of symmetry protected topological phases, it is realized that continuous quantum phase transition can also occur between states with the same symmetry but different topology. Here in this paper we study a specific class of such phase transitions in 1+1 dimensions – the phase transition between bosonic topological phases protected by Z n × Z n. We find in all cases the critical point possesses two gap opening relevant operators: one leads to a Landau-forbidden symmetry breaking phase transitionmore » and the other to the topological phase transition. We also obtained a constraint on the central charge for general phase transitions between symmetry protected bosonic topological phases in 1+1D.« less

Topological superconductivity in monolayer transition metal dichalcogenides.

PubMed

Hsu, Yi-Ting; Vaezi, Abolhassan; Fischer, Mark H; Kim, Eun-Ah

2017-04-11

Theoretically, it has been known that breaking spin degeneracy and effectively realizing spinless fermions is a promising path to topological superconductors. Yet, topological superconductors are rare to date. Here we propose to realize spinless fermions by splitting the spin degeneracy in momentum space. Specifically, we identify monolayer hole-doped transition metal dichalcogenide (TMD)s as candidates for topological superconductors out of such momentum-space-split spinless fermions. Although electron-doped TMDs have recently been found superconducting, the observed superconductivity is unlikely topological because of the near spin degeneracy. Meanwhile, hole-doped TMDs with momentum-space-split spinless fermions remain unexplored. Employing a renormalization group analysis, we propose that the unusual spin-valley locking in hole-doped TMDs together with repulsive interactions selectively favours two topological superconducting states: interpocket paired state with Chern number 2 and intrapocket paired state with finite pair momentum. A confirmation of our predictions will open up possibilities for manipulating topological superconductors on the device-friendly platform of monolayer TMDs.

The phase transitions between Z n × Z n bosonic topological phases in 1 + 1D, and a constraint on the central charge for the critical points between bosonic symmetry protected topological phases

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

Tsui, Lokman; Huang, Yen-Ta; Jiang, Hong-Chen

The study of continuous phase transitions triggered by spontaneous symmetry breaking has brought revolutionary ideas to physics. Recently, through the discovery of symmetry protected topological phases, it is realized that continuous quantum phase transition can also occur between states with the same symmetry but different topology. Here in this paper we study a specific class of such phase transitions in 1+1 dimensions – the phase transition between bosonic topological phases protected by Z n × Z n. We find in all cases the critical point possesses two gap opening relevant operators: one leads to a Landau-forbidden symmetry breaking phase transitionmore » and the other to the topological phase transition. We also obtained a constraint on the central charge for general phase transitions between symmetry protected bosonic topological phases in 1+1D.« less

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency

PubMed Central

Chen, Yuhan; Wang, Shengjun

2017-01-01

The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56%) explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs). The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially distributed regions may play a significant role in shaping the cortical connectome, in addition to the basic cost-efficiency trade-off. These findings also shed light on inherent vulnerabilities of brain networks in diseases. PMID:28961235

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency.

PubMed

Chen, Yuhan; Wang, Shengjun; Hilgetag, Claus C; Zhou, Changsong

2017-09-01

The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56%) explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs). The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially distributed regions may play a significant role in shaping the cortical connectome, in addition to the basic cost-efficiency trade-off. These findings also shed light on inherent vulnerabilities of brain networks in diseases.

Rule-based topology system for spatial databases to validate complex geographic datasets

NASA Astrophysics Data System (ADS)

Martinez-Llario, J.; Coll, E.; Núñez-Andrés, M.; Femenia-Ribera, C.

2017-06-01

A rule-based topology software system providing a highly flexible and fast procedure to enforce integrity in spatial relationships among datasets is presented. This improved topology rule system is built over the spatial extension Jaspa. Both projects are open source, freely available software developed by the corresponding author of this paper. Currently, there is no spatial DBMS that implements a rule-based topology engine (considering that the topology rules are designed and performed in the spatial backend). If the topology rules are applied in the frontend (as in many GIS desktop programs), ArcGIS is the most advanced solution. The system presented in this paper has several major advantages over the ArcGIS approach: it can be extended with new topology rules, it has a much wider set of rules, and it can mix feature attributes with topology rules as filters. In addition, the topology rule system can work with various DBMSs, including PostgreSQL, H2 or Oracle, and the logic is performed in the spatial backend. The proposed topology system allows users to check the complex spatial relationships among features (from one or several spatial layers) that require some complex cartographic datasets, such as the data specifications proposed by INSPIRE in Europe and the Land Administration Domain Model (LADM) for Cadastral data.

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

A role for chromatin topology in imprinted domain regulation.

PubMed

MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

2016-02-01

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

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.

Topological quantization of energy transport in micromechanical and nanomechanical lattices

NASA Astrophysics Data System (ADS)

Chien, Chih-Chun; Velizhanin, Kirill A.; Dubi, Yonatan; Ilic, B. Robert; Zwolak, Michael

2018-03-01

Topological effects typically discussed in the context of quantum physics are emerging as one of the central paradigms of physics. Here, we demonstrate the role of topology in energy transport through dimerized micro- and nanomechanical lattices in the classical regime, i.e., essentially "masses and springs." We show that the thermal conductance factorizes into topological and nontopological components. The former takes on three discrete values and arises due to the appearance of edge modes that prevent good contact between the heat reservoirs and the bulk, giving a length-independent reduction of the conductance. In essence, energy input at the boundary mostly stays there, an effect robust against disorder and nonlinearity. These results bridge two seemingly disconnected disciplines of physics, namely topology and thermal transport, and suggest ways to engineer thermal contacts, opening a direction to explore the ramifications of topological properties on nanoscale technology.

Topological relationships between brain and social networks.

PubMed

Sakata, Shuzo; Yamamori, Tetsuo

2007-01-01

Brains are complex networks. Previously, we revealed that specific connected structures are either significantly abundant or rare in cortical networks. However, it remains unknown whether systems from other disciplines have similar architectures to brains. By applying network-theoretical methods, here we show topological similarities between brain and social networks. We found that the statistical relevance of specific tied structures differs between social "friendship" and "disliking" networks, suggesting relation-type-specific topology of social networks. Surprisingly, overrepresented connected structures in brain networks are more similar to those in the friendship networks than to those in other networks. We found that balanced and imbalanced reciprocal connections between nodes are significantly abundant and rare, respectively, whereas these results are unpredictable by simply counting mutual connections. We interpret these results as evidence of positive selection of balanced mutuality between nodes. These results also imply the existence of underlying common principles behind the organization of brain and social networks.

Form and function of topologically associating genomic domains in budding yeast.

PubMed

Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M

2017-04-11

The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.

The Hierarchy of Brain Networks Is Related to Insulin Growth Factor-1 in a Large, Middle-Aged, Healthy Cohort: An Exploratory Magnetoencephalography Study.

PubMed

Sorrentino, Pierpaolo; Nieboer, Dagmar; Twisk, Jos W R; Stam, Cornelis J; Douw, Linda; Hillebrand, Arjan

2017-06-01

Recently, a large study demonstrated that lower serum levels of insulin growth factor-1 (IGF-1) relate to brain atrophy and to a greater risk for developing Alzheimer's disease in a healthy elderly population. We set out to test if functional brain networks relate to IGF-1 levels in the middle aged. Hence, we studied the association between IGF-1 and magnetoencephalography-based functional network characteristics in a middle-aged population. The functional connections between brain areas were estimated for six frequency bands (delta, theta, alpha1, alpha2, beta, gamma) using the phase lag index. Subsequently, the topology of the frequency-specific functional networks was characterized using the minimum spanning tree. Our results showed that lower levels of serum IGF-1 relate to a globally less integrated functional network in the beta and theta band. The associations remained significant when correcting for gender and systemic effects of IGF-1 that might indirectly affect the brain. The value of this exploratory study is the demonstration that lower levels of IGF-1 are associated with brain network topology in the middle aged.

A random spatial network model based on elementary postulates

USGS Publications Warehouse

Karlinger, Michael R.; Troutman, Brent M.

1989-01-01

A model for generating random spatial networks that is based on elementary postulates comparable to those of the random topology model is proposed. In contrast to the random topology model, this model ascribes a unique spatial specification to generated drainage networks, a distinguishing property of some network growth models. The simplicity of the postulates creates an opportunity for potential analytic investigations of the probabilistic structure of the drainage networks, while the spatial specification enables analyses of spatially dependent network properties. In the random topology model all drainage networks, conditioned on magnitude (number of first-order streams), are equally likely, whereas in this model all spanning trees of a grid, conditioned on area and drainage density, are equally likely. As a result, link lengths in the generated networks are not independent, as usually assumed in the random topology model. For a preliminary model evaluation, scale-dependent network characteristics, such as geometric diameter and link length properties, and topologic characteristics, such as bifurcation ratio, are computed for sets of drainage networks generated on square and rectangular grids. Statistics of the bifurcation and length ratios fall within the range of values reported for natural drainage networks, but geometric diameters tend to be relatively longer than those for natural networks.

Topological properties of microwave magnetoelectric fields.

PubMed

Berezin, M; Kamenetskii, E O; Shavit, R

2014-02-01

Collective excitations of electron spins in a ferromagnetic sample dominated by the magnetic dipole-dipole interaction strongly influence the field structure of microwave radiation. A small quasi-two-dimensional ferrite disk with magnetic-dipolar-mode (MDM) oscillation spectra can behave as a source of specific fields in vacuum, termed magnetoelectric (ME) fields. A coupling between the time-varying electric and magnetic fields in the ME-field structures is different from such a coupling in regular electromagnetic fields. The ME fields are characterized by strong energy confinement at a subwavelength region of microwave radiation, topologically distinctive power-flow vortices, and helicity parameters [E. O. Kamenetskii, R. Joffe, and R. Shavit, Phys. Rev. E 87, 023201 (2013)]. We study topological properties of microwave ME fields by loading a MDM ferrite particle with different dielectric samples. We establish a close connection between the permittivity parameters of dielectric environment and the topology of ME fields. We show that the topology of ME fields is strongly correlated with the Fano-resonance spectra observed at terminals of a microwave structure. We reveal specific thresholds in the Fano-resonance spectra appearing at certain permittivity parameters of dielectric samples. We show that ME fields originated from MDM ferrite disks can be distinguished by topological portraits of the helicity parameters and can have a torsion degree of freedom. Importantly, the ME-field phenomena can be viewed as implementations of space-time coordinate transformations on waves.

Bulk superconducting phase with a full energy gap in the doped topological insulator Cu(x)Bi₂Se₃.

PubMed

Kriener, M; Segawa, Kouji; Ren, Zhi; Sasaki, Satoshi; Ando, Yoichi

2011-03-25

The superconductivity recently found in the doped topological insulator Cu(x)Bi₂Se₃ offers a great opportunity to search for a topological superconductor. We have successfully prepared a single-crystal sample with a large shielding fraction and measured the specific-heat anomaly associated with the superconductivity. The temperature dependence of the specific heat suggests a fully gapped, strong-coupling superconducting state, but the BCS theory is not in full agreement with the data, which hints at a possible unconventional pairing in Cu(x)Bi₂Se₃. Also, the evaluated effective mass of 2.6m(e) (m(e) is the free electron mass) points to a large mass enhancement in this material.

Skyrme insulators: insulators at the brink of superconductivity

DOE PAGES

Ertem, Onur; Chang, Po -Yao; Coleman, Piers; ...

2017-08-04

Current theories of superfluidity are based on the idea of a coherent quantum state with topologically protected, quantized circulation. When this topological protection is absent, as in the case of 3He-A, the coherent quantum state no longer supports persistent superflow. In this paper, we argue that the loss of topological protection in a superconductor gives rise to an insulating ground state. Specifically, we introduce the concept of a Skyrme insulator to describe the coherent dielectric state that results from the topological failure of superflow carried by a complex vector order parameter. Here, we apply this idea to the case ofmore » SmB6, arguing that the observation of a diamagnetic Fermi surface within an insulating bulk can be understood as a realization of this state. Our theory enables us to understand the linear specific heat of SmB6 in terms of a neutral Majorana Fermi sea and leads us to predict that in low fields of order a Gauss, SmB6 will develop a Meissner effect.« less

Skyrme Insulators: Insulators at the Brink of Superconductivity

NASA Astrophysics Data System (ADS)

Erten, Onur; Chang, Po-Yao; Coleman, Piers; Tsvelik, Alexei M.

2017-08-01

Current theories of superfluidity are based on the idea of a coherent quantum state with topologically protected quantized circulation. When this topological protection is absent, as in the case of 3He -A , the coherent quantum state no longer supports persistent superflow. Here, we argue that the loss of topological protection in a superconductor gives rise to an insulating ground state. We specifically introduce the concept of a Skyrme insulator to describe the coherent dielectric state that results from the topological failure of superflow carried by a complex-vector order parameter. We apply this idea to the case of SmB6 , arguing that the observation of a diamagnetic Fermi surface within an insulating bulk can be understood as a realization of this state. Our theory enables us to understand the linear specific heat of SmB6 in terms of a neutral Majorana Fermi sea and leads us to predict that in low fields of order a Gauss, SmB6 will develop a Meissner effect.

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

PubMed

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

2017-01-01

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

Topological structure dynamics revealing collective evolution in active nematics

PubMed Central

Shi, Xia-qing; Ma, Yu-qiang

2013-01-01

Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

PubMed

Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

2017-01-15

During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks

PubMed Central

Pechenick, Dov A.; Payne, Joshua L.; Moore, Jason H.

2014-01-01

Many developmental, physiological, and behavioral processes depend on the precise expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of nearby genes that such binding causes. These nearby genes may themselves encode TFs, giving rise to a transcription factor network (TFN), wherein nodes represent TFs and directed edges denote regulatory interactions between TFs. Computational studies have linked several topological properties of TFNs — such as their degree distribution — with the robustness of a TFN's gene expression phenotype to genetic and environmental perturbation. Another important topological property is assortativity, which measures the tendency of nodes with similar numbers of edges to connect. In directed networks, assortativity comprises four distinct components that collectively form an assortativity signature. We know very little about how a TFN's assortativity signature affects the robustness of its gene expression phenotype to perturbation. While recent theoretical results suggest that increasing one specific component of a TFN's assortativity signature leads to increased phenotypic robustness, the biological context of this finding is currently limited because the assortativity signatures of real-world TFNs have not been characterized. It is therefore unclear whether these earlier theoretical findings are biologically relevant. Moreover, it is not known how the other three components of the assortativity signature contribute to the phenotypic robustness of TFNs. Here, we use publicly available DNaseI-seq data to measure the assortativity signatures of genome-wide TFNs in 41 distinct human cell and tissue types. We find that all TFNs share a common assortativity signature and that this signature confers phenotypic robustness to model TFNs. Lastly, we determine the extent to which each of the four components of the assortativity signature contributes to this robustness. PMID:25121490

Does the choice of nucleotide substitution models matter topologically?

PubMed

Hoff, Michael; Orf, Stefan; Riehm, Benedikt; Darriba, Diego; Stamatakis, Alexandros

2016-03-24

In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possible nucleotide substitution models in the Maximum Likelihood (ML) setting under the common Akaike, corrected Akaike, and Bayesian information criteria. We address the question if model selection matters topologically, that is, if conducting ML inferences under the optimal, instead of a standard General Time Reversible model, yields different tree topologies. We also assess, to which degree models selected and trees inferred under the three standard criteria (AIC, AICc, BIC) differ. Finally, we assess if the definition of the sample size (#sites versus #sites × #taxa) yields different models and, as a consequence, different tree topologies. We find that, all three factors (by order of impact: nucleotide model selection, information criterion used, sample size definition) can yield topologically substantially different final tree topologies (topological difference exceeding 10 %) for approximately 5 % of the tree inferences conducted on the 39 empirical datasets used in our study. We find that, using the best-fit nucleotide substitution model may change the final ML tree topology compared to an inference under a default GTR model. The effect is less pronounced when comparing distinct information criteria. Nonetheless, in some cases we did obtain substantial topological differences.

Topology-function conservation in protein-protein interaction networks.

PubMed

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

2015-05-15

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

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

PubMed Central

2017-01-01

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

Beyond Group: Multiple Person Tracking via Minimal Topology-Energy-Variation.

PubMed

Gao, Shan; Ye, Qixiang; Xing, Junliang; Kuijper, Arjan; Han, Zhenjun; Jiao, Jianbin; Ji, Xiangyang

2017-12-01

Tracking multiple persons is a challenging task when persons move in groups and occlude each other. Existing group-based methods have extensively investigated how to make group division more accurately in a tracking-by-detection framework; however, few of them quantify the group dynamics from the perspective of targets' spatial topology or consider the group in a dynamic view. Inspired by the sociological properties of pedestrians, we propose a novel socio-topology model with a topology-energy function to factor the group dynamics of moving persons and groups. In this model, minimizing the topology-energy-variance in a two-level energy form is expected to produce smooth topology transitions, stable group tracking, and accurate target association. To search for the strong minimum in energy variation, we design the discrete group-tracklet jump moves embedded in the gradient descent method, which ensures that the moves reduce the energy variation of group and trajectory alternately in the varying topology dimension. Experimental results on both RGB and RGB-D data sets show the superiority of our proposed model for multiple person tracking in crowd scenes.

A quantitative approach to the topology of large-scale structure. [for galactic clustering computation

NASA Technical Reports Server (NTRS)

Gott, J. Richard, III; Weinberg, David H.; Melott, Adrian L.

1987-01-01

A quantitative measure of the topology of large-scale structure: the genus of density contours in a smoothed density distribution, is described and applied. For random phase (Gaussian) density fields, the mean genus per unit volume exhibits a universal dependence on threshold density, with a normalizing factor that can be calculated from the power spectrum. If large-scale structure formed from the gravitational instability of small-amplitude density fluctuations, the topology observed today on suitable scales should follow the topology in the initial conditions. The technique is illustrated by applying it to simulations of galaxy clustering in a flat universe dominated by cold dark matter. The technique is also applied to a volume-limited sample of the CfA redshift survey and to a model in which galaxies reside on the surfaces of polyhedral 'bubbles'. The topology of the evolved mass distribution and 'biased' galaxy distribution in the cold dark matter models closely matches the topology of the density fluctuations in the initial conditions. The topology of the observational sample is consistent with the random phase, cold dark matter model.

Analysis of Membrane Protein Topology in the Plant Secretory Pathway.

PubMed

Guo, Jinya; Miao, Yansong; Cai, Yi

2017-01-01

Topology of membrane proteins provides important information for the understanding of protein function and intermolecular associations. Integrate membrane proteins are generally transported from endoplasmic reticulum (ER) to Golgi and downstream compartments in the plant secretory pathway. Here, we describe a simple method to study membrane protein topology along the plant secretory pathway by transiently coexpressing a fluorescent protein (XFP)-tagged membrane protein and an ER export inhibitor protein, ARF1 (T31N), in tobacco BY-2 protoplast. By fractionation, microsome isolation, and trypsin digestion, membrane protein topology could be easily detected by either direct confocal microscopy imaging or western-blot analysis using specific XFP antibodies. A similar strategy in determining membrane protein topology could be widely adopted and applied to protein analysis in a broad range of eukaryotic systems, including yeast cells and mammalian cells.

Magnetic structures of REPdBi half-Heusler bismuthides (RE = Gd, Tb, Dy, Ho, Er)

NASA Astrophysics Data System (ADS)

Pavlosiuk, Orest; Fabreges, Xavier; Gukasov, Arsen; Meven, Martin; Kaczorowski, Dariusz; Wiśniewski, Piotr

2018-05-01

We present results of neutron diffraction on single crystals of several equiatomic ternary compounds of rare-earth elements with palladium and bismuth, crystallizing with cubic MgAgAs-type structure (half-Heusler phases). Band structure calculations showed that many members of that family possess electronic band inversion, which may lead to occurrence of topological insulator or topological semimetal. But even for the compounds without intrinsic band inversion another way of topologically non-trivial state realization, through a specific antiferromagnetic order, has been theoretically proposed. Our results show that the antiferromagnetic structures of all studied bismuthides are characterized by the propagation vector, allowing for antiferromagnetic topological insulator state. Therefore, the antiferromagnetic representatives of half-Heusler family are excellent candidates for extended investigations of coexistence of superconductivity, magnetic order and non-trivial topology of electronic states.

The Volatility of Data Space: Topology Oriented Sensitivity Analysis

PubMed Central

Du, Jing; Ligmann-Zielinska, Arika

2015-01-01

Despite the difference among specific methods, existing Sensitivity Analysis (SA) technologies are all value-based, that is, the uncertainties in the model input and output are quantified as changes of values. This paradigm provides only limited insight into the nature of models and the modeled systems. In addition to the value of data, a potentially richer information about the model lies in the topological difference between pre-model data space and post-model data space. This paper introduces an innovative SA method called Topology Oriented Sensitivity Analysis, which defines sensitivity as the volatility of data space. It extends SA into a deeper level that lies in the topology of data. PMID:26368929

Optical transitions in two-dimensional topological insulators with point defects

NASA Astrophysics Data System (ADS)

Sablikov, Vladimir A.; Sukhanov, Aleksei A.

2016-12-01

Nontrivial properties of electronic states in topological insulators are inherent not only to the surface and boundary states, but to bound states localized at structure defects as well. We clarify how the unusual properties of the defect-induced bound states are manifested in optical absorption spectra in two-dimensional topological insulators. The calculations are carried out for defects with short-range potential. We find that the defects give rise to the appearance of specific features in the absorption spectrum, which are an inherent property of topological insulators. They have the form of two or three absorption peaks that are due to intracenter transitions between electron-like and hole-like bound states.

Higher-order topological insulators and superconductors protected by inversion symmetry

NASA Astrophysics Data System (ADS)

Khalaf, Eslam

2018-05-01

We study surface states of topological crystalline insulators and superconductors protected by inversion symmetry. These fall into the category of "higher-order" topological insulators and superconductors which possess surface states that propagate along one-dimensional curves (hinges) or are localized at some points (corners) on the surface. We provide a complete classification of inversion-protected higher-order topological insulators and superconductors in any spatial dimension for the 10 symmetry classes by means of a layer construction. We discuss possible physical realizations of such states starting with a time-reversal-invariant topological insulator (class AII) in three dimensions or a time-reversal-invariant topological superconductor (class DIII) in two or three dimensions. The former exhibits one-dimensional chiral or helical modes propagating along opposite edges, whereas the latter hosts Majorana zero modes localized to two opposite corners. Being protected by inversion, such states are not pinned to a specific pair of edges or corners, thus offering the possibility of controlling their location by applying inversion-symmetric perturbations such as magnetic field.

Evidence for topologically protected surface states and a superconducting phase in [Tl4](Tl(1-x)Sn(x))Te3 using photoemission, specific heat, and magnetization measurements, and density functional theory.

PubMed

Arpino, K E; Wallace, D C; Nie, Y F; Birol, T; King, P D C; Chatterjee, S; Uchida, M; Koohpayeh, S M; Wen, J-J; Page, K; Fennie, C J; Shen, K M; McQueen, T M

2014-01-10

We report the discovery of surface states in the perovskite superconductor [Tl4]TlTe3 (Tl5Te3) and its nonsuperconducting tin-doped derivative [Tl4](Tl0.4Sn0.6)Te3 as observed by angle-resolved photoemission spectroscopy. Density functional theory calculations predict that the surface states are protected by a Z2 topology of the bulk band structure. Specific heat and magnetization measurements show that Tl5Te3 has a superconducting volume fraction in excess of 95%. Thus Tl5Te3 is an ideal material in which to study the interplay of bulk band topology and superconductivity.

Development of a model of machine hand eye coordination and program specifications for a topological machine vision system

NASA Technical Reports Server (NTRS)

1972-01-01

A unified approach to computer vision and manipulation is developed which is called choreographic vision. In the model, objects to be viewed by a projected robot in the Viking missions to Mars are seen as objects to be manipulated within choreographic contexts controlled by a multimoded remote, supervisory control system on Earth. A new theory of context relations is introduced as a basis for choreographic programming languages. A topological vision model is developed for recognizing objects by shape and contour. This model is integrated with a projected vision system consisting of a multiaperture image dissector TV camera and a ranging laser system. System program specifications integrate eye-hand coordination and topological vision functions and an aerospace multiprocessor implementation is described.

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

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

Interfacial Dirac cones from alternating topological invariant superlattice structures of Bi2Se3.

PubMed

Song, Jung-Hwan; Jin, Hosub; Freeman, Arthur J

2010-08-27

When the three-dimensional topological insulators Bi2Se3 and Bi2Te3 have an interface with vacuum, i.e., a surface, they show remarkable features such as topologically protected and spin-momentum locked surface states. However, for practical applications, one often requires multiple interfaces or channels rather than a single surface. Here, for the first time, we show that an interfacial and ideal Dirac cone is realized by alternating band and topological insulators. The multichannel Dirac fermions from the superlattice structures open a new way for applications such as thermoelectric and spintronics devices. Indeed, utilizing the interfacial Dirac fermions, we also demonstrate the possible power factor improvement for thermoelectric applications.

An improved fault-tolerant control scheme for PWM inverter-fed induction motor-based EVs.

PubMed

Tabbache, Bekheïra; Benbouzid, Mohamed; Kheloui, Abdelaziz; Bourgeot, Jean-Matthieu; Mamoune, Abdeslam

2013-11-01

This paper proposes an improved fault-tolerant control scheme for PWM inverter-fed induction motor-based electric vehicles. The proposed strategy deals with power switch (IGBTs) failures mitigation within a reconfigurable induction motor control. To increase the vehicle powertrain reliability regarding IGBT open-circuit failures, 4-wire and 4-leg PWM inverter topologies are investigated and their performances discussed in a vehicle context. The proposed fault-tolerant topologies require only minimum hardware modifications to the conventional off-the-shelf six-switch three-phase drive, mitigating the IGBTs failures by specific inverter control. Indeed, the two topologies exploit the induction motor neutral accessibility for fault-tolerant purposes. The 4-wire topology uses then classical hysteresis controllers to account for the IGBT failures. The 4-leg topology, meanwhile, uses a specific 3D space vector PWM to handle vehicle requirements in terms of size (DC bus capacitors) and cost (IGBTs number). Experiments on an induction motor drive and simulations on an electric vehicle are carried-out using a European urban driving cycle to show that the proposed fault-tolerant control approach is effective and provides a simple configuration with high performance in terms of speed and torque responses. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Multifractal analysis and topological properties of a new family of weighted Koch networks

NASA Astrophysics Data System (ADS)

Huang, Da-Wen; Yu, Zu-Guo; Anh, Vo

2017-03-01

Weighted complex networks, especially scale-free networks, which characterize real-life systems better than non-weighted networks, have attracted considerable interest in recent years. Studies on the multifractality of weighted complex networks are still to be undertaken. In this paper, inspired by the concepts of Koch networks and Koch island, we propose a new family of weighted Koch networks, and investigate their multifractal behavior and topological properties. We find some key topological properties of the new networks: their vertex cumulative strength has a power-law distribution; there is a power-law relationship between their topological degree and weight strength; the networks have a high weighted clustering coefficient of 0.41004 (which is independent of the scaling factor c) in the limit of large generation t; the second smallest eigenvalue μ2 and the maximum eigenvalue μn are approximated by quartic polynomials of the scaling factor c for the general Laplacian operator, while μ2 is approximately a quartic polynomial of c and μn= 1.5 for the normalized Laplacian operator. Then, we find that weighted koch networks are both fractal and multifractal, their fractal dimension is influenced by the scaling factor c. We also apply these analyses to six real-world networks, and find that the multifractality in three of them are strong.

Constraint Embedding Technique for Multibody System Dynamics

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Cheng, Michael K.

2011-01-01

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

Entanglement convertibility by sweeping through the quantum phases of the alternating bonds XXZ chain

PubMed Central

Tzeng, Yu-Chin; Dai, Li; Chung, Ming-Chiang; Amico, Luigi; Kwek, Leong-Chuan

2016-01-01

We study the entanglement structure and the topological edge states of the ground state of the spin-1/2 XXZ model with bond alternation. We employ parity-density matrix renormalization group with periodic boundary conditions. The finite-size scaling of Rényi entropies S2 and S∞ are used to construct the phase diagram of the system. The phase diagram displays three possible phases: Haldane type (an example of symmetry protected topological ordered phases), Classical Dimer and Néel phases, the latter bounded by two continuous quantum phase transitions. The entanglement and non-locality in the ground state are studied and quantified by the entanglement convertibility. We found that, at small spatial scales, the ground state is not convertible within the topological Haldane dimer phase. The phenomenology we observe can be described in terms of correlations between edge states. We found that the entanglement spectrum also exhibits a distinctive response in the topological phase: the effective rank of the reduced density matrix displays a specifically large “susceptibility” in the topological phase. These findings support the idea that although the topological order in the ground state cannot be detected by local inspection, the ground state response at local scale can tell the topological phases apart from the non-topological phases. PMID:27216970

Entanglement convertibility by sweeping through the quantum phases of the alternating bonds XXZ chain.

PubMed

Tzeng, Yu-Chin; Dai, Li; Chung, Ming-Chiang; Amico, Luigi; Kwek, Leong-Chuan

2016-05-24

We study the entanglement structure and the topological edge states of the ground state of the spin-1/2 XXZ model with bond alternation. We employ parity-density matrix renormalization group with periodic boundary conditions. The finite-size scaling of Rényi entropies S2 and S∞ are used to construct the phase diagram of the system. The phase diagram displays three possible phases: Haldane type (an example of symmetry protected topological ordered phases), Classical Dimer and Néel phases, the latter bounded by two continuous quantum phase transitions. The entanglement and non-locality in the ground state are studied and quantified by the entanglement convertibility. We found that, at small spatial scales, the ground state is not convertible within the topological Haldane dimer phase. The phenomenology we observe can be described in terms of correlations between edge states. We found that the entanglement spectrum also exhibits a distinctive response in the topological phase: the effective rank of the reduced density matrix displays a specifically large "susceptibility" in the topological phase. These findings support the idea that although the topological order in the ground state cannot be detected by local inspection, the ground state response at local scale can tell the topological phases apart from the non-topological phases.

Topological semimetal in honeycomb lattice LnSI

NASA Astrophysics Data System (ADS)

Nie, Simin; Xu, Gang; Prinz, Fritz B.; Zhang, Shou-cheng

2017-10-01

Recognized as elementary particles in the standard model, Weyl fermions in condensed matter have received growing attention. However, most of the previously reported Weyl semimetals exhibit rather complicated electronic structures that, in turn, may have raised questions regarding the underlying physics. Here, we report promising topological phases that can be realized in specific honeycomb lattices, including ideal Weyl semimetal structures, 3D strong topological insulators, and nodal-line semimetal configurations. In particular, we highlight a semimetal featuring both Weyl nodes and nodal lines. Guided by this model, we showed that GdSI, the long-perceived ideal Weyl semimetal, has two pairs of Weyl nodes residing at the Fermi level and that LuSI (YSI) is a 3D strong topological insulator with the right-handed helical surface states. Our work provides a mechanism to study topological semimetals and proposes a platform for exploring the physics of Weyl semimetals as well as related device designs.

Topology optimization for nonlinear dynamic problems: Considerations for automotive crashworthiness

NASA Astrophysics Data System (ADS)

Kaushik, Anshul; Ramani, Anand

2014-04-01

Crashworthiness of automotive structures is most often engineered after an optimal topology has been arrived at using other design considerations. This study is an attempt to incorporate crashworthiness requirements upfront in the topology synthesis process using a mathematically consistent framework. It proposes the use of equivalent linear systems from the nonlinear dynamic simulation in conjunction with a discrete-material topology optimizer. Velocity and acceleration constraints are consistently incorporated in the optimization set-up. Issues specific to crash problems due to the explicit solution methodology employed, nature of the boundary conditions imposed on the structure, etc. are discussed and possible resolutions are proposed. A demonstration of the methodology on two-dimensional problems that address some of the structural requirements and the types of loading typical of frontal and side impact is provided in order to show that this methodology has the potential for topology synthesis incorporating crashworthiness requirements.

Topological semimetal in honeycomb lattice LnSI.

PubMed

Nie, Simin; Xu, Gang; Prinz, Fritz B; Zhang, Shou-Cheng

2017-10-03

Recognized as elementary particles in the standard model, Weyl fermions in condensed matter have received growing attention. However, most of the previously reported Weyl semimetals exhibit rather complicated electronic structures that, in turn, may have raised questions regarding the underlying physics. Here, we report promising topological phases that can be realized in specific honeycomb lattices, including ideal Weyl semimetal structures, 3D strong topological insulators, and nodal-line semimetal configurations. In particular, we highlight a semimetal featuring both Weyl nodes and nodal lines. Guided by this model, we showed that GdSI, the long-perceived ideal Weyl semimetal, has two pairs of Weyl nodes residing at the Fermi level and that LuSI (YSI) is a 3D strong topological insulator with the right-handed helical surface states. Our work provides a mechanism to study topological semimetals and proposes a platform for exploring the physics of Weyl semimetals as well as related device designs.

Topological semimetal in honeycomb lattice LnSI

PubMed Central

Nie, Simin; Xu, Gang; Prinz, Fritz B.; Zhang, Shou-cheng

2017-01-01

Recognized as elementary particles in the standard model, Weyl fermions in condensed matter have received growing attention. However, most of the previously reported Weyl semimetals exhibit rather complicated electronic structures that, in turn, may have raised questions regarding the underlying physics. Here, we report promising topological phases that can be realized in specific honeycomb lattices, including ideal Weyl semimetal structures, 3D strong topological insulators, and nodal-line semimetal configurations. In particular, we highlight a semimetal featuring both Weyl nodes and nodal lines. Guided by this model, we showed that GdSI, the long-perceived ideal Weyl semimetal, has two pairs of Weyl nodes residing at the Fermi level and that LuSI (YSI) is a 3D strong topological insulator with the right-handed helical surface states. Our work provides a mechanism to study topological semimetals and proposes a platform for exploring the physics of Weyl semimetals as well as related device designs. PMID:28928149

Topology Change and the Unity of Space

NASA Astrophysics Data System (ADS)

Callender, Craig; Weingard, Robert

Must space be a unity? This question, which exercised Aristotle, Descartes and Kant, is a specific instance of a more general one; namely, can the topology of physical space change with time? In this paper we show how the discussion of the unity of space has been altered but survives in contemporary research in theoretical physics. With a pedagogical review of the role played by the Euler characteristic in the mathematics of relativistic spacetimes, we explain how classical general relativity (modulo considerations about energy conditions) allows virtually unrestrained spatial topology change in four dimensions. We also survey the situation in many other dimensions of interest. However, topology change comes with a cost: a famous theorem by Robert Geroch shows that, for many interesting types of such change, transitions of spatial topology imply the existence of closed timelike curves or temporal non-orientability. Ways of living with this theorem and of evading it are discussed.

Broadband Control of Topological Nodes in Electromagnetic Fields

NASA Astrophysics Data System (ADS)

Song, Alex Y.; Catrysse, Peter B.; Fan, Shanhui

2018-05-01

We study topological nodes (phase singularities) in electromagnetic wave interactions with structures. We show that, when the nodes exist, it is possible to bind certain nodes to a specific plane in the structure by a combination of mirror and time-reversal symmetry. Such binding does not rely on any resonances in the structure. As a result, the nodes persist on the plane over a wide wavelength range. As an implication of such broadband binding, we demonstrate that the topological nodes can be used for hiding of metallic objects over a broad wavelength range.

Topology and Singularities in Cosmological Spacetimes Obeying the Null Energy Condition

NASA Astrophysics Data System (ADS)

Galloway, Gregory J.; Ling, Eric

2018-06-01

We consider globally hyperbolic spacetimes with compact Cauchy surfaces in a setting compatible with the presence of a positive cosmological constant. More specifically, for 3 + 1 dimensional spacetimes which satisfy the null energy condition and contain a future expanding compact Cauchy surface, we establish a precise connection between the topology of the Cauchy surfaces and the occurrence of past singularities. In addition to the Penrose singularity theorem, the proof makes use of some recent advances in the topology of 3-manifolds and of certain fundamental existence results for minimal surfaces.

Functional integrative levels in the human interactome recapitulate organ organization.

PubMed

Souiai, Ouissem; Becker, Emmanuelle; Prieto, Carlos; Benkahla, Alia; De las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This 'Largest Common Interactome Network' represents a 'functional interactome core'. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization.

Zeeman effect of the topological surface states revealed by quantum oscillations up to 91 Tesla

DOE PAGES

Zhang, Zuocheng; Wei, Wei; Yang, Fangyuan; ...

2015-12-01

In this paper, we report quantum oscillation studies on the Bi 2Te 3-xS x topological insulator single crystals in pulsed magnetic fields up to 91 T. For the x = 0.4 sample with the lowest bulk carrier density, the surface and bulk quantum oscillations can be disentangled by combined Shubnikov–de Haas and de Hass–van Alphen oscillations, as well as quantum oscillations in nanometer-thick peeled crystals. At high magnetic fields beyond the bulk quantum limit, our results suggest that the zeroth Landau level of topological surface states is shifted due to the Zeeman effect. The g factor of the topological surfacemore » states is estimated to be between 1.8 and 4.5. Lastly, these observations shed new light on the quantum transport phenomena of topological insulators in ultrahigh magnetic fields.« less

Miscibility phase diagram of ring-polymer blends: A topological effect.

PubMed

Sakaue, Takahiro; Nakajima, Chihiro H

2016-04-01

The miscibility of polymer blends, a classical problem in polymer science, may be altered, if one or both of the component do not have chain ends. Based on the idea of topological volume, we propose a mean-field theory to clarify how the topological constraints in ring polymers affect the phase behavior of the blends. While the large enhancement of the miscibility is expected for ring-linear polymer blends, the opposite trend toward demixing, albeit comparatively weak, is predicted for ring-ring polymer blends. Scaling formulas for the shift of critical point for both cases are derived. We discuss the valid range of the present theory, and the crossover to the linear polymer blends behaviors, which is expected for short chains. These analyses put forward a view that the topological constraints could be represented as an effective excluded-volume effects, in which the topological length plays a role of the screening factor.

On the generality of the topological theory of visual shape perception.

PubMed

Kanbe, Fumio

2013-01-01

This study used a series of six closely related experiments to examine whether individuals use topological structures to discriminate figures. Strict control was exerted over the selection of stimuli, which were a specific type of randomly generated lined figures that can be classified using isomorphic sets defined by graph theory. Any two figures within an isomorphic set possessed the same topological structure. The experiments described here used a same/different discrimination task with simultaneously presented pairs of figures: (a) identical pairs (Id pairs), in which each pair of figures had the same topological and superficial properties; (b) nonidentical and isomorphic pairs (Iso pairs), in which each pair had the same topological but different superficial properties; and (c) nonidentical and nonisomorphic pairs (Noniso pairs), in which each pair had different topological properties. Within these experiments I varied the conditions related to the intersecting line segments, presentation of points defining each figure, figure complexity, stimulus aspect ratios, and the parity of the total line-segment lengths between the figures in each pair. These variations showed that the latencies for making accurate discriminations were shorter for Noniso pairs than for Iso pairs, suggesting that individuals are sensitive to topology when distinguishing figures.

The application of molecular topology for ulcerative colitis drug discovery.

PubMed

Bellera, Carolina L; Di Ianni, Mauricio E; Talevi, Alan

2018-01-01

Although the therapeutic arsenal against ulcerative colitis has greatly expanded (including the revolutionary advent of biologics), there remain patients who are refractory to current medications while the safety of the available therapeutics could also be improved. Molecular topology provides a theoretic framework for the discovery of new therapeutic agents in a very efficient manner, and its applications in the field of ulcerative colitis have slowly begun to flourish. Areas covered: After discussing the basics of molecular topology, the authors review QSAR models focusing on validated targets for the treatment of ulcerative colitis, entirely or partially based on topological descriptors. Expert opinion: The application of molecular topology to ulcerative colitis drug discovery is still very limited, and many of the existing reports seem to be strictly theoretic, with no experimental validation or practical applications. Interestingly, mechanism-independent models based on phenotypic responses have recently been reported. Such models are in agreement with the recent interest raised by network pharmacology as a potential solution for complex disorders. These and other similar studies applying molecular topology suggest that some therapeutic categories may present a 'topological pattern' that goes beyond a specific mechanism of action.

On the estimation variance for the specific Euler-Poincaré characteristic of random networks.

PubMed

Tscheschel, A; Stoyan, D

2003-07-01

The specific Euler number is an important topological characteristic in many applications. It is considered here for the case of random networks, which may appear in microscopy either as primary objects of investigation or as secondary objects describing in an approximate way other structures such as, for example, porous media. For random networks there is a simple and natural estimator of the specific Euler number. For its estimation variance, a simple Poisson approximation is given. It is based on the general exact formula for the estimation variance. In two examples of quite different nature and topology application of the formulas is demonstrated.

Cherenkov sound on a surface of a topological insulator

NASA Astrophysics Data System (ADS)

Smirnov, Sergey

2013-11-01

Topological insulators are currently of considerable interest due to peculiar electronic properties originating from helical states on their surfaces. Here we demonstrate that the sound excited by helical particles on surfaces of topological insulators has several exotic properties fundamentally different from sound propagating in nonhelical or even isotropic helical systems. Specifically, the sound may have strictly forward propagation absent for isotropic helical states. Its dependence on the anisotropy of the realistic surface states is of distinguished behavior which may be used as an alternative experimental tool to measure the anisotropy strength. Fascinating from the fundamental point of view backward, or anomalous, Cherenkov sound is excited above the critical angle π/2 when the anisotropy exceeds a critical value. Strikingly, at strong anisotropy the sound localizes into a few forward and backward beams propagating along specific directions.

Structural covariance network centrality in maltreated youth with posttraumatic stress disorder

PubMed Central

Sun, Delin; Peverill, Matthew R.; Swanson, Chelsea S.; McLaughlin, Katie A.; Morey, Rajendra A.

2018-01-01

Childhood maltreatment is associated with posttraumatic stress disorder (PTSD) and elevated rates of adolescent and adult psychopathology including major depression, bipolar disorder, substance use disorders, and other medical comorbidities. Gray matter volume changes have been found in maltreated youth with (versus without) PTSD. However, little is known about the alterations of brain structural covariance network topology derived from cortical thickness in maltreated youth with PTSD. High-resolution T1-weighted magnetic resonance imaging scans were from demographically matched maltreated youth with PTSD (N = 24), without PTSD (N =64), and non-maltreated healthy controls (n = 67). Cortical thickness data from 148 cortical regions was entered into interregional partial correlation analyses across participants. The supra-threshold correlations constituted connections in a structural brain network derived from four types of centrality measures (degree, betweenness, closeness, and eigenvector) estimated network topology and the importance of nodes. Between-group differences were determined by permutation testing. Maltreated youth with PTSD exhibited larger centrality in left anterior cingulate cortex than the other two groups, suggesting cortical network topology specific to maltreated youth with PTSD. Moreover, maltreated youth with versus without PTSD showed smaller centrality in right orbitofrontal cortex, suggesting that this may represent a vulnerability factor to PTSD following maltreatment. Longitudinal follow-up of the present results will help characterize the role that altered centrality plays in vulnerability and resilience to PTSD following childhood maltreatment. PMID:29294430

Large quantum rings in the ν > 1 quantum Hall regime.

PubMed

Räsänen, E; Aichinger, M

2009-01-14

We study computationally the ground-state properties of large quantum rings in the filling-factor ν>1 quantum Hall regime. We show that the arrangement of electrons into different Landau levels leads to clear signatures in the total energies as a function of the magnetic field. In this context, we discuss possible approximations for the filling factor ν in the system. We are able to characterize integer-ν states in quantum rings in an analogy with conventional quantum Hall droplets. We also find a partially spin-polarized state between ν = 2 and 3. Despite the specific topology of a quantum ring, this state is strikingly reminiscent of the recently found ν = 5/2 state in a quantum dot.

A method for interactive specification of multiple-block topologies

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.; Mccann, Karen M.

1991-01-01

A method is presented for dealing with the vast amount of topological and other data which must be specified to generate a multiple-block computational grid. Specific uses of the graphical capabilities of a powerful scientific workstation are described which reduce the burden on the user of collecting and formatting such large amounts of data. A program to implement this method, 3DPREP, is described. A plotting transformation algorithm, some useful software tools, notes on programming, and a database organization are also presented. Example grids developed using the method are shown.

Machine learning Z2 quantum spin liquids with quasiparticle statistics

NASA Astrophysics Data System (ADS)

Zhang, Yi; Melko, Roger G.; Kim, Eun-Ah

2017-12-01

After decades of progress and effort, obtaining a phase diagram for a strongly correlated topological system still remains a challenge. Although in principle one could turn to Wilson loops and long-range entanglement, evaluating these nonlocal observables at many points in phase space can be prohibitively costly. With growing excitement over topological quantum computation comes the need for an efficient approach for obtaining topological phase diagrams. Here we turn to machine learning using quantum loop topography (QLT), a notion we have recently introduced. Specifically, we propose a construction of QLT that is sensitive to quasiparticle statistics. We then use mutual statistics between the spinons and visons to detect a Z2 quantum spin liquid in a multiparameter phase space. We successfully obtain the quantum phase boundary between the topological and trivial phases using a simple feed-forward neural network. Furthermore, we demonstrate advantages of our approach for the evaluation of phase diagrams relating to speed and storage. Such statistics-based machine learning of topological phases opens new efficient routes to studying topological phase diagrams in strongly correlated systems.

Topological properties of the electron density of solids and molecules. Recent developments in Oviedo.

PubMed

Luaña, Víctor; Costales, Aurora; Mori-Sánchez, Paula; Blanco, Miguel A; Martín Pendás, A

2004-09-01

Some of the latest advances in the analysis of electron density are reviewed, including: (a) topological indices that provide a useful characterization of the global properties of the density; (b) specific results on some prototypical metal and low heteropolarity systems; and (c) calculation of the local curvature of the interatomic surface.

Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.

PubMed

Cang, Zixuan; Wei, Guo-Wei

2018-02-01

Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein-ligand binding affinities is vital to rational drug design and the understanding of protein-ligand binding and binding induced function. Existing binding affinity prediction methods are inundated with geometric detail and involve excessively high dimensions, which undermines their predictive power for massive binding data. Topology provides the ultimate level of abstraction and thus incurs too much reduction in geometric information. Persistent homology embeds geometric information into topological invariants and bridges the gap between complex geometry and abstract topology. However, it oversimplifies biological information. This work introduces element specific persistent homology (ESPH) or multicomponent persistent homology to retain crucial biological information during topological simplification. The combination of ESPH and machine learning gives rise to a powerful paradigm for macromolecular analysis. Tests on 2 large data sets indicate that the proposed topology-based machine-learning paradigm outperforms other existing methods in protein-ligand binding affinity predictions. ESPH reveals protein-ligand binding mechanism that can not be attained from other conventional techniques. The present approach reveals that protein-ligand hydrophobic interactions are extended to 40Å  away from the binding site, which has a significant ramification to drug and protein design. Copyright © 2017 John Wiley & Sons, Ltd.

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

PubMed

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

2008-01-01

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

The physical size of transcription factors is key to transcriptional regulation in chromatin domains

NASA Astrophysics Data System (ADS)

Maeshima, Kazuhiro; Kaizu, Kazunari; Tamura, Sachiko; Nozaki, Tadasu; Kokubo, Tetsuro; Takahashi, Koichi

2015-02-01

Genetic information, which is stored in the long strand of genomic DNA as chromatin, must be scanned and read out by various transcription factors. First, gene-specific transcription factors, which are relatively small (˜50 kDa), scan the genome and bind regulatory elements. Such factors then recruit general transcription factors, Mediators, RNA polymerases, nucleosome remodellers, and histone modifiers, most of which are large protein complexes of 1-3 MDa in size. Here, we propose a new model for the functional significance of the size of transcription factors (or complexes) for gene regulation of chromatin domains. Recent findings suggest that chromatin consists of irregularly folded nucleosome fibres (10 nm fibres) and forms numerous condensed domains (e.g., topologically associating domains). Although the flexibility and dynamics of chromatin allow repositioning of genes within the condensed domains, the size exclusion effect of the domain may limit accessibility of DNA sequences by transcription factors. We used Monte Carlo computer simulations to determine the physical size limit of transcription factors that can enter condensed chromatin domains. Small gene-specific transcription factors can penetrate into the chromatin domains and search their target sequences, whereas large transcription complexes cannot enter the domain. Due to this property, once a large complex binds its target site via gene-specific factors it can act as a ‘buoy’ to keep the target region on the surface of the condensed domain and maintain transcriptional competency. This size-dependent specialization of target-scanning and surface-tethering functions could provide novel insight into the mechanisms of various DNA transactions, such as DNA replication and repair/recombination.

Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

PubMed

Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

2014-11-07

Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

PubMed Central

Mustoe, Anthony M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2014-01-01

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. PMID:25217593

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Topological entanglement entropy with a twist.

PubMed

Brown, Benjamin J; Bartlett, Stephen D; Doherty, Andrew C; Barrett, Sean D

2013-11-27

Defects in topologically ordered models have interesting properties that are reminiscent of the anyonic excitations of the models themselves. For example, dislocations in the toric code model are known as twists and possess properties that are analogous to Ising anyons. We strengthen this analogy by using the topological entanglement entropy as a diagnostic tool to identify properties of both defects and excitations in the toric code. Specifically, we show, through explicit calculation, that the toric code model including twists and dyon excitations has the same quantum dimensions, the same total quantum dimension, and the same fusion rules as an Ising anyon model.

In-surface confinement of topological insulator nanowire surface states

NASA Astrophysics Data System (ADS)

Chen, Fan W.; Jauregui, Luis A.; Tan, Yaohua; Manfra, Michael; Klimeck, Gerhard; Chen, Yong P.; Kubis, Tillmann

2015-09-01

The bandstructures of [110] and [001] Bi2Te3 nanowires are solved with the atomistic 20 band tight binding functionality of NEMO5. The theoretical results reveal: The popular assumption that all topological insulator (TI) wire surfaces are equivalent is inappropriate. The Fermi velocity of chemically distinct wire surfaces differs significantly which creates an effective in-surface confinement potential. As a result, topological insulator surface states prefer specific surfaces. Therefore, experiments have to be designed carefully not to probe surfaces unfavorable to the surface states (low density of states) and thereby be insensitive to the TI-effects.

On the design of a hierarchical SS7 network: A graph theoretical approach

NASA Astrophysics Data System (ADS)

Krauss, Lutz; Rufa, Gerhard

1994-04-01

This contribution is concerned with the design of Signaling System No. 7 networks based on graph theoretical methods. A hierarchical network topology is derived by combining the advantage of the hierarchical network structure with the realization of node disjoint routes between nodes of the network. By using specific features of this topology, we develop an algorithm to construct circle-free routing data and to assure bidirectionality also in case of failure situations. The methods described are based on the requirements that the network topology, as well as the routing data, may be easily changed.

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

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

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

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

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

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

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

Zhang, Zuocheng; Wei, Wei; Yang, Fangyuan

In this paper, we report quantum oscillation studies on the Bi 2Te 3-xS x topological insulator single crystals in pulsed magnetic fields up to 91 T. For the x = 0.4 sample with the lowest bulk carrier density, the surface and bulk quantum oscillations can be disentangled by combined Shubnikov–de Haas and de Hass–van Alphen oscillations, as well as quantum oscillations in nanometer-thick peeled crystals. At high magnetic fields beyond the bulk quantum limit, our results suggest that the zeroth Landau level of topological surface states is shifted due to the Zeeman effect. The g factor of the topological surfacemore » states is estimated to be between 1.8 and 4.5. Lastly, these observations shed new light on the quantum transport phenomena of topological insulators in ultrahigh magnetic fields.« less

Functional Integrative Levels in the Human Interactome Recapitulate Organ Organization

PubMed Central

Prieto, Carlos; Benkahla, Alia; De Las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This ‘Largest Common Interactome Network’ represents a ‘functional interactome core’. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization. PMID:21799769

Andreev Reflection in an s-Type Superconductor Proximized 3D Topological Insulator.

PubMed

Tikhonov, E S; Shovkun, D V; Snelder, M; Stehno, M P; Huang, Y; Golden, M S; Golubov, A A; Brinkman, A; Khrapai, V S

2016-09-30

We investigate transport and shot noise in lateral normal-metal-3D topological-insulator-superconductor contacts, where the 3D topological insulator (TI) is based on Bi. In the normal state, the devices are in the elastic diffusive transport regime, as demonstrated by a nearly universal value of the shot noise Fano factor F_{N}≈1/3 in magnetic field and in a reference normal-metal contact. In the absence of magnetic field, we identify the Andreev reflection (AR) regime, which gives rise to the effective charge doubling in shot noise measurements. Surprisingly, the Fano factor F_{AR}≈0.22±0.02 is considerably reduced in the AR regime compared to F_{N}, in contrast to previous AR experiments in normal metals and semiconductors. We suggest that this effect is related to a finite thermal conduction of the proximized, superconducting TI owing to a residual density of states at low energies.

Influence of the number of topologically interacting neighbors on swarm dynamics

PubMed Central

Shang, Yilun; Bouffanais, Roland

2014-01-01

Recent empirical and theoretical works on collective behaviors based on a topological interaction are beginning to offer some explanations as for the physical reasons behind the selection of a particular number of nearest neighbors locally affecting each individual's dynamics. Recently, flocking starlings have been shown to topologically interact with a very specific number of neighbors, between six to eight, while metric-free interactions were found to govern human crowd dynamics. Here, we use network- and graph-theoretic approaches combined with a dynamical model of locally interacting self-propelled particles to study how the consensus reaching process and its dynamics are influenced by the number k of topological neighbors. Specifically, we prove exactly that, in the absence of noise, consensus is always attained with a speed to consensus strictly increasing with k. The analysis of both speed and time to consensus reveals that, irrespective of the swarm size, a value of k ~ 10 speeds up the rate of convergence to consensus to levels close to the one of the optimal all-to-all interaction signaling. Furthermore, this effect is found to be more pronounced in the presence of environmental noise. PMID:24567077

Coherent Structure Detection using Persistent Homology and other Topological Tools

NASA Astrophysics Data System (ADS)

Smith, Spencer; Roberts, Eric; Sindi, Suzanne; Mitchell, Kevin

2017-11-01

For non-autonomous, aperiodic fluid flows, coherent structures help organize the dynamics, much as invariant manifolds and periodic orbits do for autonomous or periodic systems. The prevalence of such flows in nature and industry has motivated many successful techniques for defining and detecting coherent structures. However, often these approaches require very fine trajectory data to reconstruct velocity fields and compute Cauchy-Green-tensor-related quantities. We use topological techniques to help detect coherent trajectory sets in relatively sparse 2D advection problems. More specifically, we have developed a homotopy-based algorithm, the ensemble-based topological entropy calculation (E-tec), which assigns to each edge in an initial triangulation of advected points a topologically forced lower bound on its future stretching rate. The triangulation and its weighted edges allow us to analyze flows using persistent homology. This topological data analysis tool detects clusters and loops in the triangulation that are robust in the presence of noise and in this case correspond to coherent trajectory sets.

Topological Phase Transitions in Line-nodal Superconductors

NASA Astrophysics Data System (ADS)

Cho, Gil Young; Han, Sangeun; Moon, Eun-Gook

Fathoming interplay between symmetry and topology of many-electron wave-functions deepens our understanding in quantum nature of many particle systems. Topology often protects zero-energy excitation, and in a certain class, symmetry is intrinsically tied to the topological protection. Namely, unless symmetry is broken, topological nature is intact. We study one specific case of such class, symmetry-protected line-nodal superconductors in three spatial dimensions (3d). Mismatch between phase spaces of order parameter fluctuation and line-nodal fermion excitation induces an exotic universality class in a drastic contrast to one of the conventional ϕ4 theory in 3d. Hyper-scaling violation and relativistic dynamic scaling with unusually large quantum critical region are main characteristics, and their implication in experiments is discussed. For example, continuous phase transition out of line-nodal superconductors has a linear phase boundary in a temperature-tuning parameter phase-diagram. This work was supported by the Brain Korea 21 PLUS Project of Korea Government and KAIST start-up funding.

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.

The connectivity of the brain: multi-level quantitative analysis.

PubMed

Murre, J M; Sturdy, D P

1995-11-01

We develop a mathematical formalism or calculating connectivity volumes generated by specific topologies with various physical packing strategies. We consider four topologies (full, random, nearest-neighbor, and modular connectivity) and three physical models: (i) interior packing, where neurons and connection fibers are intermixed, (ii) sheeted packing where neurons are located on a sheet with fibers running underneath, and (iii) exterior packing where the neurons are located at the surfaces of a cube or sphere with fibers taking up the internal volume. By extensive cross-referencing of available human neuroanatomical data we produce a consistent set of parameters for the whole brain, the cerebral cortex, and the cerebellar cortex. By comparing these inferred values with those predicted by the expressions, we draw the following general conclusions for the human brain, cortex, and cerebellum: (i) Interior packing is less efficient than exterior packing (in a sphere). (ii) Fully and randomly connected topologies are extremely inefficient. More specifically we find evidence that different topologies and physical packing strategies might be used at different scales. (iii) For the human brain at a macro-structural level, modular topologies on an exterior sphere approach the data most closely. (iv) On a mesostructural level, laminarization and columnarization are evidence of the superior efficiency of organizing the wiring as sheets. (v) Within sheets, microstructures emerge in which interior models are shown to be the most efficient. With regard to interspecies similarities and differences we conjecture (vi) that the remarkable constancy of number of neurons per underlying square millimeter of cortex may be the result of evolution minimizing interneuron distance in grey matter, and (vii) that the topologies that best fit the human brain data should not be assumed to apply to other mammals, such as the mouse for which we show that a random topology may be feasible for the cortex.

Topological and Historical Considerations for Infectious Disease Transmission among Injecting Drug Users in Bushwick, Brooklyn (USA)

PubMed Central

Dombrowski, Kirk; Curtis, Richard; Friedman, Samuel; Khan, Bilal

2014-01-01

Recent interest by physicists in social networks and disease transmission factors has prompted debate over the topology of degree distributions in sexual networks. Social network researchers have been critical of “scale-free” Barabasi-Albert approaches, and largely rejected the preferential attachment, “rich-get-richer” assumptions that underlie that model. Instead, research on sexual networks has pointed to the importance of homophily and local sexual norms in dictating degree distributions, and thus disease transmission thresholds. Injecting Drug User (IDU) network topologies may differ from the emerging models of sexual networks, however. Degree distribution analysis of a Brooklyn, NY, IDU network indicates a different topology than the spanning tree configurations discussed for sexual networks, instead featuring comparatively short cycles and high concurrency. Our findings suggest that IDU networks do in some ways conform to a “scale-free” topology, and thus may represent “reservoirs” of potential infection despite seemingly low transmission thresholds. PMID:24672745

Topological and Functional Characterization of an Insect Gustatory Receptor

PubMed Central

Zhang, Hui-Jie; Anderson, Alisha R.; Trowell, Stephen C.; Luo, A-Rong; Xiang, Zhong-Huai; Xia, Qing-You

2011-01-01

Insect gustatory receptors are predicted to have a seven-transmembrane structure and are distantly related to insect olfactory receptors, which have an inverted topology compared with G-protein coupled receptors, including mammalian olfactory receptors. In contrast, the topology of insect gustatory receptors remains unknown. Except for a few examples from Drosophila, the specificity of individual insect gustatory receptors is also unknown. In this study, the total number of identified gustatory receptors in Bombyx mori was expanded from 65 to 69. BmGr8, a silkmoth gustatory receptor from the sugar receptor subfamily, was expressed in insect cells. Membrane topology studies on BmGr8 indicate that, like insect olfactory receptors, it has an inverted topology relative to G protein-coupled receptors. An orphan GR from the bitter receptor family, BmGr53, yielded similar results. We infer, from the finding that two distantly related BmGrs have an intracellular N-terminus and an odd number of transmembrane spans, that this is likely to be a general topology for all insect gustatory receptors. We also show that BmGr8 functions independently in Sf9 cells and responds in a concentration-dependent manner to the polyalcohols myo-inositol and epi-inositol but not to a range of mono- and di-saccharides. BmGr8 is the first chemoreceptor shown to respond specifically to inositol, an important or essential nutrient for some Lepidoptera. The selectivity of BmGr8 responses is consistent with the known responses of one of the gustatory receptor neurons in the lateral styloconic sensilla of B. mori, which responds to myo-inositol and epi-inositol but not to allo-inositol. PMID:21912618

Homogeneous, anisotropic three-manifolds of topologically massive gravity

NASA Astrophysics Data System (ADS)

Nutku, Y.; Baekler, P.

1989-10-01

We present a new class of exact solutions of Deser, Jackiw, and Templeton's theory (DJT) of topologically massive gravity which consists of homogeneous, anisotropic manifolds. In these solutions the coframe is given by the left-invariant 1-forms of 3-dimensional Lie algebras up to constant scale factors. These factors are fixed in terms of the DJT coupling constant μ which is the constant of proportionality between the Einstein and Cotton tensors in 3-dimensions. Differences between the scale factors result in anisotropy which is a common feature of topologically massive 3-manifolds. We have found that only Bianchi Types VI, VIII, and IX lead to nontrivial solutions. Among these, a Bianchi Type IX, squashed 3-sphere solution of the Euclideanized DJT theory has finite action. Bianchi Type VIII, IX solutions can variously be embedded in the de Sitter/anti-de Sitter space. That is, some DJT 3-manifolds that we shall present here can be regarded as the basic constituent of anti-de Sitter space which is the ground state solution in higher dimensional generalization of Einstein's general relativity.

Homogeneous, anisotropic three-manifolds of topologically massive gravity

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

Nutku, Y.; Baekler, P.

1989-10-01

We present a new class of exact solutions of Deser, Jackiw, and Templeton's theory (DJT) of topologically massive gravity which consists of homogeneous, anisotropic manifolds. In these solutions the coframe is given by the left-invariant 1-forms of 3-dimensional Lie algebras up to constant scale factors. These factors are fixed in terms of the DJT coupling constant {mu}m which is the constant of proportionality between the Einstein and Cotton tensors in 3-dimensions. Differences between the scale factors result in anisotropy which is a common feature of topologically massive 3-manifolds. We have found that only Bianchi Types VI, VIII, and IX leadmore » to nontrivial solutions. Among these, a Bianchi Type IX, squashed 3-sphere solution of the Euclideanized DJT theory has finite action, Bianchi Type VIII, IX solutions can variously be embedded in the de Sitter/anti-de Sitter space. That is, some DJT 3-manifolds that we shall present here can be regarded as the basic constitent of anti-de Sitter space which is the ground state solution in higher dimensional generalizations of Einstein's general relativity. {copyright} 1989 Academic Press, Inc.« less

A Scalable Distribution Network Risk Evaluation Framework via Symbolic Dynamics

PubMed Central

Yuan, Kai; Liu, Jian; Liu, Kaipei; Tan, Tianyuan

2015-01-01

Background Evaluations of electric power distribution network risks must address the problems of incomplete information and changing dynamics. A risk evaluation framework should be adaptable to a specific situation and an evolving understanding of risk. Methods This study investigates the use of symbolic dynamics to abstract raw data. After introducing symbolic dynamics operators, Kolmogorov-Sinai entropy and Kullback-Leibler relative entropy are used to quantitatively evaluate relationships between risk sub-factors and main factors. For layered risk indicators, where the factors are categorized into four main factors – device, structure, load and special operation – a merging algorithm using operators to calculate the risk factors is discussed. Finally, an example from the Sanya Power Company is given to demonstrate the feasibility of the proposed method. Conclusion Distribution networks are exposed and can be affected by many things. The topology and the operating mode of a distribution network are dynamic, so the faults and their consequences are probabilistic. PMID:25789859

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

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

PubMed Central

2009-01-01

Background The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for essential genes discovery are labor-intensive and time-consuming. Considering these experimental constraints, a computational approach capable of accurately predicting essential genes would be of great value. We therefore present here a machine learning-based computational approach relying on network topological features, cellular localization and biological process information for prediction of essential genes. Results We constructed a decision tree-based meta-classifier and trained it on datasets with individual and grouped attributes-network topological features, cellular compartments and biological processes-to generate various predictors of essential genes. We showed that the predictors with better performances are those generated by datasets with integrated attributes. Using the predictor with all attributes, i.e., network topological features, cellular compartments and biological processes, we obtained the best predictor of essential genes that was then used to classify yeast genes with unknown essentiality status. Finally, we generated decision trees by training the J48 algorithm on datasets with all network topological features, cellular localization and biological process information to discover cellular rules for essentiality. We found that the number of protein physical interactions, the nuclear localization of proteins and the number of regulating transcription factors are the most important factors determining gene essentiality. Conclusion We were able to demonstrate that network topological features, cellular localization and biological process information are reliable predictors of essential genes. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing essentiality. PMID:19758426

Hormonal induction of transfected genes depends on DNA topology.

PubMed Central

Piña, B; Haché, R J; Arnemann, J; Chalepakis, G; Slater, E P; Beato, M

1990-01-01

Plasmids containing the hormone regulatory element of mouse mammary tumor virus linked to the thymidine kinase promoter of herpes simplex virus and the reporter gene chloramphenicol acetyltransferase of Escherichia coli respond to glucocorticoids and progestins when transfected into appropriate cells. In the human mammary tumor cell line T47D, the response to progestins, but not to glucocorticoids, is highly dependent on the topology of the transfected DNA. Although negatively supercoiled plasmids respond optimally to the synthetic progestin R5020, their linearized counterparts exhibit markedly reduced progestin inducibility. This is not due to changes in the efficiency of DNA transfection, since the amount of DNA incorporated into the cell nucleus is not significantly dependent on the initial topology of the plasmids. In contrast, cotransfection experiments with glucocorticoid receptor cDNA in the same cell line show no significant influence of DNA topology on induction by dexamethasone. A similar result was obtained with fibroblasts that contain endogenous glucocorticoid receptors. When the distance between receptor-binding sites or between the binding sites and the promoter was increased, the dependence of progestin induction on DNA topology was more pronounced. In contrast to the original plasmid, these constructs also revealed a similar topological dependence for induction by glucocorticoids. The differential influence of DNA topology is not due to differences in the affinity of the two hormone receptors for DNA of various topologies, but probably reflects an influence of DNA topology on the interaction between different DNA-bound receptor molecules and between receptors and other transcription factors. Images PMID:2153920

Nexus fermions in topological symmorphic crystalline metals

DOE PAGES

Chang, Guoqing; Xu, Su-Yang; Huang, Shin-Ming; ...

2017-05-10

Topological metals and semimetals (TMs) have recently drawn significant interest. These materials give rise to condensed matter realizations of many important concepts in high-energy physics, leading to wide-ranging protected properties in transport and spectroscopic experiments. It has been well-established that the known TMs can be classified by the dimensionality of the topologically protected band degeneracies. While Weyl and Dirac semimetals feature zero-dimensional points, the band crossing of nodal-line semimetals forms a one-dimensional closed loop. In this paper, we identify a TM that goes beyond the above paradigms. It shows an exotic configuration of degeneracies without a well-defined dimensionality. Specifically, itmore » consists of 0D nexus with triple-degeneracy that interconnects 1D lines with double-degeneracy. We show that, because of the novel form of band crossing, the new TM cannot be described by the established results that characterize the topology of the Dirac and Weyl nodes. Moreover, triply-degenerate nodes realize emergent fermionic quasiparticles not present in relativistic quantum field theory. We present materials candidates. Thus, our results open the door for realizing new topological phenomena and fermions including transport anomalies and spectroscopic responses in metallic crystals with nontrivial topology beyond the Weyl/Dirac paradigm.« less

Glycosylatable GFP as a compartment-specific membrane topology reporter

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

Lee, Hunsang; Min, Jisoo; Heijne, Gunnar von

2012-11-02

Highlights: Black-Right-Pointing-Pointer An N-linked glycosylation site is introduced near the GFP fluorophore. Black-Right-Pointing-Pointer gGFP is not glycosylated and is fully fluorescent in the cytosol. Black-Right-Pointing-Pointer gGFP is glycosylated and non-fluorescent in the lumen of the ER. Black-Right-Pointing-Pointer gGFP is fused to membrane proteins of known topology. Black-Right-Pointing-Pointer Its applicability as a membrane topology reporter is demonstrated. -- Abstract: Determination of the membrane topology is an essential step in structural and functional studies of integral membrane proteins, yet the choices of membrane topology reporters are limited and the experimental analysis can be laborious, especially in eukaryotic cells. Here, we present amore » robust membrane topology reporter, glycosylatable green fluorescent protein (gGFP). gGFP is fully fluorescent in the yeast cytosol but becomes glycosylated and does not fluoresce in the lumen of the endoplasmic reticulum (ER). Thus, by assaying fluorescence and the glycosylation status of C-terminal fusions of gGFP to target membrane proteins in whole-cell lysates, the localization of the gGFP moiety (and hence the fusion joint) relative to the ER membrane can be unambiguously determined.« less

Planck 2015 results. XVIII. Background geometry and topology of the Universe

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Basak, S.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bucher, M.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, H. C.; Christensen, P. R.; Church, S.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; 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.; Désert, F.-X.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Feeney, S.; Fergusson, J.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; 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.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; McEwen, J. D.; McGehee, P.; Meinhold, P. R.; 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.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Peiris, H. V.; Perdereau, O.; Perotto, L.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pogosyan, D.; Pointecouteau, E.; Polenta, G.; Popa, L.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rowan-Robinson, M.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, F.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Yvon, D.; Zacchei, A.; Zonca, A.

2016-09-01

Maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χrec), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius ℛI of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio Δlnℒ > -5 relative to a simply-connected flat Planck best-fit model) are: ℛI > 0.97 χrec for the T3 cubic torus; and ℛI > 0.56 χrec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, ℛI > 0.97 χrec at 99% confidence level from polarization data alone. 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 temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. 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 < 7.6 × 10-10 (95% CL).

DNA Knots: Theory and Experiments

NASA Astrophysics Data System (ADS)

Sumners, D. W.

Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

Retinal artery-vein classification via topology estimation

PubMed Central

Estrada, Rolando; Allingham, Michael J.; Mettu, Priyatham S.; Cousins, Scott W.; Tomasi, Carlo; Farsiu, Sina

2015-01-01

We propose a novel, graph-theoretic framework for distinguishing arteries from veins in a fundus image. We make use of the underlying vessel topology to better classify small and midsized vessels. We extend our previously proposed tree topology estimation framework by incorporating expert, domain-specific features to construct a simple, yet powerful global likelihood model. We efficiently maximize this model by iteratively exploring the space of possible solutions consistent with the projected vessels. We tested our method on four retinal datasets and achieved classification accuracies of 91.0%, 93.5%, 91.7%, and 90.9%, outperforming existing methods. Our results show the effectiveness of our approach, which is capable of analyzing the entire vasculature, including peripheral vessels, in wide field-of-view fundus photographs. This topology-based method is a potentially important tool for diagnosing diseases with retinal vascular manifestation. PMID:26068204

Linking network topology to function. Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O.C. Martin, A. Krzywicki and M. Zagorski

NASA Astrophysics Data System (ADS)

di Bernardo, Diego

2016-07-01

The review by Martin et al. deals with a long standing problem at the interface of complex systems and molecular biology, that is the relationship between the topology of a complex network and its function. In biological terms the problem translates to relating the topology of gene regulatory networks (GRNs) to specific cellular functions. GRNs control the spatial and temporal activity of the genes encoded in the cell's genome by means of specialised proteins called Transcription Factors (TFs). A TF is able to recognise and bind specifically to a sequence (TF biding site) of variable length (order of magnitude of 10) found upstream of the sequence encoding one or more genes (at least in prokaryotes) and thus activating or repressing their transcription. TFs can thus be distinguished in activator and repressor. The picture can become more complex since some classes of TFs can form hetero-dimers consisting of a protein complex whose subunits are the individual TFs. Heterodimers can have completely different binding sites and activity compared to their individual parts. In this review the authors limit their attention to prokaryotes where the complexity of GRNs is somewhat reduced. Moreover they exploit a unique feature of living systems, i.e. evolution, to understand whether function can shape network topology. Indeed, prokaryotes such as bacteria are among the oldest living systems that have become perfectly adapted to their environment over geological scales and thus have reached an evolutionary steady-state where the fitness of the population has reached a plateau. By integrating in silico analysis and comparative evolution, the authors show that indeed function does tend to shape the structure of a GRN, however this trend is not always present and depends on the properties of the network being examined. Interestingly, the trend is more apparent for sparse networks, i.e. where the density of edges is very low. Sparsity is indeed one of the most prominent features of natural occurring GRNs, and more specifically GRNs have been found to approximate a power-law ;scale-free; degree distribution by Barabasi and Albert [2]. Why sparsity arises is still under debate, but Price in 1976 proposed a model [1], later renamed ;preferential attachment; by Barabasi and Albert [2], able to give rise to sparse scale-free networks. In this model, a network grows over time (such as GRN during evolution) by sequential addition of new nodes (caused by genome duplications) that attach with higher probability to nodes with higher degree. In this review, Martin et al. propose that sparsity could also be caused phenotypic constrains even in the absence of genome duplications, in order for the network to be robust against random mutations in the genome sequence, which in turn affect the specificity of TF binding sites. The authors also found that network motifs, i.e. subnetworks consisting of 3 or 4 nodes with a specific topology that are over-represented in the network, are also shaped by phenotypic constrains. Theoretical and computational approaches to understand the forces that shape network topology are of extreme interest in biology, although at this stage their impact has been limited. Neverteless, these approaches may soon have important practical applications. The era of synthetic biology is upon us, novel organisms with ;minimal genomes; are being built with the dual aim of simplifying engineering of new functions useful to humans and to understand which is the minimal set of genes needed to support life [3]. The first minimal organism has just been created [3] by randomly deleting genes and genomic regions until a minimal set supporting cell growth and replication was found. The GRN of this minimal organism has not been investigated yet, but it will be of limited complexity. What is the GRN structure in this organism? Will the cell phenotypes be robust to mutations? Is it possible to re-engineer the GRN in order to find an optimal structure that confers phenotypic robustness to the cell? All of these questions can be tackled only by understanding the guiding principles linking network topology to network function.

Analysis on the urban street network of Korea: Connections between topology and meta-information

NASA Astrophysics Data System (ADS)

Lee, Byoung-Hwa; Jung, Woo-Sung

2018-05-01

Cities consist of infrastructure that enables transportation, which can be considered as topology in abstract terms. Once cities are physically organized in terms of infrastructure, people interact with each other to form the values, which can be regarded as the meta-information of the cities. The topology and meta-information coevolve together as the cities are developed. In this study, we investigate the relationship between the topology and meta-information for a street network, which has aspects of both a complex network and planar graph. The degree of organization of a street structure determines the efficiency and productivity of the city in that they act as blood vessels to transport people, goods, and information. We analyze the topological aspect of a street network using centralities including the betweenness, closeness, straightness, and information. We classify the cities into several groups that share common meta-information based on the centrality, indicating that the topological factor of the street structure is closely related to meta-information through coevolution. We also obtain the coevolution in the planned cities using the regularity. Another footprint is the relation between the street segment length and the population, which shows the sublinear scaling.

Circuit Design Features of a Stable Two-Cell System.

PubMed

Zhou, Xu; Franklin, Ruth A; Adler, Miri; Jacox, Jeremy B; Bailis, Will; Shyer, Justin A; Flavell, Richard A; Mayo, Avi; Alon, Uri; Medzhitov, Ruslan

2018-02-08

Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit with specific properties that ensure homeostasis. Here, we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. Analytical screening of all possible two-cell circuit topologies revealed the circuit features sufficient for stability, including environmental constraint and negative-feedback regulation. Moreover, we found that cell-cell contact is essential for the stability of the macrophage-fibroblast circuit. These findings illustrate principles of cell circuit design and provide a quantitative perspective on cell interactions. Copyright © 2018 Elsevier Inc. All rights reserved.

Revealing topological Dirac fermions at the surface of strained HgTe thin films via quantum Hall transport spectroscopy

NASA Astrophysics Data System (ADS)

Thomas, C.; Crauste, O.; Haas, B.; Jouneau, P.-H.; Bäuerle, C.; Lévy, L. P.; Orignac, E.; Carpentier, D.; Ballet, P.; Meunier, T.

2017-12-01

We demonstrate evidences of electronic transport via topological Dirac surface states in a thin film of strained HgTe. At high perpendicular magnetic fields, we show that the electron transport reaches the quantum Hall regime with vanishing resistance. Furthermore, quantum Hall transport spectroscopy reveals energy splittings of relativistic Landau levels specific to coupled Dirac surface states. This study provides insights in the quantum Hall effect of topological insulator (TI) slabs, in the crossover regime between two- and three-dimensional TIs, and in the relevance of thin TI films to explore circuit functionalities in spintronics and quantum nanoelectronics.

An Integrated Multilevel Converter with Sigma Delta Control for LED Lighting

NASA Astrophysics Data System (ADS)

Gerber, Daniel L.

High brightness LEDs have become a mainstream lighting technology due to their efficiency, life span, and environmental benefits. As such, the lighting industry values LED drivers with low cost, small form factor, and long life span. Additional specifications that define a high quality LED driver are high efficiency, high power factor, wide-range dimming, minimal flicker, and a galvanically isolated output. The flyback LED driver is a popular topology that satisfies all these specifications, but it requires a bulky and costly flyback transformer. In addition, its passive methods for cancelling AC power ripple require electrolytic capacitors, which have been known to have life span issues. This dissertation details the design, construction, and verification of a novel LED driver that satisfies all the specifications. In addition, it does not require a flyback transformer or electrolytic capacitors, thus marking an improvement over the flyback driver on size, cost, and life span. This dissertation presents an integrated circuit (IC) LED driver, which features a pair of generalized multilevel converters that are controlled via sigma-delta modulation. The first is a multilevel rectifier responsible for power factor correction (PFC) and dimming. The PFC rectifier employs a second order sigma-delta loop to precisely control the input current harmonics and amplitude. The second is a bidirectional multilevel inverter used to cancel AC power ripple from the DC bus. This ripple-cancellation module transfers energy to and from a storage capacitor. It uses a first order sigma-delta loop with a preprogrammed waveform to swing the storage capacitor voltage. The system also contains an output stage that powers the LEDs with DC and provides for galvanic isolation. The output stage consists of an H-bridge stack that connects to the output through a small toroid transformer. The IC LED driver was simulated and prototyped on an ABCD silicon test chip. Testing and verification indicates functional performance for all the modules in the LED driver. The driver exhibits moderate efficiency at half voltage. Although the part was only testable to half voltage, loss models predict that its efficiency would be much higher at full voltage. The driver also meets specifications on the line current harmonics and ripple cancellation. This dissertation introduces multilevel circuit techniques to the IC and LED research space. The prototype's functional performance indicates that integrated multilevel converters are a viable topology for lighting and other similar applications.

Branch age and light conditions determine leaf-area-specific conductivity in current shoots of Scots pine.

PubMed

Grönlund, Leila; Hölttä, Teemu; Mäkelä, Annikki

2016-08-01

Shoot size and other shoot properties more or less follow the availability of light, but there is also evidence that the topological position in a tree crown has an influence on shoot development. Whether the hydraulic properties of new shoots are more regulated by the light or the position affects the shoot acclimation to changing light conditions and thereby to changing evaporative demand. We investigated the leaf-area-specific conductivity (and its components sapwood-specific conductivity and Huber value) of the current-year shoots of Scots pine (Pinus sylvestris L.) in relation to light environment and topological position in three different tree classes. The light environment was quantified in terms of simulated transpiration and the topological position was quantified by parent branch age. Sample shoot measurements included length, basal and tip diameter, hydraulic conductivity of the shoot, tracheid area and density, and specific leaf area. In our results, the leaf-area-specific conductivity of new shoots declined with parent branch age and increased with simulated transpiration rate of the shoot. The relation to transpiration demand seemed more decisive, since it gave higher R(2) values than branch age and explained the differences between the tree classes. The trend of leaf-area-specific conductivity with simulated transpiration was closely related to Huber value, whereas the trend of leaf-area-specific conductivity with parent branch age was related to a similar trend in sapwood-specific conductivity. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Psychometric Validation of a Multidimensional Schema of Substance Use Topology: Discrimination of High and Low Risk Youth and Prediction of Substance Use Disorder.

ERIC Educational Resources Information Center

Kirisci, Levent; Tarter, Ralph E.

2001-01-01

Designs and evaluates a multidimensional schema for the assessment of alcohol, tobacco and other drug use topology. Findings illustrate the value of multidimensional assessment for identifying youth at high risk for substance use disorder (SUD) as well as for elucidating the factors contributing to the transition to suprathreshold SUD. (Contains…

Suggested Mechanisms of Tracheal Occlusion Mediated Accelerated Fetal Lung Growth: A Case for Heterogeneous Topological Zones

PubMed Central

Marwan, Ahmed I.; Shabeka, Uladzimir; Dobrinskikh, Evgenia

2018-01-01

In this article, we report an up-to-date summary on tracheal occlusion (TO) as an approach to drive accelerated lung growth and strive to review the different maternal- and fetal-derived local and systemic signals and mechanisms that may play a significant biological role in lung growth and formation of heterogeneous topological zones following TO. Pulmonary hypoplasia is a condition whereby branching morphogenesis and embryonic pulmonary vascular development are globally affected and is classically seen in congenital diaphragmatic hernia. TO is an innovative approach aimed at driving accelerated lung growth in the most severe forms of diaphragmatic hernia and has been shown to result in improved neonatal outcomes. Currently, most research on mechanisms of TO-induced lung growth is focused on mechanical forces and is viewed from the perspective of homogeneous changes within the lung. We suggest that the key principle in understanding changes in fetal lungs after TO is taking into account formation of unique variable topological zones. Following TO, fetal lungs might temporarily look like a dynamically changing topologic mosaic with varying proliferation rates, dissimilar scale of vasculogenesis, diverse patterns of lung tissue damage, variable metabolic landscape, and different structures. The reasons for this dynamic topological mosaic pattern may include distinct degree of increased hydrostatic pressure in different parts of the lung, dissimilar degree of tissue stress/damage and responses to this damage, and incomparable patterns of altered lung zones with variable response to systemic maternal and fetal factors, among others. The local interaction between these factors and their accompanying processes in addition to the potential role of other systemic factors might lead to formation of a common vector of biological response unique to each zone. The study of the interaction between various networks formed after TO (action of mechanical forces, activation of mucosal mast cells, production and secretion of damage-associated molecular pattern substances, low-grade local pulmonary inflammation, and cardiac contraction-induced periodic agitation of lung tissue, among others) will bring us closer to an appreciation of the biological phenomenon of topological heterogeneity within the fetal lungs. PMID:29376042

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.

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

PubMed Central

Mustoe, Anthony M.; Al-Hashimi, Hashim M.; Brooks, Charles L.

2016-01-01

A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding. PMID:26481360

Structural covariance network centrality in maltreated youth with posttraumatic stress disorder.

PubMed

Sun, Delin; Peverill, Matthew R; Swanson, Chelsea S; McLaughlin, Katie A; Morey, Rajendra A

2018-03-01

Childhood maltreatment is associated with posttraumatic stress disorder (PTSD) and elevated rates of adolescent and adult psychopathology including major depression, bipolar disorder, substance use disorders, and other medical comorbidities. Gray matter volume changes have been found in maltreated youth with (versus without) PTSD. However, little is known about the alterations of brain structural covariance network topology derived from cortical thickness in maltreated youth with PTSD. High-resolution T1-weighted magnetic resonance imaging scans were from demographically matched maltreated youth with PTSD (N = 24), without PTSD (N = 64), and non-maltreated healthy controls (n = 67). Cortical thickness data from 148 cortical regions was entered into interregional partial correlation analyses across participants. The supra-threshold correlations constituted connections in a structural brain network derived from four types of centrality measures (degree, betweenness, closeness, and eigenvector) estimated network topology and the importance of nodes. Between-group differences were determined by permutation testing. Maltreated youth with PTSD exhibited larger centrality in left anterior cingulate cortex than the other two groups, suggesting cortical network topology specific to maltreated youth with PTSD. Moreover, maltreated youth with versus without PTSD showed smaller centrality in right orbitofrontal cortex, suggesting that this may represent a vulnerability factor to PTSD following maltreatment. Longitudinal follow-up of the present results will help characterize the role that altered centrality plays in vulnerability and resilience to PTSD following childhood maltreatment. Copyright © 2017. Published by Elsevier Ltd.

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

PubMed

Heled, Joseph; Drummond, Alexei J

2015-05-01

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

Quantum transport in topological semimetals under magnetic fields

NASA Astrophysics Data System (ADS)

Lu, Hai-Zhou; Shen, Shun-Qing

2017-06-01

Topological semimetals are three-dimensional topological states of matter, in which the conduction and valence bands touch at a finite number of points, i.e., the Weyl nodes. Topological semimetals host paired monopoles and antimonopoles of Berry curvature at the Weyl nodes and topologically protected Fermi arcs at certain surfaces. We review our recent works on quantum transport in topological semimetals, according to the strength of the magnetic field. At weak magnetic fields, there are competitions between the positive magnetoresistivity induced by the weak anti-localization effect and negative magnetoresistivity related to the nontrivial Berry curvature. We propose a fitting formula for the magnetoconductivity of the weak anti-localization. We expect that the weak localization may be induced by inter-valley effects and interaction effect, and occur in double-Weyl semimetals. For the negative magnetoresistance induced by the nontrivial Berry curvature in topological semimetals, we show the dependence of the negative magnetoresistance on the carrier density. At strong magnetic fields, specifically, in the quantum limit, the magnetoconductivity depends on the type and range of the scattering potential of disorder. The high-field positive magnetoconductivity may not be a compelling signature of the chiral anomaly. For long-range Gaussian scattering potential and half filling, the magnetoconductivity can be linear in the quantum limit. A minimal conductivity is found at the Weyl nodes although the density of states vanishes there.

Origins of enhanced thermoelectric power factor in topologically insulating Bi{sub 0.64}Sb{sub 1.36}Te{sub 3} thin films

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

Liu, Wei; State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070; Chi, Hang

2016-01-25

In this research, we report the enhanced thermoelectric power factor in topologically insulating thin films of Bi{sub 0.64}Sb{sub 1.36}Te{sub 3} with a thickness of 6–200 nm. Measurements of scanning tunneling spectroscopy and electronic transport show that the Fermi level lies close to the valence band edge, and that the topological surface state (TSS) is electron dominated. We find that the Seebeck coefficient of the 6 nm and 15 nm thick films is dominated by the valence band, while the TSS chiefly contributes to the electrical conductivity. In contrast, the electronic transport of the reference 200 nm thick film behaves similar to bulk thermoelectric materialsmore » with low carrier concentration, implying the effect of the TSS on the electronic transport is merely prominent in the thin region. The conductivity of the 6 nm and 15 nm thick film is obviously higher than that in the 200 nm thick film owing to the highly mobile TSS conduction channel. As a consequence of the enhanced electrical conductivity and the suppressed bipolar effect in transport properties for the 6 nm thick film, an impressive power factor of about 2.0 mW m{sup −1} K{sup −2} is achieved at room temperature for this film. Further investigations of the electronic transport properties of TSS and interactions between TSS and the bulk band might result in a further improved thermoelectric power factor in topologically insulating Bi{sub 0.64}Sb{sub 1.36}Te{sub 3} thin films.« less

Macroscopic Floquet topological crystalline steel and superconductor pump

NASA Astrophysics Data System (ADS)

Rossi, Anna M. E. B.; Bugase, Jonas; Fischer, Thomas M.

2017-08-01

The transport of a macroscopic steel sphere and a superconducting sphere on top of two-dimensional periodic magnetic patterns is studied experimentally and compared with the theory and with experiments on topological transport of magnetic colloids. Transport of the steel and superconducting sphere is achieved by moving an external permanent magnet on a closed loop around the two-dimensional crystal. The transport is topological, i.e., the spheres are transported by a primitive unit vector of the lattice when the external magnet loop winds around specific directions. We experimentally determine the set of directions the loops must enclose for nontrivial transport of the spheres into various directions. We show that the loops can be used to sort steel and superconducting spheres. We show that the topological transport is robust with respect to the scale of the system and therefore speculate on its down scalability to the molecular scale.

Topological properties of robust biological and computational networks

PubMed Central

Navlakha, Saket; He, Xin; Faloutsos, Christos; Bar-Joseph, Ziv

2014-01-01

Network robustness is an important principle in biology and engineering. Previous studies of global networks have identified both redundancy and sparseness as topological properties used by robust networks. By focusing on molecular subnetworks, or modules, we show that module topology is tightly linked to the level of environmental variability (noise) the module expects to encounter. Modules internal to the cell that are less exposed to environmental noise are more connected and less robust than external modules. A similar design principle is used by several other biological networks. We propose a simple change to the evolutionary gene duplication model which gives rise to the rich range of module topologies observed within real networks. We apply these observations to evaluate and design communication networks that are specifically optimized for noisy or malicious environments. Combined, joint analysis of biological and computational networks leads to novel algorithms and insights benefiting both fields. PMID:24789562

Adiabatic photo-steering theory in topological insulators.

PubMed

Inoue, Jun-Ichi

2014-12-01

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

Adiabatic photo-steering theory in topological insulators

NASA Astrophysics Data System (ADS)

Inoue, Jun-ichi

2014-12-01

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

The Born-Infeld vortices induced from a generalized Higgs mechanism.

PubMed

Han, Xiaosen

2016-04-01

We construct self-dual Born-Infeld vortices induced from a generalized Higgs mechanism. Two specific models of the theory are of focused interest where the Higgs potential is either of a | ϕ | 4 - or | ϕ | 6 -type. For the | ϕ | 4 -model, we obtain a sharp existence and uniqueness theorem for doubly periodic and planar vortices. For doubly periodic solutions, a necessary and sufficient condition for the existence is explicitly derived in terms of the vortex number, the Born-Infeld parameter, and the size of the periodic lattice domain. For the | ϕ | 6 -model, we show that both topological and non-topological vortices are present. This new phenomenon distinguishes the model from the classical Born-Infeld-Higgs theory studied earlier in the literature. A series of results regarding doubly periodic, topological, and non-topological vortices in the | ϕ | 6 -model are also established.

The precedence of topological change over top-down attention in masked priming.

PubMed

Huang, Yan; Zhou, Tiangang; Chen, Lin

2011-10-14

Recent data indicate that unconscious masked priming can be mediated by top-down attentional set, so that priming effects of congruence between a masked prime and a subsequent probe vanish when the congruence ceases to be task relevant. Here, we show that, while the attentional set determines masked priming for color and orientation features, it does not fully determine priming based on the topological properties of stimuli. Specifically, across a series of different choice-RT tasks, we find that topological congruence between prime and probe stimuli affects RTs for the probes even when other stimulus information (e.g., color or orientation) is required for the response, whereas congruence priming effects of color or orientation occur only when these features are response relevant. Our results suggest that changes in topological properties take precedence over task-directed top-down attentional modulation in masked priming.

The Born–Infeld vortices induced from a generalized Higgs mechanism

PubMed Central

2016-01-01

We construct self-dual Born–Infeld vortices induced from a generalized Higgs mechanism. Two specific models of the theory are of focused interest where the Higgs potential is either of a |ϕ|4- or |ϕ|6-type. For the |ϕ|4-model, we obtain a sharp existence and uniqueness theorem for doubly periodic and planar vortices. For doubly periodic solutions, a necessary and sufficient condition for the existence is explicitly derived in terms of the vortex number, the Born–Infeld parameter, and the size of the periodic lattice domain. For the |ϕ|6-model, we show that both topological and non-topological vortices are present. This new phenomenon distinguishes the model from the classical Born–Infeld–Higgs theory studied earlier in the literature. A series of results regarding doubly periodic, topological, and non-topological vortices in the |ϕ|6-model are also established. PMID:27274694

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.

Quon 3D language for quantum information

PubMed Central

Liu, Zhengwei; Wozniakowski, Alex; Jaffe, Arthur M.

2017-01-01

We present a 3D topological picture-language for quantum information. Our approach combines charged excitations carried by strings, with topological properties that arise from embedding the strings in the interior of a 3D manifold with boundary. A quon is a composite that acts as a particle. Specifically, a quon is a hemisphere containing a neutral pair of open strings with opposite charge. We interpret multiquons and their transformations in a natural way. We obtain a type of relation, a string–genus “joint relation,” involving both a string and the 3D manifold. We use the joint relation to obtain a topological interpretation of the C∗-Hopf algebra relations, which are widely used in tensor networks. We obtain a 3D representation of the controlled NOT (CNOT) gate that is considerably simpler than earlier work, and a 3D topological protocol for teleportation. PMID:28167790

Supersymmetric extensions of K field theories

NASA Astrophysics Data System (ADS)

Adam, C.; Queiruga, J. M.; Sanchez-Guillen, J.; Wereszczynski, A.

2012-02-01

We review the recently developed supersymmetric extensions of field theories with non-standard kinetic terms (so-called K field theories) in two an three dimensions. Further, we study the issue of topological defect formation in these supersymmetric theories. Specifically, we find supersymmetric K field theories which support topological kinks in 1+1 dimensions as well as supersymmetric extensions of the baby Skyrme model for arbitrary nonnegative potentials in 2+1 dimensions.

Multilayer Joint Gait-Pose Manifolds for Human Gait Motion Modeling.

PubMed

Ding, Meng; Fan, Guolian

2015-11-01

We present new multilayer joint gait-pose manifolds (multilayer JGPMs) for complex human gait motion modeling, where three latent variables are defined jointly in a low-dimensional manifold to represent a variety of body configurations. Specifically, the pose variable (along the pose manifold) denotes a specific stage in a walking cycle; the gait variable (along the gait manifold) represents different walking styles; and the linear scale variable characterizes the maximum stride in a walking cycle. We discuss two kinds of topological priors for coupling the pose and gait manifolds, i.e., cylindrical and toroidal, to examine their effectiveness and suitability for motion modeling. We resort to a topologically-constrained Gaussian process (GP) latent variable model to learn the multilayer JGPMs where two new techniques are introduced to facilitate model learning under limited training data. First is training data diversification that creates a set of simulated motion data with different strides. Second is the topology-aware local learning to speed up model learning by taking advantage of the local topological structure. The experimental results on the Carnegie Mellon University motion capture data demonstrate the advantages of our proposed multilayer models over several existing GP-based motion models in terms of the overall performance of human gait motion modeling.

Topological Insulators: A New Platform for Fundamental Science and Applications

NASA Astrophysics Data System (ADS)

Bansil, Arun

2013-03-01

Topological insulators constitute a new phase of quantum matter whose recent discovery has focused world-wide attention on wide-ranging phenomena in materials driven by spin-orbit coupling effects well beyond their traditional role in determining magnetic properties. I will discuss how by exploiting electronic structure techniques we have been able to predict and understand the characteristics of many new classes of binary, ternary and quaternary topologically interesting systems. The flexibility of chemical, structural and magnetic parameters so obtained is the key ingredient for exploring fundamental science questions, including novel spin-textures and exotic superconducting states, as well as for the realization of multi-functional topological devices for thermoelectric, spintronics, information processing and other applications. I will also highlight new insights that have been enabled through our material-specific modeling of angle-resolved photoemission (ARPES) and scanning tunneling (STS) spectroscopies of topological surface states, including effects of the photoemission and tunneling matrix element, which is well-known to be important for a robust interpretation of various highly resolved spectroscopies. Work supported by the Materials Science & Engineering Division, Basic Energy Sciences, U. S. D. O. E.

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

PubMed Central

Guo, Ya; Xu, Quan; Canzio, Daniele; Shou, Jia; Li, Jinhuan; Gorkin, David U.; Jung, Inkyung; Wu, Haiyang; Zhai, Yanan; Tang, Yuanxiao; Lu, Yichao; Wu, Yonghu; Jia, Zhilian; Li, Wei; Zhang, Michael Q.; Ren, Bing; Krainer, Adrian R.; Maniatis, Tom; Wu, Qiang

2015-01-01

SUMMARY CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters, and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. The findings reveal how 3D chromosome architecture can be encoded by genome sequence. PMID:26276636

A novel algorithm using an orthotropic material model for topology optimization

NASA Astrophysics Data System (ADS)

Tong, Liyong; Luo, Quantian

2017-09-01

This article presents a novel algorithm for topology optimization using an orthotropic material model. Based on the virtual work principle, mathematical formulations for effective orthotropic material properties of an element containing two materials are derived. An algorithm is developed for structural topology optimization using four orthotropic material properties, instead of one density or area ratio, in each element as design variables. As an illustrative example, minimum compliance problems for linear and nonlinear structures are solved using the present algorithm in conjunction with the moving iso-surface threshold method. The present numerical results reveal that: (1) chequerboards and single-node connections are not present even without filtering; (2) final topologies do not contain large grey areas even using a unity penalty factor; and (3) the well-known numerical issues caused by low-density material when considering geometric nonlinearity are resolved by eliminating low-density elements in finite element analyses.

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.

Topological RPdBi half-Heusler semimetals: A new family of noncentrosymmetric magnetic superconductors.

PubMed

Nakajima, Yasuyuki; Hu, Rongwei; Kirshenbaum, Kevin; Hughes, Alex; Syers, Paul; Wang, Xiangfeng; Wang, Kefeng; Wang, Renxiong; Saha, Shanta R; Pratt, Daniel; Lynn, Jeffrey W; Paglione, Johnpierre

2015-06-01

We report superconductivity and magnetism in a new family of topological semimetals, the ternary half-Heusler compound RPdBi (R: rare earth). In this series, tuning of the rare earth f-electron component allows for simultaneous control of both lattice density via lanthanide contraction and the strength of magnetic interaction via de Gennes scaling, allowing for a unique tuning of the normal-state band inversion strength, superconducting pairing, and magnetically ordered ground states. Antiferromagnetism with ordering vector (½,½,½) occurs below a Néel temperature that scales with de Gennes factor dG, whereas a superconducting transition is simultaneously supressed with increasing dG. With superconductivity appearing in a system with noncentrosymmetric crystallographic symmetry, the possibility of spin-triplet Cooper pairing with nontrivial topology analogous to that predicted for the normal-state electronic structure provides a unique and rich opportunity to realize both predicted and new exotic excitations in topological materials.

Topological Constraints and Their Conformational Entropic Penalties on RNA Folds.

PubMed

Mak, Chi H; Phan, Ethan N H

2018-05-08

Functional RNAs can fold into intricate structures using a number of different secondary and tertiary structural motifs. Many factors contribute to the overall free energy of the target fold. This study aims at quantifying the entropic costs coming from the loss of conformational freedom when the sugar-phosphate backbone is subjected to constraints imposed by secondary and tertiary contacts. Motivated by insights from topology theory, we design a diagrammatic scheme to represent different types of RNA structures so that constraints associated with a folded structure may be segregated into mutually independent subsets, enabling the total conformational entropy loss to be easily calculated as a sum of independent terms. We used high-throughput Monte Carlo simulations to simulate large ensembles of single-stranded RNA sequences in solution to validate the assumptions behind our diagrammatic scheme, examining the entropic costs for hairpin initiation and formation of many multiway junctions. Our diagrammatic scheme aids in the factorization of secondary/tertiary constraints into distinct topological classes and facilitates the discovery of interrelationships among multiple constraints on RNA folds. This perspective, which to our knowledge is novel, leads to useful insights into the inner workings of some functional RNA sequences, demonstrating how they might operate by transforming their structures among different topological classes. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantum Hall effect in dual gated BiSbTeSe2 topological insulator

NASA Astrophysics Data System (ADS)

Chong, Su Kong; Han, Kyu Bum; Nagaoka, Akira; Harmer, Jared; Tsuchikawa, Ryuichi; Sparks, Taylor D.; Deshpande, Vikram V.

The discovery of topological insulators (TIs) has expanded the family of Dirac materials and enables the probing of exotic matter such as Majorana fermions and magnetic monopoles. Different from conventional 2D electron gas, 3D TIs exhibit a gapped insulating bulk and gapless topological surface states as a result of the strong spin-orbit coupling. BiSbTeSe2 is also known to be a 3D TI with a large intrinsic bulk gap of about 0.3 eV and a single Dirac cone surface state. The highly bulk insulating BiSbTeSe2 permits surface dominated conduction, which is an ideal system for the study of quantum Hall effect (QHE). Due to the spin-momentum locking, the Dirac fermions at the topological surface states have a degeneracy of one. In the QH regime, the Hall conductance is quantized to (n + 1 / 2) e2 / h , where n is an integer and the factor of half is related to Berry curvature. In this work, we study the QHE 3D TI using a dual gated BiSbTeSe2 device. By tuning the chemical potentials on top and bottom surfaces, integer QHE with Landau filling factors, ν = 0, +/-1, and +/-2 are observed.

Quantum transport of two-species Dirac fermions in dual-gated three-dimensional topological insulators

DOE PAGES

Xu, Yang; Miotkowski, Ireneusz; Chen, Yong P.

2016-05-04

Topological insulators are a novel class of quantum matter with a gapped insulating bulk, yet gapless spin-helical Dirac fermion conducting surface states. Here, we report local and non-local electrical and magneto transport measurements in dual-gated BiSbTeSe 2 thin film topological insulator devices, with conduction dominated by the spatially separated top and bottom surfaces, each hosting a single species of Dirac fermions with independent gate control over the carrier type and density. We observe many intriguing quantum transport phenomena in such a fully tunable two-species topological Dirac gas, including a zero-magnetic-field minimum conductivity close to twice the conductance quantum at themore » double Dirac point, a series of ambipolar two-component half-integer Dirac quantum Hall states and an electron-hole total filling factor zero state (with a zero-Hall plateau), exhibiting dissipationless (chiral) and dissipative (non-chiral) edge conduction, respectively. As a result, such a system paves the way to explore rich physics, ranging from topological magnetoelectric effects to exciton condensation.« less

Topological analysis of long-chain branching patterns in polyolefins.

PubMed

Bonchev, D; Markel, E; Dekmezian, A

2001-01-01

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

Effects of topologies on signal propagation in feedforward networks

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Effects of topologies on signal propagation in feedforward networks.

PubMed

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

2018-01-01

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

Engineering hybrid epitaxial InAsSb/Al nanowires for stronger topological protection

NASA Astrophysics Data System (ADS)

Sestoft, Joachim E.; Kanne, Thomas; Gejl, Aske Nørskov; von Soosten, Merlin; Yodh, Jeremy S.; Sherman, Daniel; Tarasinski, Brian; Wimmer, Michael; Johnson, Erik; Deng, Mingtang; Nygârd, Jesper; Jespersen, Thomas Sand; Marcus, Charles M.; Krogstrup, Peter

2018-04-01

The combination of strong spin-orbit coupling, large g factors, and the coupling to a superconductor can be used to create a topologically protected state in a semiconductor nanowire. Here we report on growth and characterization of hybrid epitaxial InAsSb/Al nanowires, with varying composition and crystal structure. We find the strongest spin-orbit interaction at intermediate compositions in zinc-blende InAs1 -xSbx nanowires, exceeding that of both InAs and InSb materials, confirming recent theoretical studies. We show that the epitaxial InAsSb/Al interface allows for a hard induced superconducting gap and 2 e transport in Coulomb charging experiments, similarly to experiments on InAs/Al and InSb/Al materials, and find measurements consistent with topological phase transitions at low magnetic fields due to large effective g factors. Finally we present a method to grow pure wurtzite InAsSb nanowires which are predicted to exhibit even stronger spin-orbit coupling than the zinc-blende structure.

Consequences of population topology for studying gene flow using link-based landscape genetic methods.

PubMed

van Strien, Maarten J

2017-07-01

Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link-based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link-based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link-based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link-based landscape genetic studies.

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.

Dual frequency parametric excitation of a nonlinear, multi degree of freedom mechanical amplifier with electronically modified topology

NASA Astrophysics Data System (ADS)

Dolev, A.; Bucher, I.

2018-04-01

Mechanical or electromechanical amplifiers can exploit the high-Q and low noise features of mechanical resonance, in particular when parametric excitation is employed. Multi-frequency parametric excitation introduces tunability and is able to project weak input signals on a selected resonance. The present paper addresses multi degree of freedom mechanical amplifiers or resonators whose analysis and features require treatment of the spatial as well as temporal behavior. In some cases, virtual electronic coupling can alter the given topology of the resonator to better amplify specific inputs. An analytical development is followed by a numerical and experimental sensitivity and performance verifications, illustrating the advantages and disadvantages of such topologies.

Sensitivity and network topology in chemical reaction systems

NASA Astrophysics Data System (ADS)

Okada, Takashi; Mochizuki, Atsushi

2017-08-01

In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved concentrations, which allows us to study any reaction system. We also propose network characteristics quantifying robustness. We compare E. coli metabolic network with randomly rewired networks, and find that the robustness of the E. coli network is significantly higher than that of the random networks.

Investigation of Positron Sticking to the Surfaces of Topological Insulators

NASA Astrophysics Data System (ADS)

Shastry, K.; Joglekar, P. V.; Olenga, A. Y.; Fazleev, N. G.; Weiss, A. H.; Barniellini, B.

2013-03-01

We describe experiments aimed at probing the sticking of positrons to the surfaces of topological insulators. In these experiments, a magnetically beam will be used to deposit positrons at the surface of Bi2Te2Se. The energy spectra and intensities of electrons emitted as a result of Positron Annihilation induced Auger electron Spectroscopy (PAES) provides a distinct element specific signal which can be used to determine if positrons can be trapped efficiently into a surface localized bound state. The experiments are aimed at determining the practicality of using positron annihilation to selectively probe the critically important top most layer of topological insulator system. Welch Y1100, NSF DMR 0907679

Large magnetoresistance dips and perfect spin-valley filter induced by topological phase transitions in silicene

NASA Astrophysics Data System (ADS)

Prarokijjak, Worasak; Soodchomshom, Bumned

2018-04-01

Spin-valley transport and magnetoresistance are investigated in silicene-based N/TB/N/TB/N junction where N and TB are normal silicene and topological barriers. The topological phase transitions in TB's are controlled by electric, exchange fields and circularly polarized light. As a result, we find that by applying electric and exchange fields, four groups of spin-valley currents are perfectly filtered, directly induced by topological phase transitions. Control of currents, carried by single, double and triple channels of spin-valley electrons in silicene junction, may be achievable by adjusting magnitudes of electric, exchange fields and circularly polarized light. We may identify that the key factor behind the spin-valley current filtered at the transition points may be due to zero and non-zero Chern numbers. Electrons that are allowed to transport at the transition points must obey zero-Chern number which is equivalent to zero mass and zero-Berry's curvature, while electrons with non-zero Chern number are perfectly suppressed. Very large magnetoresistance dips are found directly induced by topological phase transition points. Our study also discusses the effect of spin-valley dependent Hall conductivity at the transition points on ballistic transport and reveals the potential of silicene as a topological material for spin-valleytronics.

Network topology and resilience analysis of South Korean power grid

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

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.

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.

Observation of Dirac-like energy band and ring-torus Fermi surface associated with the nodal line in topological insulator CaAgAs

NASA Astrophysics Data System (ADS)

Takane, Daichi; Nakayama, Kosuke; Souma, Seigo; Wada, Taichi; Okamoto, Yoshihiko; Takenaka, Koshi; Yamakawa, Youichi; Yamakage, Ai; Mitsuhashi, Taichi; Horiba, Koji; Kumigashira, Hiroshi; Takahashi, Takashi; Sato, Takafumi

2018-01-01

One of key challenges in current material research is to search for new topological materials with inverted bulk-band structure. In topological insulators, the band inversion caused by strong spin-orbit coupling leads to opening of a band gap in the entire Brillouin zone, whereas an additional crystal symmetry such as point-group and nonsymmorphic symmetries sometimes prohibits the gap opening at/on specific points or line in momentum space, giving rise to topological semimetals. Despite many theoretical predictions of topological insulators/semimetals associated with such crystal symmetries, the experimental realization is still relatively scarce. Here, using angle-resolved photoemission spectroscopy with bulk-sensitive soft-x-ray photons, we experimentally demonstrate that hexagonal pnictide CaAgAs belongs to a new family of topological insulators characterized by the inverted band structure and the mirror reflection symmetry of crystal. We have established the bulk valence-band structure in three-dimensional Brillouin zone, and observed the Dirac-like energy band and ring-torus Fermi surface associated with the line node, where bulk valence and conducting bands cross on a line in the momentum space under negligible spin-orbit coupling. Intriguingly, we found that no other bands cross the Fermi level and therefore the low-energy excitations are solely characterized by the Dirac-like band. CaAgAs provides an excellent platform to study the interplay among low-energy electron dynamics, crystal symmetry, and exotic topological properties.

High power density dc/dc converter: Selection of converter topology

NASA Technical Reports Server (NTRS)

Divan, Deepakraj M.

1990-01-01

The work involved in the identification and selection of a suitable converter topology is described. Three new dc/dc converter topologies are proposed: Phase-Shifted Single Active Bridge DC/DC Converter; Single Phase Dual Active Bridges DC/DC Converter; and Three Phase Dual Active Bridges DC/DC Converter (Topology C). The salient features of these topologies are: (1) All are minimal in structure, i.e., each consists of an input and output bridge, input and output filter and a transformer, all components essential for a high power dc/dc conversion process; (2) All devices of both the bridges can operate under near zero-voltage conditions, making possible a reduction of device switching losses and hence, an increase in switching frequency; (3) All circuits operate at a constant frequency, thus simplifying the task of the magnetic and filter elements; (4) Since, the leakage inductance of the transformer is used as the main current transfer element, problems associated with the diode reverse recovery are eliminated. Also, this mode of operation allows easy paralleling of multiple modules for extending the power capacity of the system; (5) All circuits are least sensitive to parasitic impedances, infact the parasitics are efficently utilized; and (6) The soft switching transitions, result in low electromagnetic interference. A detailed analysis of each topology was carried out. Based on the analysis, the various device and component ratings for each topology operating at an optimum point, and under the given specifications, are tabulated and discussed.

National law enforcement telecommunications network

NASA Technical Reports Server (NTRS)

Reilly, N. B.; Garrison, G. W.; Sohn, R. L.; Gallop, D. L.; Goldstein, B. L.

1975-01-01

Alternative approaches are analyzed to a National Law Enforcement Telecommunications Network (NALECOM) designed to service all state-to-state and state-to-national criminal justice communications traffic needs in the United States. Network topology options were analyzed, and equipment and personnel requirements for each option were defined in accordance with NALECOM functional specifications and design guidelines. Evaluation criteria were developed and applied to each of the options leading to specific conclusions. Detailed treatments of methods for determining traffic requirements, communication line costs, switcher configurations and costs, microwave costs, satellite system configurations and costs, facilities, operations and engineering costs, network delay analysis and network availability analysis are presented. It is concluded that a single regional switcher configuration is the optimum choice based on cost and technical factors. A two-region configuration is competitive. Multiple-region configurations are less competitive due to increasing costs without attending benefits.

On the contributions of topological features to transcriptional regulatory network robustness

PubMed Central

2012-01-01

Background Because biological networks exhibit a high-degree of robustness, a systemic understanding of their architecture and function requires an appraisal of the network design principles that confer robustness. In this project, we conduct a computational study of the contribution of three degree-based topological properties (transcription factor-target ratio, degree distribution, cross-talk suppression) and their combinations on the robustness of transcriptional regulatory networks. We seek to quantify the relative degree of robustness conferred by each property (and combination) and also to determine the extent to which these properties alone can explain the robustness observed in transcriptional networks. Results To study individual properties and their combinations, we generated synthetic, random networks that retained one or more of the three properties with values derived from either the yeast or E. coli gene regulatory networks. Robustness of these networks were estimated through simulation. Our results indicate that the combination of the three properties we considered explains the majority of the structural robustness observed in the real transcriptional networks. Surprisingly, scale-free degree distribution is, overall, a minor contributor to robustness. Instead, most robustness is gained through topological features that limit the complexity of the overall network and increase the transcription factor subnetwork sparsity. Conclusions Our work demonstrates that (i) different types of robustness are implemented by different topological aspects of the network and (ii) size and sparsity of the transcription factor subnetwork play an important role for robustness induction. Our results are conserved across yeast and E Coli, which suggests that the design principles examined are present within an array of living systems. PMID:23194062

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.

PubMed

Hamed, Mohamed; Spaniol, Christian; Nazarieh, Maryam; Helms, Volkhard

2015-07-01

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states

PubMed Central

2014-01-01

Background At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a σ-factor to recognize the genomic location at which the process initiates. Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function. Results Using multiple genome-scale measurements, we elucidated the network of σ-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 σ-factor-specific promoters corresponding to transcription units (TUs), representing an increase of more than 300% over what has been previously reported. The reconstructed network was used to investigate competition between alternative σ-factors (the σ70 and σ38 regulons), confirming the competition model of σ substitution and negative regulation by alternative σ-factors. Comparison with σ-factor binding in Klebsiella pneumoniae showed that transcriptional regulation of conserved genes in closely related species is unexpectedly divergent. Conclusions The reconstructed network reveals the regulatory complexity of the promoter architecture in prokaryotic genomes, and opens a path to the direct determination of the systems biology of their transcriptional regulatory networks. PMID:24461193

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.

Planck 2015 results: XVIII. Background geometry and topology of the Universe

DOE PAGES

Ade, P. A. R.; Aghanim, N.; Arnaud, M.; ...

2016-09-20

We report that maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χ rec), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. Wemore » specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio ΔlnL > -5 relative to a simply-connected flat Planck best-fit model) are: R i > 0.97 χ rec for the T3 cubic torus; and R i > 0.56 χ rec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R i > 0.97 χ rec at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. 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 VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 7.6 × 10 -10 (95% CL).« less

Modulators of heterogeneous protein surface water dynamics

NASA Astrophysics Data System (ADS)

Han, Songi

The hydration water that solvates proteins is a major factor in driving or enabling biological events, including protein-protein and protein-ligand interactions. We investigate the role of the protein surface in modulating the hydration water fluctuations on both the picosecond and nanosecond timescale with an emerging experimental NMR technique known as Overhauser Dynamic Nuclear Polarization (ODNP). We carry out site-specific ODNP measurements of the hydration water fluctuations along the surface of Chemotaxis Y (CheY), and correlate the measured fluctuations to hydropathic and topological properties of the CheY surface as derived from molecular dynamics (MD) simulation. Furthermore, we compare hydration water fluctuations measured on the CheY surface to that of other globular proteins, as well as intrinsically disordered proteins, peptides, and liposome surfaces to systematically test characteristic effects of the biomolecular surface on the hydration water dynamics. Our results suggest that the labile (ps) hydration water fluctuations are modulated by the chemical nature of the surface, while the bound (ns) water fluctuations are present on surfaces that feature a rough topology and chemical heterogeneity such as the surface of a folded and structured protein. In collaboration with: Ryan Barnes, Dept of Chemistry and Biochemistry, University of California Santa Barbara

A model for evolution of overlapping community networks

NASA Astrophysics Data System (ADS)

Karan, Rituraj; Biswal, Bibhu

2017-05-01

A model is proposed for the evolution of network topology in social networks with overlapping community structure. Starting from an initial community structure that is defined in terms of group affiliations, the model postulates that the subsequent growth and loss of connections is similar to the Hebbian learning and unlearning in the brain and is governed by two dominant factors: the strength and frequency of interaction between the members, and the degree of overlap between different communities. The temporal evolution from an initial community structure to the current network topology can be described based on these two parameters. It is possible to quantify the growth occurred so far and predict the final stationary state to which the network is likely to evolve. Applications in epidemiology or the spread of email virus in a computer network as well as finding specific target nodes to control it are envisaged. While facing the challenge of collecting and analyzing large-scale time-resolved data on social groups and communities one faces the most basic questions: how do communities evolve in time? This work aims to address this issue by developing a mathematical model for the evolution of community networks and studying it through computer simulation.

The N-Terminal Amphipathic Helix of the Topological Specificity Factor MinE Is Associated with Shaping Membrane Curvature

PubMed Central

Shih, Yu-Ling; Huang, Kai-Fa; Lai, Hsin-Mei; Liao, Jiahn-Haur; Lee, Chai-Siah; Chang, Chiao-Min; Mak, Huey-Ming; Hsieh, Cheng-Wei; Lin, Chu-Chi

2011-01-01

Pole-to-pole oscillations of the Min proteins in Escherichia coli are required for the proper placement of the division septum. Direct interaction of MinE with the cell membrane is critical for the dynamic behavior of the Min system. In vitro, this MinE-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. Here we report that MinE-induced membrane deformation involves the formation of an amphipathic helix of MinE2–9, which, together with the adjacent basic residues, function as membrane anchors. Biochemical evidence suggested that the membrane association induces formation of the helix, with the helical face, consisting of A2, L3, and F6, inserted into the membrane. Insertion of this helix into the cell membrane can influence local membrane curvature and lead to drastic changes in membrane topology. Accordingly, MinE showed characteristic features of protein-induced membrane tubulation and lipid clustering in in vitro reconstituted systems. In conclusion, MinE shares common protein signatures with a group of membrane trafficking proteins in eukaryotic cells. These MinE signatures appear to affect membrane curvature. PMID:21738659

Symmetry breaking: a tool to unveil the topology of chaotic scattering with three degrees of freedom

NASA Astrophysics Data System (ADS)

Jung, Christof; Zapfe, W. P. Karel; Merlo, Olivier; Seligman, T. H.

2010-12-01

We shall use symmetry breaking as a tool to attack the problem of identifying the topology of chaotic scatteruing with more then two degrees of freedom. specifically we discuss the structure of the homoclinic/heteroclinic tangle and the connection between the chaotic invariant set, the scattering functions and the singularities in the cross section for a class of scattering systems with one open and two closed degrees of freedom.

Symmetry breaking: a tool to unveil the topology of chaotic scattering with three degrees of freedom

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

Jung, Christof; Zapfe, W. P. Karel; Seligman, T. H.

2010-12-23

We shall use symmetry breaking as a tool to attack the problem of identifying the topology of chaotic scatteruing with more then two degrees of freedom. specifically we discuss the structure of the homoclinic/heteroclinic tangle and the connection between the chaotic invariant set, the scattering functions and the singularities in the cross section for a class of scattering systems with one open and two closed degrees of freedom.

Towards A Topological Framework for Integrating Semantic Information Sources

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

Joslyn, Cliff A.; Hogan, Emilie A.; Robinson, Michael

2014-09-07

In this position paper we argue for the role that topological modeling principles can play in providing a framework for sensor integration. While used successfully in standard (quantitative) sensors, we are developing this methodology in new directions to make it appropriate specifically for semantic information sources, including keyterms, ontology terms, and other general Boolean, categorical, ordinal, and partially-ordered data types. We illustrate the basics of the methodology in an extended use case/example, and discuss path forward.

Topological Structures in Multiferroics - Domain Walls, Skyrmions and Vortices

DOE PAGES

Seidel, Jan; Vasudevan, Rama K.; Valanoor, Nagarajan

2015-12-15

Topological structures in multiferroic materials have recently received considerable attention because of their potential use as nanoscale functional elements. Their reduced size in conjunction with exotic arrangement of the ferroic order parameter and potential order parameter coupling allows for emergent and unexplored phenomena in condensed matter and functional materials systems. This will lead to exciting new fundamental discoveries as well as application concepts that exploit their response to external stimuli such as mechanical strain, electric and magnetic fields. In this review we capture the current development of this rapidly moving field with specific emphasis on key achievements that have castmore » light on how such topological structures in multiferroic materials systems can be exploited for use in complex oxide nanoelectronics and spintronics.« less

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.

A topological extension of GR: Black holes induce dark energy

NASA Astrophysics Data System (ADS)

Spaans, M.

2013-02-01

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

Stock market network’s topological stability: Evidence from planar maximally filtered graph and minimal spanning tree

NASA Astrophysics Data System (ADS)

Yan, Xin-Guo; Xie, Chi; Wang, Gang-Jin

2015-08-01

We study the topological stability of stock market network by investigating the topological robustness, namely the ability of the network to resist structural or topological changes. The stock market network is extracted by minimal spanning tree (MST) and planar maximally filtered graph (PMFG). We find that the specific delisting thresholds of the listed companies exist in both MST and PMFG networks. In comparison with MST, PMFG provides more information and is better for the aim of exploring stock market network’s robustness. The PMFG before the US sub-prime crisis (i.e., from June 2005 to May 2007) has a stronger robustness against the intentional topological damage than the other two sub-periods (i.e., from June 2007 to May 2009 and from June 2009 to May 2011). We also find that the nonfractal property exists in MSTs of S&P 500, i.e., the highly connected nodes link with each other directly, which indicates that the MSTs are vulnerable to the removal of such important nodes. Moreover, the financial institutions and high technology companies are important in maintaining the stability of S&P 500 network.

Modes of Interaction between Individuals Dominate the Topologies of Real World Networks

PubMed Central

Lee, Insuk; Kim, Eiru; Marcotte, Edward M.

2015-01-01

We find that the topologies of real world networks, such as those formed within human societies, by the Internet, or among cellular proteins, are dominated by the mode of the interactions considered among the individuals. Specifically, a major dichotomy in previously studied networks arises from modeling networks in terms of pairwise versus group tasks. The former often intrinsically give rise to scale-free, disassortative, hierarchical networks, whereas the latter often give rise to single- or broad-scale, assortative, nonhierarchical networks. These dependencies explain contrasting observations among previous topological analyses of real world complex systems. We also observe this trend in systems with natural hierarchies, in which alternate representations of the same networks, but which capture different levels of the hierarchy, manifest these signature topological differences. For example, in both the Internet and cellular proteomes, networks of lower-level system components (routers within domains or proteins within biological processes) are assortative and nonhierarchical, whereas networks of upper-level system components (internet domains or biological processes) are disassortative and hierarchical. Our results demonstrate that network topologies of complex systems must be interpreted in light of their hierarchical natures and interaction types. PMID:25793969

Topological String Theory and Enumerative Geometry

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

Song, Y. S

In this thesis we investigate several problems which have their roots in both topological string theory and enumerative geometry. In the former case, underlying theories are topological field theories, whereas the latter case is concerned with intersection theories on moduli spaces. A permeating theme in this thesis is to examine the close interplay between these two complementary fields of study. The main problems addressed are as follows: In considering the Hurwitz enumeration problem of branched covers of compact connected Riemann surfaces, we completely solve the problem in the case of simple Hurwitz numbers. In addition, utilizing the connection between Hurwitzmore » numbers and Hodge integrals, we derive a generating function for the latter on the moduli space {bar M}{sub g,2} of 2-pointed, genus-g Deligne-Mumford stable curves. We also investigate Givental's recent conjecture regarding semisimple Frobenius structures and Gromov-Witten invariants, both of which are closely related to topological field theories; we consider the case of a complex projective line P{sup 1} as a specific example and verify his conjecture at low genera. In the last chapter, we demonstrate that certain topological open string amplitudes can be computed via relative stable morphisms in the algebraic category.« less

From Sensor Networks to Internet of Things. Bluetooth Low Energy, a Standard for This Evolution

PubMed Central

Hortelano, Diego; Olivares, Teresa; Ruiz, M. Carmen; Garrido-Hidalgo, Celia; López, Vicente

2017-01-01

Current sensor networks need to be improved and updated to satisfy new essential requirements of the Internet of Things, where cutting-edge applications will appear. These requirements are: total coverage, zero fails (high performance), scalability and sustainability (hardware and software). We are going to evaluate Bluetooth Low Energy as wireless transmission technology and as the ideal candidate for these improvements, due to its low power consumption, its low cost radio chips and its ability to communicate with users directly, using their smartphones or smartbands. However, this technology is relatively recent, and standard network topologies are not able to fulfil its new requirements. To address these shortcomings, the implementation of other more flexible topologies (as the mesh topology) will be very interesting. After studying it in depth, we have identified certain weaknesses, for example, specific devices are needed to provide network scalability, and the need to choose between high performance or sustainability. In this paper, after presenting the studies carried out on these new technologies, we propose a new packet format and a new BLE mesh topology, with two different configurations: Individual Mesh and Collaborative Mesh. Our results show how this topology improves the scalability, sustainability, coverage and performance. PMID:28216560

From Sensor Networks to Internet of Things. Bluetooth Low Energy, a Standard for This Evolution.

PubMed

Hortelano, Diego; Olivares, Teresa; Ruiz, M Carmen; Garrido-Hidalgo, Celia; López, Vicente

2017-02-14

Current sensor networks need to be improved and updated to satisfy new essential requirements of the Internet of Things, where cutting-edge applications will appear. These requirements are: total coverage, zero fails (high performance), scalability and sustainability (hardware and software). We are going to evaluate Bluetooth Low Energy as wireless transmission technology and as the ideal candidate for these improvements, due to its low power consumption, its low cost radio chips and its ability to communicate with users directly, using their smartphones or smartbands. However, this technology is relatively recent, and standard network topologies are not able to fulfil its new requirements. To address these shortcomings, the implementation of other more flexible topologies (as the mesh topology) will be very interesting. After studying it in depth, we have identified certain weaknesses, for example, specific devices are needed to provide network scalability, and the need to choose between high performance or sustainability. In this paper, after presenting the studies carried out on these new technologies, we propose a new packet format and a new BLE mesh topology, with two different configurations: Individual Mesh and Collaborative Mesh . Our results show how this topology improves the scalability, sustainability, coverage and performance.

Odd-frequency superconducting pairing and subgap density of states at the edge of a two-dimensional topological insulator without magnetism

NASA Astrophysics Data System (ADS)

Cayao, Jorge; Black-Schaffer, Annica M.

2017-10-01

We investigate the emergence and consequences of odd-frequency spin-triplet s -wave pairing in superconducting hybrid junctions at the edge of a two-dimensional topological insulator without any magnetism. More specifically, we consider several different normal-superconductor hybrid systems at the topological insulator edge, where spin-singlet s -wave superconducting pairing is proximity induced from an external conventional superconductor. We perform fully analytical calculations and show that odd-frequency mixed spin-triplet s -wave pairing arises due to the unique spin-momentum locking in the topological insulator edge state and the naturally nonconstant pairing potential profile in hybrid systems. Importantly, we establish a one-to-one correspondence between the local density of states (LDOS) at low energies and the odd-frequency spin-triplet pairing in NS, NSN, and SNS junctions along the topological insulator edge; at interfaces the enhancement in the LDOS can directly be attributed to the contribution of odd-frequency pairing. Furthermore, in SNS junctions we show that the emergence of the zero-energy LDOS peak at the superconducting phase ϕ =π is associated purely with odd-frequency pairing in the middle of the junction.

Detection of topological phase transitions through entropy measurements: The case of germanene

NASA Astrophysics Data System (ADS)

Grassano, D.; Pulci, O.; Shubnyi, V. O.; Sharapov, S. G.; Gusynin, V. P.; Kavokin, A. V.; Varlamov, A. A.

2018-05-01

We propose a characterization tool for studies of the band structure of new materials promising for the observation of topological phase transitions. We show that a specific resonant feature in the entropy per electron dependence on the chemical potential may be considered as a fingerprint of the transition between topological and trivial insulator phases. The entropy per electron in a honeycomb two-dimensional crystal of germanene subjected to the external electric field is obtained from the first-principles calculation of the density of electronic states and the Maxwell relation. We demonstrate that, in agreement with the recent prediction of the analytical model, strong spikes in the entropy per particle dependence on the chemical potential appear at low temperatures. They are observed at the values of the applied bias both below and above the critical value that corresponds to the transition between the topological insulator and trivial insulator phases, whereas the giant resonant feature in the vicinity of the zero chemical potential is strongly suppressed at the topological transition point, in the low-temperature limit. In a wide energy range, the van Hove singularities in the electronic density of states manifest themselves as zeros in the entropy per particle dependence on the chemical potential.

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

Renner, J.; Farbin, A.; Vidal, J. Muñoz

Here, we investigate the potential of using deep learning techniques to reject background events in searches for neutrinoless double beta decay with high pressure xenon time projection chambers capable of detailed track reconstruction. The differences in the topological signatures of background and signal events can be learned by deep neural networks via training over many thousands of events. These networks can then be used to classify further events as signal or background, providing an additional background rejection factor at an acceptable loss of efficiency. The networks trained in this study performed better than previous methods developed based on the usemore » of the same topological signatures by a factor of 1.2 to 1.6, and there is potential for further improvement.« less

Gene network interconnectedness and the generalized topological overlap measure

PubMed Central

Yip, Andy M; Horvath, Steve

2007-01-01

Background Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. [1] can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness. Results We generalize the topological overlap measure from m = 1 step neighborhoods to m ≥ 2 step neighborhoods. This allows us to define the m-th order generalized topological overlap measure (GTOM) by (i) counting the number of m-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis. Conclusion Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The m-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules. PMID:17250769

Whole-lake invasive crayfish removal and qualitative modeling reveal habitat-specific food web topology

DOE PAGES

Hansen, Gretchen J. A.; Tunney, Tyler D.; Winslow, Luke A.; ...

2017-02-10

Patterning of the presence/absence of food web linkages (hereafter topology) is a fundamental characteristic of ecosystems that can influence species responses to perturbations. However, the insight from food web topology into dynamic effects of perturbations on species is potentially hindered because most described topologies represent data integrated across spatial and temporal scales. We conducted a 10-year, whole-lake experiment in which we removed invasive rusty crayfish ( Orconectes rusticus) from a 64-ha north-temperate lake and monitored responses of multiple trophic levels. We compared species responses observed in two sub-habitats to the responses predicted from all topologies of an integrated, literature-informed basemore » food web model of 32 potential links. Out of 4.3 billion possible topologies, only 308,833 (0.0072%) predicted responses that qualitatively matched observed species responses in cobble habitat, and only 12,673 (0.0003%) matched observed responses in sand habitat. Furthermore, when constrained to predictions that both matched observed responses and were highly reliable (i.e., predictions were robust to link strength values), only 5040 (0.0001%) and 140 (0.000003%) topologies were identified for cobble and sand habitats, respectively. A small number of linkages were nearly always present in these valid, reliable networks in sand, while a greater variety of possible network configurations were possible in cobble. Direct links involving invasive rusty crayfish were more important in cobble, while indirect effects involving Lepomis spp. were more important in sand. Importantly, the importance of individual species linkages differed dramatically among cobble and sand sub-habitats within a single lake, even though species composition was identical. Furthermore the true topology of food webs is difficult to determine, constraining topologies to include spatial resolution that matches observed experimental outcomes may reduce possibilities to a small number of plausible alternatives.« less

Whole-lake invasive crayfish removal and qualitative modeling reveal habitat-specific food web topology

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

Hansen, Gretchen J. A.; Tunney, Tyler D.; Winslow, Luke A.

Patterning of the presence/absence of food web linkages (hereafter topology) is a fundamental characteristic of ecosystems that can influence species responses to perturbations. However, the insight from food web topology into dynamic effects of perturbations on species is potentially hindered because most described topologies represent data integrated across spatial and temporal scales. We conducted a 10-year, whole-lake experiment in which we removed invasive rusty crayfish ( Orconectes rusticus) from a 64-ha north-temperate lake and monitored responses of multiple trophic levels. We compared species responses observed in two sub-habitats to the responses predicted from all topologies of an integrated, literature-informed basemore » food web model of 32 potential links. Out of 4.3 billion possible topologies, only 308,833 (0.0072%) predicted responses that qualitatively matched observed species responses in cobble habitat, and only 12,673 (0.0003%) matched observed responses in sand habitat. Furthermore, when constrained to predictions that both matched observed responses and were highly reliable (i.e., predictions were robust to link strength values), only 5040 (0.0001%) and 140 (0.000003%) topologies were identified for cobble and sand habitats, respectively. A small number of linkages were nearly always present in these valid, reliable networks in sand, while a greater variety of possible network configurations were possible in cobble. Direct links involving invasive rusty crayfish were more important in cobble, while indirect effects involving Lepomis spp. were more important in sand. Importantly, the importance of individual species linkages differed dramatically among cobble and sand sub-habitats within a single lake, even though species composition was identical. Furthermore the true topology of food webs is difficult to determine, constraining topologies to include spatial resolution that matches observed experimental outcomes may reduce possibilities to a small number of plausible alternatives.« less

Localization of functional receptor epitopes on the structure of ciliary neurotrophic factor indicates a conserved, function-related epitope topography among helical cytokines.

PubMed

Panayotatos, N; Radziejewska, E; Acheson, A; Somogyi, R; Thadani, A; Hendrickson, W A; McDonald, N Q

1995-06-09

By rational mutagenesis, receptor-specific functional analysis, and visualization of complex formation in solution, we identified individual amino acid side chains involved specifically in the interaction of ciliary neurotrophic factor (CNTF) with CNTFR alpha and not with the beta-components, gp130 and LIFR. In the crystal structure, the side chains of these residues, which are located in helix A, the AB loop, helix B, and helix D, are surface accessible and are clustered in space, thus constituting an epitope for CNTFR alpha. By the same analysis, a partial epitope for gp130 was also identified on the surface of helix A that faces away from the alpha-epitope. Superposition of the CNTF and growth hormone structures showed that the location of these epitopes on CNTF is analogous to the location of the first and second receptor epitopes on the surface of growth hormone. Further comparison with proposed binding sites for alpha- and beta-receptors on interleukin-6 and leukemia inhibitory factor indicated that this epitope topology is conserved among helical cytokines. In each case, epitope I is utilized by the specificity-conferring component, whereas epitopes II and III are used by accessory components. Thus, in addition to a common fold, helical cytokines share a conserved order of receptor epitopes that is function related.

Topological Structures of Gravitational Vacuum as a Factor of Unclustered DM

NASA Astrophysics Data System (ADS)

Burdyuzha, V.; Pacheco, J.; Vereshkov, G.

2003-03-01

Topological structures of gravitational vacuum which could be produced in the result of the first relativistic phase transition or in the result of defect creation of the Universe from "nothing" are discussed. The concrete physical meaning is imparted to the parametrizational noninvariant members of Wheeler -DeWitt equation which may be considered as vacuum topological defects of different dimensions (worm-holes, micromembranes, microstrings and monopoles). After Universe inflation defects smoothed, stretches and broken up. They must be isotropic distributed on background of the expanding Universe. The part of them has survived and now they are perceiving as the structures of Λ -term, quintessence and unclustered dark matter. Mathematical illustration of these processes may be spontaneous breaking of global Lorentz-invariance of quantum geometrodynamics equations.

Influence of film thickness on topology and related magnetic interactions in Fe nanoparticle films

NASA Astrophysics Data System (ADS)

Ausanio, G.; Iannotti, V.; Amoruso, S.; Bruzzese, R.; Wang, X.; Aruta, C.; Arzeo, M.; Lanotte, L.

2013-08-01

Fe nanoparticle (NP)-assembled thin films with different thickness were prepared by femtosecond-pulsed laser deposition using different deposition times. The proper selection of the deposition time allows to control, to a certain degree, the morphology and topology of the deposited Fe nanoparticles (NPs) assembly, fostering non-uniform dense assemblies of NPs, with the consequent reduction of the influence of the exchange interactions on the macroscopic magnetic properties with decreasing thickness. The magnetic behavior of the Fe NP-assembled films with decreasing thickness is characterized by higher coercive field ( H c) values (a factor ≈4.5) and a good compromise between the hysteresis loops squareness and moderate exchange interactions, strongly correlated with the NPs topology.

Two-dimensional symmetry-protected topological orders and their protected gapless edge excitations

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

Chen Xie; Liu Zhengxin; Wen Xiaogang

2011-12-15

Topological insulators in free fermion systems have been well characterized and classified. However, it is not clear in strongly interacting boson or fermion systems what symmetry-protected topological orders exist. In this paper, we present a model in a two-dimensional (2D) interacting spin system with nontrivial onsite Z{sub 2} symmetry-protected topological order. The order is nontrivial because we can prove that the one-dimensional (1D) system on the boundary must be gapless if the symmetry is not broken, which generalizes the gaplessness of Wess-Zumino-Witten model for Lie symmetry groups to any discrete symmetry groups. The construction of this model is related tomore » a nontrivial 3-cocycle of the Z{sub 2} group and can be generalized to any symmetry group. It potentially leads to a complete classification of symmetry-protected topological orders in interacting boson and fermion systems of any dimension. Specifically, this exactly solvable model has a unique gapped ground state on any closed manifold and gapless excitations on the boundary if Z{sub 2} symmetry is not broken. We prove the latter by developing the tool of a matrix product unitary operator to study the nonlocal symmetry transformation on the boundary and reveal the nontrivial 3-cocycle structure of this transformation. Similar ideas are used to construct a 2D fermionic model with onsite Z{sub 2} symmetry-protected topological order.« less

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

NASA Astrophysics Data System (ADS)

Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H.-J.; Castro, C. E.

2016-05-01

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.

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

PubMed Central

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

2013-01-01

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

Experimental observation of the topological structure of exceptional points in an ultrathin hybridized metamaterial

NASA Astrophysics Data System (ADS)

Kang, Ming; Zhu, Weiren; Rukhlenko, Ivan D.

2017-12-01

The exceptional point (EP), which is one of the most important branch-type singularities exclusive to non-Hermitian systems, has been observed recently in various synthetic materials, giving rise to counterintuitive phenomena due to the nontrivial topology of the EP. Here, we present a direct experimental observation of the topological structure of the EPs via the angle-resolved transmission measurement of a hybridized metamaterial. Both eigenvalues and eigenvectors show branch-point singularities in the investigated biparametric space of frequency and incident angle. Importantly, the angle-resolved transmission coefficients provide all the information about the eigenvalues as well as the corresponding eigenvectors in the biparametric space, revealing the nontrivial topological structure of the EP, such as mode switching and the topological phase for a parameter loop encircling the EP. It is shown that the appearance of the EP in the scattering matrix is related directly to the perfect unidirectional transmission and the chirality of the EP corresponds to the maximum or minimum value of the asymmetric factor. Our investigation uncovers the capabilities of metamaterials for exploring the physics of EPs and their potential for having extreme optical properties, which provide potential applications in the spectral band ranging from microwaves to visible frequencies.

Fermionic topological quantum states as tensor networks

NASA Astrophysics Data System (ADS)

Wille, C.; Buerschaper, O.; Eisert, J.

2017-06-01

Tensor network states, and in particular projected entangled pair states, play an important role in the description of strongly correlated quantum lattice systems. They do not only serve as variational states in numerical simulation methods, but also provide a framework for classifying phases of quantum matter and capture notions of topological order in a stringent and rigorous language. The rapid development in this field for spin models and bosonic systems has not yet been mirrored by an analogous development for fermionic models. In this work, we introduce a tensor network formalism capable of capturing notions of topological order for quantum systems with fermionic components. At the heart of the formalism are axioms of fermionic matrix-product operator injectivity, stable under concatenation. Building upon that, we formulate a Grassmann number tensor network ansatz for the ground state of fermionic twisted quantum double models. A specific focus is put on the paradigmatic example of the fermionic toric code. This work shows that the program of describing topologically ordered systems using tensor networks carries over to fermionic models.

WKB solutions of difference equations and reconstruction by the topological recursion

NASA Astrophysics Data System (ADS)

Marchal, Olivier

2018-01-01

The purpose of this article is to analyze the connection between Eynard-Orantin topological recursion and formal WKB solutions of a \\hbar -difference equation: \\Psi(x+\\hbar)=≤ft(e\\hbar\\fracd{dx}\\right) \\Psi(x)=L(x;\\hbar)\\Psi(x) with L(x;\\hbar)\\in GL_2( ({C}(x))[\\hbar]) . In particular, we extend the notion of determinantal formulas and topological type property proposed for formal WKB solutions of \\hbar -differential systems to this setting. We apply our results to a specific \\hbar -difference system associated to the quantum curve of the Gromov-Witten invariants of {P}1 for which we are able to prove that the correlation functions are reconstructed from the Eynard-Orantin differentials computed from the topological recursion applied to the spectral curve y=\\cosh-1\\frac{x}{2} . Finally, identifying the large x expansion of the correlation functions, proves a recent conjecture made by Dubrovin and Yang regarding a new generating series for Gromov-Witten invariants of {P}1 .

Designing patient-specific 3D printed craniofacial implants using a novel topology optimization method.

PubMed

Sutradhar, Alok; Park, Jaejong; Carrau, Diana; Nguyen, Tam H; Miller, Michael J; Paulino, Glaucio H

2016-07-01

Large craniofacial defects require efficient bone replacements which should not only provide good aesthetics but also possess stable structural function. The proposed work uses a novel multiresolution topology optimization method to achieve the task. Using a compliance minimization objective, patient-specific bone replacement shapes can be designed for different clinical cases that ensure revival of efficient load transfer mechanisms in the mid-face. In this work, four clinical cases are introduced and their respective patient-specific designs are obtained using the proposed method. The optimized designs are then virtually inserted into the defect to visually inspect the viability of the design . Further, once the design is verified by the reconstructive surgeon, prototypes are fabricated using a 3D printer for validation. The robustness of the designs are mechanically tested by subjecting them to a physiological loading condition which mimics the masticatory activity. The full-field strain result through 3D image correlation and the finite element analysis implies that the solution can survive the maximum mastication of 120 lb. Also, the designs have the potential to restore the buttress system and provide the structural integrity. Using the topology optimization framework in designing the bone replacement shapes would deliver surgeons new alternatives for rather complicated mid-face reconstruction.

Refining Pathways: A Model Comparison Approach

PubMed Central

Moffa, Giusi; Erdmann, Gerrit; Voloshanenko, Oksana; Hundsrucker, Christian; Sadeh, Mohammad J.; Boutros, Michael; Spang, Rainer

2016-01-01

Cellular signalling pathways consolidate multiple molecular interactions into working models of signal propagation, amplification, and modulation. They are described and visualized as networks. Adjusting network topologies to experimental data is a key goal of systems biology. While network reconstruction algorithms like nested effects models are well established tools of computational biology, their data requirements can be prohibitive for their practical use. In this paper we suggest focussing on well defined aspects of a pathway and develop the computational tools to do so. We adapt the framework of nested effect models to focus on a specific aspect of activated Wnt signalling in HCT116 colon cancer cells: Does the activation of Wnt target genes depend on the secretion of Wnt ligands or do mutations in the signalling molecule β-catenin make this activation independent from them? We framed this question into two competing classes of models: Models that depend on Wnt ligands secretion versus those that do not. The model classes translate into restrictions of the pathways in the network topology. Wnt dependent models are more flexible than Wnt independent models. Bayes factors are the standard Bayesian tool to compare different models fairly on the data evidence. In our analysis, the Bayes factors depend on the number of potential Wnt signalling target genes included in the models. Stability analysis with respect to this number showed that the data strongly favours Wnt ligands dependent models for all realistic numbers of target genes. PMID:27248690

Self-determined mechanisms in complex networks

NASA Astrophysics Data System (ADS)

Liu, Yang; Yuan, Jian; Shan, Xiuming; Ren, Yong; Ma, Zhengxin

2008-03-01

Self-organized networks are pervasive in communication systems such as the Internet, overlay networks, peer-to-peer networks, and cluster-based services. These networks evolve into complex topologies, under specific driving forces, i.e. user demands, technological innovations, design objectives and so on. Our study focuses on the driving forces behind individual evolutions of network components, and their stimulation and domination to the self-organized networks which are defined as self-determined mechanisms in this paper. Understanding forces underlying the evolution of networks should enable informed design decisions and help to avoid unwanted surprises, such as congestion collapse. A case study on the macroscopic evolution of the Internet topology of autonomous systems under a specific driving force is then presented. Using computer simulations, it is found that the power-law degree distribution can originate from a connection preference to larger numbers of users, and that the small-world property can be caused by rapid growth in the number of users. Our results provide a new feasible perspective to understand intrinsic fundamentals in the topological evolution of complex networks.

Induced unconventional superconductivity on the surface states of Bi2Te3 topological insulator.

PubMed

Charpentier, Sophie; Galletti, Luca; Kunakova, Gunta; Arpaia, Riccardo; Song, Yuxin; Baghdadi, Reza; Wang, Shu Min; Kalaboukhov, Alexei; Olsson, Eva; Tafuri, Francesco; Golubev, Dmitry; Linder, Jacob; Bauch, Thilo; Lombardi, Floriana

2017-12-08

Topological superconductivity is central to a variety of novel phenomena involving the interplay between topologically ordered phases and broken-symmetry states. The key ingredient is an unconventional order parameter, with an orbital component containing a chiral p x  + ip y wave term. Here we present phase-sensitive measurements, based on the quantum interference in nanoscale Josephson junctions, realized by using Bi 2 Te 3 topological insulator. We demonstrate that the induced superconductivity is unconventional and consistent with a sign-changing order parameter, such as a chiral p x  + ip y component. The magnetic field pattern of the junctions shows a dip at zero externally applied magnetic field, which is an incontrovertible signature of the simultaneous existence of 0 and π coupling within the junction, inherent to a non trivial order parameter phase. The nano-textured morphology of the Bi 2 Te 3 flakes, and the dramatic role played by thermal strain are the surprising key factors for the display of an unconventional induced order parameter.

Topological π Junctions from Crossed Andreev Reflection in the Quantum Hall Regime

NASA Astrophysics Data System (ADS)

Finocchiaro, F.; Guinea, F.; San-Jose, P.

2018-03-01

We consider a two-dimensional electron gas (2DEG) in the quantum Hall regime in the presence of a Zeeman field, with the Fermi level tuned to a filling factor of ν =1 . We show that, in the presence of spin-orbit coupling, contacting the 2DEG with a narrow strip of an s -wave superconductor produces a topological superconducting gap along the contact as a result of crossed Andreev reflection (CAR) processes across the strip. The sign of the topological gap, controlled by the CAR amplitude, depends periodically on the Fermi wavelength and strip width and can be externally tuned. An interface between two halves of a long strip with topological gaps of opposite sign implements a robust π junction, hosting a pair of Majorana zero modes that do not split despite their overlap. We show that such a configuration can be exploited to perform protected non-Abelian tunnel-braid operations without any fine tuning.

Quantifying climatic controls on river network topology across scales

NASA Astrophysics Data System (ADS)

Ranjbar Moshfeghi, S.; Hooshyar, M.; Wang, D.; Singh, A.

2017-12-01

Branching structure of river networks is an important topologic and geomorphologic feature that depends on several factors (e.g. climate, tectonic). However, mechanisms that cause these drainage patterns in river networks are poorly understood. In this study, we investigate the effects of varying climatic forcing on river network topology and geomorphology. For this, we select 20 catchments across the United States with different long-term climatic conditions quantified by climate aridity index (AI), defined here as the ratio of mean annual potential evaporation (Ep) to precipitation (P), capturing variation in runoff and vegetation cover. The river networks of these catchments are extracted, using a curvature-based method, from high-resolution (1 m) digital elevation models and several metrics such as drainage density, branching angle, and width functions are computed. We also use a multiscale-entropy-based approach to quantify the topologic irregularity and structural richness of these river networks. Our results reveal systematic impacts of climate forcing on the structure of river networks.

Topological Reorganization of the Default Mode Network in Severe Male Obstructive Sleep Apnea

PubMed Central

Chen, Liting; Fan, Xiaole; Li, Haijun; Ye, Chenglong; Yu, Honghui; Gong, Honghan; Zeng, Xianjun; Peng, Dechang; Yan, Liping

2018-01-01

Impaired spontaneous regional activity and altered topology of the brain network have been observed in obstructive sleep apnea (OSA). However, the mechanisms of disrupted functional connectivity (FC) and topological reorganization of the default mode network (DMN) in patients with OSA remain largely unknown. We explored whether the FC is altered within the DMN and examined topological changes occur in the DMN in patients with OSA using a graph theory analysis of resting-state functional magnetic resonance imaging data and evaluated the relationship between neuroimaging measures and clinical variables. Resting-state data were obtained from 46 male patients with untreated severe OSA and 46 male good sleepers (GSs). We specifically selected 20 DMN subregions to construct the DMN architecture. The disrupted FC and topological properties of the DMN in patients with OSA were characterized using graph theory. The OSA group showed significantly decreased FC of the anterior–posterior DMN and within the posterior DMN, and also showed increased FC within the DMN. The DMN exhibited small-world topology in both OSA and GS groups. Compared to GSs, patients with OSA showed a decreased clustering coefficient (Cp) and local efficiency, and decreased nodal centralities in the left posterior cingulate cortex and dorsal medial prefrontal cortex, and increased nodal centralities in the ventral medial prefrontal cortex and the right parahippocampal cortex. Finally, the abnormal DMN FC was significantly related to Cp, path length, global efficiency, and Montreal cognitive assessment score. OSA showed disrupted FC within the DMN, which may have contributed to the observed topological reorganization. These findings may provide further evidence of cognitive deficits in patients with OSA.

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

PubMed Central

Ganguly, Debabani; Zhang, Weihong; Chen, Jianhan

2013-01-01

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via “electrostatic steering” and at the same time promote “folding-competent” encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation. PMID:24278008

Complexity of chemical graphs in terms of size, branching, and cyclicity.

PubMed

Balaban, A T; Mills, D; Kodali, V; Basak, S C

2006-08-01

Chemical graph complexity depends on many factors, but the main ones are size, branching, and cyclicity. Some molecular descriptors embrace together all these three parameters, which cannot then be disentangled. The topological index J (and its refinements that include accounting for bond multiplicity and the presence of heteroatoms) was designed to compensate in a significant measure for graph size and cyclicity, and therefore it contains information mainly on branching. In order to separate these factors, two new indices (F and G) related with J are proposed, which allow to group together graphs with the same size into families of constitutional formulas differing in their branching and cyclicity. A comparison with other topological indices revealed that a few other topological indices vary similarly with index G, notably DN2S4 among the triplet indices, and TOTOP among the indices contained in the Molconn-Z program. This comparison involved all possible chemical graphs (i.e. connected planar graphs with vertex degrees not higher than four) with four through six vertices, and all possible alkanes with four through nine carbon atoms.

Dynamical behaviours and control measures of rumour-spreading model with consideration of network topology

NASA Astrophysics Data System (ADS)

Zhu, Linhe; Zhao, Hongyong

2017-07-01

A series of online rumours have seriously influenced the normal production and living of people. This paper aims to study the combined impact of psychological factor, propagation delay, network topology and control strategy on rumour diffusion over the online social networks. Based on an online social network, which is seen as a scale-free network, we model the spread of rumours by using a delayed SIS (Susceptible and Infected) epidemic-like model with consideration of psychological factor and network topology. First, through theoretical analysis, we illustrate the boundedness of the density of rumour-susceptible individuals and rumour-infected individuals. Second, we obtain the basic reproduction number R0 and prove the stability of the non-rumour equilibrium point and the rumour-spreading equilibrium point. Third, control strategies, such as uniform immunisation control, proportional immunisation control, targeted immunisation control and optimum control, are put forward to restrain rumour diffusion. Meanwhile, we have compared the differences of these control strategies. Finally, some representative numerical simulations are performed to verify the theoretical analysis results.

The Coordinated Positive Regulation of Topoisomerase Genes Maintains Topological Homeostasis in Streptomyces coelicolor

PubMed Central

Gongerowska, Martyna; Gutkowski, Paweł; Zakrzewska-Czerwińska, Jolanta; Jakimowicz, Dagmara

2016-01-01

ABSTRACT Maintaining an optimal level of chromosomal supercoiling is critical for the progression of DNA replication and transcription. Moreover, changes in global supercoiling affect the expression of a large number of genes and play a fundamental role in adapting to stress. Topoisomerase I (TopA) and gyrase are key players in the regulation of bacterial chromosomal topology through their respective abilities to relax and compact DNA. Soil bacteria such as Streptomyces species, which grow as branched, multigenomic hyphae, are subject to environmental stresses that are associated with changes in chromosomal topology. The topological fluctuations modulate the transcriptional activity of a large number of genes and in Streptomyces are related to the production of antibiotics. To better understand the regulation of topological homeostasis in Streptomyces coelicolor, we investigated the interplay between the activities of the topoisomerase-encoding genes topA and gyrBA. We show that the expression of both genes is supercoiling sensitive. Remarkably, increased chromosomal supercoiling induces the topA promoter but only slightly influences gyrBA transcription, while DNA relaxation affects the topA promoter only marginally but strongly activates the gyrBA operon. Moreover, we showed that exposure to elevated temperatures induces rapid relaxation, which results in changes in the levels of both topoisomerases. We therefore propose a unique mechanism of S. coelicolor chromosomal topology maintenance based on the supercoiling-dependent stimulation, rather than repression, of the transcription of both topoisomerase genes. These findings provide important insight into the maintenance of topological homeostasis in an industrially important antibiotic producer. IMPORTANCE We describe the unique regulation of genes encoding two topoisomerases, topoisomerase I (TopA) and gyrase, in a model Streptomyces species. Our studies demonstrate the coordination of topoisomerase gene regulation, which is crucial for maintenance of topological homeostasis. Streptomyces species are producers of a plethora of biologically active secondary metabolites, including antibiotics, antitumor agents, and immunosuppressants. The significant regulatory factor controlling the secondary metabolism is the global chromosomal topology. Thus, the investigation of chromosomal topology homeostasis in Streptomyces strains is crucial for their use in industrial applications as producers of secondary metabolites. PMID:27551021

Segmentation of radiologic images with self-organizing maps: the segmentation problem transformed into a classification task

NASA Astrophysics Data System (ADS)

Pelikan, Erich; Vogelsang, Frank; Tolxdorff, Thomas

1996-04-01

The texture-based segmentation of x-ray images of focal bone lesions using topological maps is introduced. Texture characteristics are described by image-point correlation of feature images to feature vectors. For the segmentation, the topological map is labeled using an improved labeling strategy. Results of the technique are demonstrated on original and synthetic x-ray images and quantified with the aid of quality measures. In addition, a classifier-specific contribution analysis is applied for assessing the feature space.

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).

Network evolution model for supply chain with manufactures as the core.

PubMed

Fang, Haiyang; Jiang, Dali; Yang, Tinghong; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model.

Network evolution model for supply chain with manufactures as the core

PubMed Central

Jiang, Dali; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model. PMID:29370201

Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by Protein-DNA Photo-Cross-Linking

PubMed Central

Douziech, Maxime; Coin, Frédéric; Chipoulet, Jean-Marc; Arai, Yoko; Ohkuma, Yoshiaki; Egly, Jean-Marc; Coulombe, Benoit

2000-01-01

The p89/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNAPII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact, which is in the region where promoter melting occurs (positions −9 to +2), requires tight DNA wrapping around RNAPII. The addition of hydrolyzable ATP tethers the template strand at positions −5 and +1 to RNAPII subunits. A mutation in p89/XPB found in a xeroderma pigmentosum patient impairs the ability of TFIIH to associate correctly with the complex and thereby melt promoter DNA. A model for open complex formation is proposed. PMID:11027286

Topology of correlation-based minimal spanning trees in real and model markets

NASA Astrophysics Data System (ADS)

Bonanno, Giovanni; Caldarelli, Guido; Lillo, Fabrizio; Mantegna, Rosario N.

2003-10-01

We compare the topological properties of the minimal spanning tree obtained from a large group of stocks traded at the New York Stock Exchange during a 12-year trading period with the one obtained from surrogated data simulated by using simple market models. We find that the empirical tree has features of a complex network that cannot be reproduced, even as a first approximation, by a random market model and by the widespread one-factor model.

Universal features in the genome-level evolution of protein domains.

PubMed

Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

2009-01-01

Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.

Topologically protected modes in non-equilibrium stochastic systems.

PubMed

Murugan, Arvind; Vaikuntanathan, Suriyanarayanan

2017-01-10

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

Research on Collection System Optimal Design of Wind Farm with Obstacles

NASA Astrophysics Data System (ADS)

Huang, W.; Yan, B. Y.; Tan, R. S.; Liu, L. F.

2017-05-01

To the collection system optimal design of offshore wind farm, the factors considered are not only the reasonable configuration of the cable and switch, but also the influence of the obstacles on the topology design of the offshore wind farm. This paper presents a concrete topology optimization algorithm with obstacles. The minimal area rectangle encasing box of the obstacle is obtained by using the method of minimal area encasing box. Then the optimization algorithm combining the advantages of Dijkstra algorithm and Prim algorithm is used to gain the scheme of avoidance obstacle path planning. Finally a fuzzy comprehensive evaluation model based on the analytic hierarchy process is constructed to compare the performance of the different topologies. Case studies demonstrate the feasibility of the proposed algorithm and model.

DNA topology and transcription

PubMed Central

Kouzine, Fedor; Levens, David; Baranello, Laura

2014-01-01

Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

Background rejection in NEXT using deep neural networks

DOE PAGES

Renner, J.; Farbin, A.; Vidal, J. Muñoz; ...

2017-01-16

Here, we investigate the potential of using deep learning techniques to reject background events in searches for neutrinoless double beta decay with high pressure xenon time projection chambers capable of detailed track reconstruction. The differences in the topological signatures of background and signal events can be learned by deep neural networks via training over many thousands of events. These networks can then be used to classify further events as signal or background, providing an additional background rejection factor at an acceptable loss of efficiency. The networks trained in this study performed better than previous methods developed based on the usemore » of the same topological signatures by a factor of 1.2 to 1.6, and there is potential for further improvement.« less

Abnormal brain white matter network in young smokers: a graph theory analysis study.

PubMed

Zhang, Yajuan; Li, Min; Wang, Ruonan; Bi, Yanzhi; Li, Yangding; Yi, Zhang; Liu, Jixin; Yu, Dahua; Yuan, Kai

2018-04-01

Previous diffusion tensor imaging (DTI) studies had investigated the white matter (WM) integrity abnormalities in some specific fiber bundles in smokers. However, little is known about the changes in topological organization of WM structural network in young smokers. In current study, we acquired DTI datasets from 58 male young smokers and 51 matched nonsmokers and constructed the WM networks by the deterministic fiber tracking approach. Graph theoretical analysis was used to compare the topological parameters of WM network (global and nodal) and the inter-regional fractional anisotropy (FA) weighted WM connections between groups. The results demonstrated that both young smokers and nonsmokers had small-world topology in WM network. Further analysis revealed that the young smokers exhibited the abnormal topological organization, i.e., increased network strength, global efficiency, and decreased shortest path length. In addition, the increased nodal efficiency predominately was located in frontal cortex, striatum and anterior cingulate gyrus (ACG) in smokers. Moreover, based on network-based statistic (NBS) approach, the significant increased FA-weighted WM connections were mainly found in the PFC, ACG and supplementary motor area (SMA) regions. Meanwhile, the network parameters were correlated with the nicotine dependence severity (FTND) scores, and the nodal efficiency of orbitofrontal cortex was positive correlation with the cigarette per day (CPD) in young smokers. We revealed the abnormal topological organization of WM network in young smokers, which may improve our understanding of the neural mechanism of young smokers form WM topological organization level.

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 New Supercapacitor and Li-ion Battery Hybrid System for Electric Vehicle in ADVISOR

NASA Astrophysics Data System (ADS)

Peng, Xiao; Shuhai, Quan; Changjun, Xie

2017-02-01

The supercapacitor (SC) and Li-ion battery(BT) hybrid energy storage system(HESS) electric vehicle(EV) is gaining universal attention. The topology is of importance for the SC/BT HESS. A new SC/BT topology HESS with a rule-based energy management strategy for EV was proposed. The BT pack is connected directly to the DC link via a controlled switch. The SC pack is connected to the DC link via a controlled switch. A uni-directional DC/DC converter is connected between the SC pack and the BT pack. The braking regeneration energy is all harvested by the SC pack. The output power of BT pack is limited. The different SC/BT configurations with varied BT maximum Ah capacity factor and SC maximum capacity factor are simulated in ADVISOR. Simulation results show that BT maximum Ah capacity factor has little impact on vehicle acceleration performance and maximum speed. SC maximum capacity factor has significant impact on vehicle acceleration performance and maximum speed. The fuel economy isn’t affected.

Fatigue performance of additively manufactured meta-biomaterials: The effects of topology and material type.

PubMed

Ahmadi, S M; Hedayati, R; Li, Y; Lietaert, K; Tümer, N; Fatemi, A; Rans, C D; Pouran, B; Weinans, H; Zadpoor, A A

2018-01-01

Additive manufacturing (AM) techniques enable fabrication of bone-mimicking meta-biomaterials with unprecedented combinations of topological, mechanical, and mass transport properties. The mechanical performance of AM meta-biomaterials is a direct function of their topological design. It is, however, not clear to what extent the material type is important in determining the fatigue behavior of such biomaterials. We therefore aimed to determine the isolated and modulated effects of topological design and material type on the fatigue response of metallic meta-biomaterials fabricated with selective laser melting. Towards that end, we designed and additively manufactured Co-Cr meta-biomaterials with three types of repeating unit cells and three to four porosities per type of repeating unit cell. The AM meta-biomaterials were then mechanically tested to obtain their normalized S-N curves. The obtained S-N curves of Co-Cr meta-biomaterials were compared to those of meta-biomaterials with same topological designs but made from other materials, i.e. Ti-6Al-4V, tantalum, and pure titanium, available from our previous studies. We found the material type to be far more important than the topological design in determining the normalized fatigue strength of our AM metallic meta-biomaterials. This is the opposite of what we have found for the quasi-static mechanical properties of the same meta-biomaterials. The effects of material type, manufacturing imperfections, and topological design were different in the high and low cycle fatigue regions. That is likely because the cyclic response of meta-biomaterials depends not only on the static and fatigue strengths of the bulk material but also on other factors that may include strut roughness, distribution of the micro-pores created inside the struts during the AM process, and plasticity. Meta-biomaterials are a special class of metamaterials with unusual or unprecedented combinations of mechanical, physical (e.g. mass transport), and biological properties. Topologically complex and additively manufactured meta-biomaterials have been shown to improve bone regeneration and osseointegration. The mechanical properties of such biomaterials are directly related to their topological design and material type. However, previous studies of such biomaterials have largely neglected the effects of material type, instead focusing on topological design. We show here that neglecting the effects of material type is unjustified. We studied the isolated and combined effects of topological design and material type on the normalized S-N curves of metallic bone-mimicking biomaterials and found them to be more strongly dependent on the material type than topological design. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Topology driven modeling: the IS metaphor.

PubMed

Merelli, Emanuela; Pettini, Marco; Rasetti, Mario

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

Graphite Web: web tool for gene set analysis exploiting pathway topology

PubMed Central

Sales, Gabriele; Calura, Enrica; Martini, Paolo; Romualdi, Chiara

2013-01-01

Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into ‘topological’ and ‘non-topological’ methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by researchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpretation. Specifically, Graphite web implements five different gene set analyses on three model organisms and two pathway databases. Graphite Web is freely available at http://graphiteweb.bio.unipd.it/. PMID:23666626

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Topological Principles of Control in Dynamical Networks

NASA Astrophysics Data System (ADS)

Kim, Jason; Pasqualetti, Fabio; Bassett, Danielle

Networked biological systems, such as the brain, feature complex patterns of interactions. To predict and correct the dynamic behavior of such systems, it is imperative to understand how the underlying topological structure affects and limits the function of the system. Here, we use network control theory to extract topological features that favor or prevent network controllability, and to understand the network-wide effect of external stimuli on large-scale brain systems. Specifically, we treat each brain region as a dynamic entity with real-valued state, and model the time evolution of all interconnected regions using linear, time-invariant dynamics. We propose a simplified feed-forward scheme where the effect of upstream regions (drivers) on the connected downstream regions (non-drivers) is characterized in closed-form. Leveraging this characterization of the simplified model, we derive topological features that predict the controllability properties of non-simplified networks. We show analytically and numerically that these predictors are accurate across a large range of parameters. Among other contributions, our analysis shows that heterogeneity in the network weights facilitate controllability, and allows us to implement targeted interventions that profoundly improve controllability. By assuming an underlying dynamical mechanism, we are able to understand the complex topology of networked biological systems in a functionally meaningful way.

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

PubMed

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

2016-08-30

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

Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-alpha-helix bundle.

PubMed

Grosset, A M; Gibney, B R; Rabanal, F; Moser, C C; Dutton, P L

2001-05-08

New understanding of the engineering and allosteric regulation of natural protein conformational switches (such as those that couple chemical and ionic signals, mechanical force, and electro/chemical free energy for biochemical activation, catalysis, and motion) can be derived from simple de novo designed synthetic protein models (maquettes). We demonstrate proof of principle of both reversible switch action and allosteric regulation in a tetra-alpha-helical bundle protein composed of two identical di-helical subunits containing heme coordinated at a specific position close to the disulfide loop region. Individual bundles assume one of two switch states related by large-scale mechanical changes: a syn-topology (helices of the different subunits parallel) or anti-topology (helices antiparallel). Both the spectral properties of a coproporphyrin probe appended to the loop region and the distance-dependent redox interaction between the hemes identify the topologies. Beginning from a syn-topology, introduction of ferric heme in each subunit (either binding or redox change) shifts the topological balance by 25-50-fold (1.9-2.3 kcal/mol) to an anti-dominance. Charge repulsion between the two internal cationic ferric hemes drives the syn- to anti-switch, as demonstrated in two ways. When fixed in the syn-topology, the second ferric heme binding is 25-80-fold (1.9-2.6 kcal/mol) weaker than the first, and adjacent heme redox potentials are split by 80 mV (1.85 kcal/mol), values that energetically match the shift in topological balance. Allosteric and cooperative regulation of the switch by ionic strength exploits the shielded charge interactions between the two hemes and the exposed, cooperative interactions between the coproporphyrin carboxylates.

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

PubMed Central

Normanno, Davide; Vanzi, Francesco; Pavone, Francesco Saverio

2008-01-01

Gene expression regulation is a fundamental biological process which deploys specific sets of genomic information depending on physiological or environmental conditions. Several transcription factors (including lac repressor, LacI) are present in the cell at very low copy number and increase their local concentration by binding to multiple sites on DNA and looping the intervening sequence. In this work, we employ single-molecule manipulation to experimentally address the role of DNA supercoiling in the dynamics and stability of LacI-mediated DNA looping. We performed measurements over a range of degrees of supercoiling between −0.026 and +0.026, in the absence of axial stretching forces. A supercoiling-dependent modulation of the lifetimes of both the looped and unlooped states was observed. Our experiments also provide evidence for multiple structural conformations of the LacI–DNA complex, depending on torsional constraints. The supercoiling-dependent modulation demonstrated here adds an important element to the model of the lac operon. In fact, the complex network of proteins acting on the DNA in a living cell constantly modifies its topological and mechanical properties: our observations demonstrate the possibility of establishing a signaling pathway from factors affecting DNA supercoiling to transcription factors responsible for the regulation of specific sets of genes. PMID:18310101

Topological Insulator Bi2Se3/Si-Nanowire-Based p-n Junction Diode for High-Performance Near-Infrared Photodetector.

PubMed

Das, Biswajit; Das, Nirmalya S; Sarkar, Samrat; Chatterjee, Biplab K; Chattopadhyay, Kalyan K

2017-07-12

Chemically derived topological insulator Bi 2 Se 3 nanoflake/Si nanowire (SiNWs) heterojunctions were fabricated employing all eco-friendly cost-effective chemical route for the first time. X-ray diffraction studies confirmed proper phase formation of Bi 2 Se 3 nanoflakes. The morphological features of the individual components and time-evolved hybrid structures were studied using field emission scanning electron microscope. High resolution transmission electron microscopic studies were performed to investigate the actual nature of junction whereas elemental distributions at junction, along with overall stoichiometry of the samples were analyzed using energy dispersive X-ray studies. Temperature dependent current-voltage characteristics and variation of barrier height and ideality factor was studied between 50 and 300 K. An increase in barrier height and decrease in the ideality factor were observed with increasing temperature for the sample. The rectification ratio (I + /I - ) for SiNWs substrate over pristine Si substrate under dark and near-infrared (NIR) irradiation of 890 nm was found to be 3.63 and 10.44, respectively. Furthermore, opto-electrical characterizations were performed for different light power intensities and highest photo responsivity and detectivity were determined to be 934.1 A/W and 2.30 × 10 13 Jones, respectively. Those values are appreciably higher than previous reports for topological insulator based devices. Thus, this work establishes a hybrid system based on topological insulator Bi 2 Se 3 nanoflake and Si nanowire as the newest efficient candidate for advanced optoelectronic materials.

Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling

PubMed Central

Sims, Joshua J.; Scavone, Francesco; Cooper, Eric M.; Kane, Lesley A.; Youle, Richard J.; Boeke, Jef D.; Cohen, Robert E.

2012-01-01

Polyubiquitin (polyUb) chain topology is thought to direct modified substrates to specific fates, but this function-topology relationship is poorly understood, as are the dynamics and subcellular locations of specific polyUb signals. Experimental access to these questions has been limited because linkage-specific inhibitors and in vivo sensors have been unavailable. Here we present a general strategy to track linkage-specific polyUb signals in yeast and mammalian cells, and to probe their functions. We designed several high-affinity lysine-63-polyUb-binding proteins and demonstrate their specificity both in vitro and in cells. We apply these tools as competitive inhibitors to dissect the polyUb-linkage dependence of NF-κB activation in several cell types, inferring the essential role of lysine-63-polyUb for signaling via the IL-1β and TNF-related weak inducer of apoptosis (TWEAK) but not TNF-α receptors. We anticipate live-cell imaging, proteomic, and biochemical applications for these tools, and extension of the design strategy to other polymeric ubiquitin-like protein modifications. PMID:22306808

Reliability of nine programs of topological predictions and their application to integral membrane channel and carrier proteins.

PubMed

Reddy, Abhinay; Cho, Jaehoon; Ling, Sam; Reddy, Vamsee; Shlykov, Maksim; Saier, Milton H

2014-01-01

We evaluated topological predictions for nine different programs, HMMTOP, TMHMM, SVMTOP, DAS, SOSUI, TOPCONS, PHOBIUS, MEMSAT-SVM (hereinafter referred to as MEMSAT), and SPOCTOPUS. These programs were first evaluated using four large topologically well-defined families of secondary transporters, and the three best programs were further evaluated using topologically more diverse families of channels and carriers. In the initial studies, the order of accuracy was: SPOCTOPUS > MEMSAT > HMMTOP > TOPCONS > PHOBIUS > TMHMM > SVMTOP > DAS > SOSUI. Some families, such as the Sugar Porter Family (2.A.1.1) of the Major Facilitator Superfamily (MFS; TC #2.A.1) and the Amino Acid/Polyamine/Organocation (APC) Family (TC #2.A.3), were correctly predicted with high accuracy while others, such as the Mitochondrial Carrier (MC) (TC #2.A.29) and the K(+) transporter (Trk) families (TC #2.A.38), were predicted with much lower accuracy. For small, topologically homogeneous families, SPOCTOPUS and MEMSAT were generally most reliable, while with large, more diverse superfamilies, HMMTOP often proved to have the greatest prediction accuracy. We next developed a novel program, TM-STATS, that tabulates HMMTOP, SPOCTOPUS or MEMSAT-based topological predictions for any subdivision (class, subclass, superfamily, family, subfamily, or any combination of these) of the Transporter Classification Database (TCDB; www.tcdb.org) and examined the following subclasses: α-type channel proteins (TC subclasses 1.A and 1.E), secreted pore-forming toxins (TC subclass 1.C) and secondary carriers (subclass 2.A). Histograms were generated for each of these subclasses, and the results were analyzed according to subclass, family and protein. The results provide an update of topological predictions for integral membrane transport proteins as well as guides for the development of more reliable topological prediction programs, taking family-specific characteristics into account. © 2014 S. Karger AG, Basel.

Classification and characterization of topological insulators and superconductors

NASA Astrophysics Data System (ADS)

Mong, Roger

Topological insulators (TIs) are a new class of materials which, until recently, have been overlooked despite decades of study in band insulators. Like semiconductors and ordinary insulators, TIs have a bulk gap, but feature robust surfaces excitations which are protected from disorder and interactions which do not close the bulk gap. TIs are distinguished from ordinary insulators not by the symmetries they possess (or break), but by topological invariants characterizing their bulk band structures. These two pictures, the existence of gapless surface modes, and the nontrivial topology of the bulk states, yield two contrasting approaches to the study of TIs. At the heart of the subject, they are connected by the bulk-boundary correspondence, relating bulk and surface degrees of freedom. In this work, we study both aspects of topological insulators, at the same time providing an illumination to their mysterious connection. First, we present a systematic approach to the classification of bulk states of systems with inversion-like symmetries, deriving a complete set of topological invariants for such ensembles. We find that the topological invariants in all dimensions may be computed algebraically via exact sequences. In particular, systems with spatial inversion symmetries in one-, two-, and three-dimensions can be classified by, respectively, 2, 5, and 11 integer invariants. The values of these integers are related to physical observables such as polarization, Hall conductivity, and magnetoelectric coupling. We also find that, for systems with “antiferromagnetic symmetry,” there is a Z2 classification in three-dimensions, and hence a class of “antiferromagnetic topological insulators” (AFTIs) which are distinguished from ordinary antiferromagnets. From the perspective of the bulk, AFTI exhibits the quantized magnetoelectric effect, whereas on the surface, gapless one-dimensional chiral modes emerge at step-defects. Next, we study how the surface spectrum can be computed from bulk quantities. Specifically, we present an analytic prescription for computing the edge dispersion E(k) of a tight-binding Dirac Hamiltonian terminated at an abrupt crystalline edge, based on the bulk Hamiltonian. The result is presented as a geometric formula, relating the existence of surface states as well as their energy dispersion to properties of the bulk Hamiltonian. We further prove the bulk-boundary correspondence for this specific class of systems, connecting the Chern number and the chiral edge modes for quantum Hall systems given in terms of Dirac Hamiltonians. In similar spirit, we examine the existence of Majorana zero modes in superconducting doped-TIs. We find that Majorana zero modes indeed appear but only if the doped Fermi energy is below a critical chemical potential. The critical doping is associated with a topological phase transition of vortex lines, which supports gapless excitations spanning their length. For weak pairing, the critical point is dependent on the non-abelian Berry phase of the bulk Fermi surface. Finally, we investigate the transport properties on the surfaces of TIs. While the surfaces of “strong topological insulators” - TIs with an odd number of Dirac cones in their surface spectrum - have been well studied in literature, studies of their counterpart “weak topological insulators” (WTIs) are meager, with conflicting claims. Because WTIs have an even number of Dirac cones in their surface spectrum, they are thought to be unstable to disorder, which leads to an insulating surface. Here we argue that the presence of disorder alone will not localize the surface states, rather, presence of a time-reversal symmetric mass term is required for localization. Through numerical simulations, we show that in the absence of the mass term the surface always flow to a stable metallic phase and the conductivity obeys a one-parameter scaling relation, just as in the case of a strong topological insulator surface. With the inclusion of the mass, the transport properties of the surface of a weak topological insulator follow a two-parameter scaling form, reminiscent of the quantum Hall phase transition.

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.

Understanding network concepts in modules

PubMed Central

2007-01-01

Background Network concepts are increasingly used in biology and genetics. For example, the clustering coefficient has been used to understand network architecture; the connectivity (also known as degree) has been used to screen for cancer targets; and the topological overlap matrix has been used to define modules and to annotate genes. Dozens of potentially useful network concepts are known from graph theory. Results Here we study network concepts in special types of networks, which we refer to as approximately factorizable networks. In these networks, the pairwise connection strength (adjacency) between 2 network nodes can be factored into node specific contributions, named node 'conformity'. The node conformity turns out to be highly related to the connectivity. To provide a formalism for relating network concepts to each other, we define three types of network concepts: fundamental-, conformity-based-, and approximate conformity-based concepts. Fundamental concepts include the standard definitions of connectivity, density, centralization, heterogeneity, clustering coefficient, and topological overlap. The approximate conformity-based analogs of fundamental network concepts have several theoretical advantages. First, they allow one to derive simple relationships between seemingly disparate networks concepts. For example, we derive simple relationships between the clustering coefficient, the heterogeneity, the density, the centralization, and the topological overlap. The second advantage of approximate conformity-based network concepts is that they allow one to show that fundamental network concepts can be approximated by simple functions of the connectivity in module networks. Conclusion Using protein-protein interaction, gene co-expression, and simulated data, we show that a) many networks comprised of module nodes are approximately factorizable and b) in these types of networks, simple relationships exist between seemingly disparate network concepts. Our results are implemented in freely available R software code, which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/ModuleConformity/ModuleNetworks PMID:17547772

A single-phase multi-level D-STATCOM inverter using modular multi-level converter (MMC) topology for renewable energy sources

NASA Astrophysics Data System (ADS)

Sotoodeh, Pedram

This dissertation presents the design of a novel multi-level inverter with FACTS capability for small to mid-size (10-20kW) permanent-magnet wind installations using modular multi-level converter (MMC) topology. The aim of the work is to design a new type of inverter with D-STATCOM option to provide utilities with more control on active and reactive power transfer of distribution lines. The inverter is placed between the renewable energy source, specifically a wind turbine, and the distribution grid in order to fix the power factor of the grid at a target value, regardless of wind speed, by regulating active and reactive power required by the grid. The inverter is capable of controlling active and reactive power by controlling the phase angle and modulation index, respectively. The unique contribution of the proposed work is to combine the two concepts of inverter and D-STATCOM using a novel voltage source converter (VSC) multi-level topology in a single unit without additional cost. Simulations of the proposed inverter, with 5 and 11 levels, have been conducted in MATLAB/Simulink for two systems including 20 kW/kVAR and 250 W/VAR. To validate the simulation results, a scaled version (250 kW/kVAR) of the proposed inverter with 5 and 11 levels has been built and tested in the laboratory. Experimental results show that the reduced-scale 5- and 11-level inverter is able to fix PF of the grid as well as being compatible with IEEE standards. Furthermore, total cost of the prototype models, which is one of the major objectives of this research, is comparable with market prices.

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

PubMed

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

2014-02-01

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

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.

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires

NASA Astrophysics Data System (ADS)

Dufouleur, J.; Veyrat, L.; Dassonneville, B.; Xypakis, E.; Bardarson, J. H.; Nowka, C.; Hampel, S.; Schumann, J.; Eichler, B.; Schmidt, O. G.; Büchner, B.; Giraud, R.

2017-04-01

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder.

Topology optimization based design of unilateral NMR for generating a remote homogeneous field.

PubMed

Wang, Qi; Gao, Renjing; Liu, Shutian

2017-06-01

This paper presents a topology optimization based design method for the design of unilateral nuclear magnetic resonance (NMR), with which a remote homogeneous field can be obtained. The topology optimization is actualized by seeking out the optimal layout of ferromagnetic materials within a given design domain. The design objective is defined as generating a sensitive magnetic field with optimal homogeneity and maximal field strength within a required region of interest (ROI). The sensitivity of the objective function with respect to the design variables is derived and the method for solving the optimization problem is presented. A design example is provided to illustrate the utility of the design method, specifically the ability to improve the quality of the magnetic field over the required ROI by determining the optimal structural topology for the ferromagnetic poles. Both in simulations and experiments, the sensitive region of the magnetic field achieves about 2 times larger than that of the reference design, validating validates the feasibility of the design method. Copyright © 2017. Published by Elsevier Inc.

Spin and topological order in a periodically driven spin chain

NASA Astrophysics Data System (ADS)

Russomanno, Angelo; Friedman, Bat-el; Dalla Torre, Emanuele G.

2017-07-01

The periodically driven quantum Ising chain has recently attracted a large attention in the context of Floquet engineering. In addition to the common paramagnet and ferromagnet, this driven model can give rise to new topological phases. In this work, we systematically explore its quantum phase diagram by examining the properties of its Floquet ground state. We specifically focus on driving protocols with time-reversal invariant points, and demonstrate the existence of an infinite number of distinct phases. These phases are separated by second-order quantum phase transitions, accompanied by continuous changes of local and string order parameters, as well as sudden changes of a topological winding number and of the number of protected edge states. When one of these phase transitions is adiabatically crossed, the correlator associated to the order parameter is nonvanishing over a length scale which shows a Kibble-Zurek scaling. In some phases, the Floquet ground state spontaneously breaks the discrete time-translation symmetry of the Hamiltonian. Our findings provide a better understanding of topological phases in periodically driven clean integrable models.

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires

PubMed Central

Dufouleur, J.; Veyrat, L.; Dassonneville, B.; Xypakis, E.; Bardarson, J. H.; Nowka, C.; Hampel, S.; Schumann, J.; Eichler, B.; Schmidt, O. G.; Büchner, B.; Giraud, R.

2017-01-01

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder. PMID:28374744

Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector

PubMed Central

Masulis, Irina S.; Babaeva, Zaira Sh.; Chernyshov, Sergey V.; Ozoline, Olga N.

2015-01-01

Mosaic pattern of transcription in alternating directions is a common feature of prokaryotic and eukaryotic genomes which rationality and origin remain enigmatic. In Escherichia coli approximately 25% of genes comprise pairs of topologically linked divergently transcribed units. Given that transcriptional complex formation at each promoter in the pair induces topological changes and is itself sensitive to DNA structural perturbations, study of the functional anatomy in such areas requires special approaches. Here we suggested the dual-colour promoter probe vector which may become an ideal tool for divergent transcription profiling. The vector was used to characterize the specific genomic region nearby appY with multiple bidirectional promoters predicted in silico. Only three promoters of this region were shown to be engaged in the transcription initiation resulting in the expression of reporter genes. RNA product transcribed in antisense direction is suggested as a novel RNA. Nalidixin-induced topological modulation differentially affected transcription in sense and antisense directions thus exemplifying anticooperative mode in the response to topological alterations. PMID:26081797

Bondonic effects in group-IV honeycomb nanoribbons with Stone-Wales topological defects.

PubMed

Putz, Mihai V; Ori, Ottorino

2014-04-03

This work advances the modeling of bondonic effects on graphenic and honeycomb structures, with an original two-fold generalization: (i) by employing the fourth order path integral bondonic formalism in considering the high order derivatives of the Wiener topological potential of those 1D systems; and (ii) by modeling a class of honeycomb defective structures starting from graphene, the carbon-based reference case, and then generalizing the treatment to Si (silicene), Ge (germanene), Sn (stannene) by using the fermionic two-degenerate statistical states function in terms of electronegativity. The honeycomb nanostructures present η-sized Stone-Wales topological defects, the isomeric dislocation dipoles originally called by authors Stone-Wales wave or SWw. For these defective nanoribbons the bondonic formalism foresees a specific phase-transition whose critical behavior shows typical bondonic fast critical time and bonding energies. The quantum transition of the ideal-to-defect structural transformations is fully described by computing the caloric capacities for nanostructures triggered by η-sized topological isomerisations. Present model may be easily applied to hetero-combinations of Group-IV elements like C-Si, C-Ge, C-Sn, Si-Ge, Si-Sn, Ge-Sn.

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires.

PubMed

Dufouleur, J; Veyrat, L; Dassonneville, B; Xypakis, E; Bardarson, J H; Nowka, C; Hampel, S; Schumann, J; Eichler, B; Schmidt, O G; Büchner, B; Giraud, R

2017-04-04

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi 2 Te 3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder.

Modeling Natural Anti-Inflammatory Compounds by Molecular Topology

PubMed Central

Galvez-Llompart, María; Zanni, Riccardo; García-Domenech, Ramón

2011-01-01

One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with the remaining compounds (those not used in building up the model), has been carried out. Finally, a virtual screening on natural products was performed and 74 compounds showed actual anti-inflammatory activity. From them, 54 had been previously described as anti-inflammatory in the literature. This can be seen as a plus in the model validation and as a reinforcement of the role of Molecular Topology as an efficient tool for the discovery of new anti-inflammatory natural compounds. PMID:22272145

The Origin of Improved Electrical Double-Layer Capacitance by Inclusion of Topological Defects and Dopants in Graphene for Supercapacitors.

PubMed

Chen, Jiafeng; Han, Yulei; Kong, Xianghua; Deng, Xinzhou; Park, Hyo Ju; Guo, Yali; Jin, Song; Qi, Zhikai; Lee, Zonghoon; Qiao, Zhenhua; Ruoff, Rodney S; Ji, Hengxing

2016-10-24

Low-energy density has long been the major limitation to the application of supercapacitors. Introducing topological defects and dopants in carbon-based electrodes in a supercapacitor improves the performance by maximizing the gravimetric capacitance per mass of the electrode. However, the main mechanisms governing this capacitance improvement are still unclear. We fabricated planar electrodes from CVD-derived single-layer graphene with deliberately introduced topological defects and nitrogen dopants in controlled concentrations and of known configurations, to estimate the influence of these defects on the electrical double-layer (EDL) capacitance. Our experimental study and theoretical calculations show that the increase in EDL capacitance due to either the topological defects or the nitrogen dopants has the same origin, yet these two factors improve the EDL capacitance in different ways. Our work provides a better understanding of the correlation between the atomic-scale structure and the EDL capacitance and presents a new strategy for the development of experimental and theoretical models for understanding the EDL capacitance of carbon electrodes. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geometrization of quantum physics

NASA Astrophysics Data System (ADS)

Ol'Khov, O. A.

2009-12-01

It is shown that the Dirac equation for free particle can be considered as a description of specific distortion of the space euclidean geometry (space topological defect). This approach is based on possibility of interpretation of the wave function as vector realizing representation of the fundamental group of the closed topological space-time 4-manifold. Mass and spin appear to be topological invariants. Such concept explains all so called “strange” properties of quantum formalism: probabilities, wave-particle duality, nonlocal instantaneous correlation between noninteracting particles (EPR-paradox) and so on. Acceptance of suggested geometrical concept means rejection of atomistic concept where all matter is considered as consisting of more and more small elementary particles. There is no any particles a priori, before measurement: the notions of particles appear as a result of classical interpretation of the contact of the region of the curved space with a device.

Bullied no more:when and how DNA shoves proteins around

PubMed Central

Pettitt, B. Montgomery; Sumners, De Witt L.; Harris, Sarah A.; Zechiedrich, Lynn

2016-01-01

The predominant protein-centric perspective in protein–DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism. PMID:22850561

Visualization of a Unidirectional Electromagnetic Waveguide Using Topological Photonic Crystals Made of Dielectric Materials

NASA Astrophysics Data System (ADS)

Yang, Yuting; Xu, Yun Fei; Xu, Tao; Wang, Hai-Xiao; Jiang, Jian-Hua; Hu, Xiao; Hang, Zhi Hong

2018-05-01

We demonstrate experimentally that a photonic crystal made of Al2O3 cylinders exhibits topological time-reversal symmetric electromagnetic propagation, similar to the quantum spin Hall effect in electronic systems. A pseudospin degree of freedom in the electromagnetic system representing different states of orbital angular momentum arises due to a deformation of the photonic crystal from the ideal honeycomb lattice. It serves as the photonic analogue to the electronic Kramers pair. We visualized qualitatively and measured quantitatively that microwaves of a specific pseudospin propagate only in one direction along the interface between a topological photonic crystal and a trivial one. As only a conventional dielectric material is used and only local real-space manipulations are required, our scheme can be extended to visible light to inspire many future applications in the field of photonics and beyond.

Use of nonlinear design optimization techniques in the comparison of battery discharger topologies for the space platform

NASA Technical Reports Server (NTRS)

Sable, Dan M.; Cho, Bo H.; Lee, Fred C.

1990-01-01

A detailed comparison of a boost converter, a voltage-fed, autotransformer converter, and a multimodule boost converter, designed specifically for the space platform battery discharger, is performed. Computer-based nonlinear optimization techniques are used to facilitate an objective comparison. The multimodule boost converter is shown to be the optimum topology at all efficiencies. The margin is greatest at 97 percent efficiency. The multimodule, multiphase boost converter combines the advantages of high efficiency, light weight, and ample margin on the component stresses, thus ensuring high reliability.

Introduction of functionality, selection of topology, and enhancement of gas adsorption in multivariate metal-organic framework-177.

PubMed

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun; Nie, Weixuan; Park, Hye Jeong; Okajima, Satoshi; Cordova, Kyle E; Deng, Hexiang; Kim, Jaheon; Yaghi, Omar M

2015-02-25

Metal-organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn4O(-COO)6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We find that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH2, and -C4H4) is an important strategy for the incorporation of a specific functionality (-NO2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.

Introduction of Functionality, Selection of Topology, and Enhancement of Gas Adsorption in Multivariate Metal–Organic Framework-177

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

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun

2015-02-25

Metal–organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn 4O(-COO) 6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We findmore » that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH 2, and -C 4H 4) is an important strategy for the incorporation of a specific functionality (-NO 2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.« less

Three-Dimensional Reconstruction of the Virtual Plant Branching Structure Based on Terrestrial LIDAR Technologies and L-System

NASA Astrophysics Data System (ADS)

Gong, Y.; Yang, Y.; Yang, X.

2018-04-01

For the purpose of extracting productions of some specific branching plants effectively and realizing its 3D reconstruction, Terrestrial LiDAR data was used as extraction source of production, and a 3D reconstruction method based on Terrestrial LiDAR technologies combined with the L-system was proposed in this article. The topology structure of the plant architectures was extracted using the point cloud data of the target plant with space level segmentation mechanism. Subsequently, L-system productions were obtained and the structural parameters and production rules of branches, which fit the given plant, was generated. A three-dimensional simulation model of target plant was established combined with computer visualization algorithm finally. The results suggest that the method can effectively extract a given branching plant topology and describes its production, realizing the extraction of topology structure by the computer algorithm for given branching plant and also simplifying the extraction of branching plant productions which would be complex and time-consuming by L-system. It improves the degree of automation in the L-system extraction of productions of specific branching plants, providing a new way for the extraction of branching plant production rules.

Edge-entanglement spectrum correspondence in a nonchiral topological phase and Kramers-Wannier duality

NASA Astrophysics Data System (ADS)

Ho, Wen Wei; Cincio, Lukasz; Moradi, Heidar; Gaiotto, Davide; Vidal, Guifre

2015-03-01

In a system with chiral topological order, there is a remarkable correspondence between the edge and entanglement spectra: the low-energy spectrum of the system in the presence of a physical edge coincides with the lowest part of the entanglement spectrum (ES) across a virtual cut of the system into two parts, up to rescaling and shifting. This correspondence is believed to be due to the existence of protected gapless edge modes. In this paper, we explore whether the edge-entanglement spectrum correspondence extends to nonchiral topological phases, where there are no protected gapless edge modes. Specifically, we consider the Wen-plaquette model, which is equivalent to the Kitaev toric code model and has Z2 topological order (quantum double of Z2) . The unperturbed Wen-plaquette model displays an exact correspondence: both the edge and entanglement spectra within each topological sector a (a =1 ,⋯,4 ) are flat and equally degenerate. Here, we show, through a detailed microscopic calculation, that in the presence of generic local perturbations: (i) the effective degrees of freedom for both the physical edge and the entanglement cut consist of a (spin-1 /2 ) spin chain, with effective Hamiltonians Hedgea and Henta, respectively, both of which have a Z2 symmetry enforced by the bulk topological order; (ii) there is in general no match between the low-energy spectra of Hedgea and Henta, that is, there is no edge-ES correspondence. However, if supplement the Z2 topological order with a global symmetry (translational invariance along the edge/entanglement cut), i.e., by considering the Wen-plaquette model as a symmetry-enriched topological phase (SET), then there is a finite domain in Hamiltonian space in which both Hedgea and Henta realize the critical Ising model, whose low-energy effective theory is the c =1 /2 Ising CFT. This is achieved because the presence of the global symmetry implies that the effective degrees of freedom of both the edge and entanglement cut are governed by Kramers-Wannier self-dual Hamiltonians, in addition to them being Z2 symmetric, which is imposed by the topological order. Thus, by considering the Wen-plaquette model as a SET, the topological order in the bulk together with the translation invariance of the perturbations along the edge/cut imply an edge-ES correspondence at least in some finite domain in Hamiltonian space.

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

PubMed

Pancaldi, Vera; Carrillo-de-Santa-Pau, Enrique; Javierre, Biola Maria; Juan, David; Fraser, Peter; Spivakov, Mikhail; Valencia, Alfonso; Rico, Daniel

2016-07-08

Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts. We use high-resolution promoter capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse embryonic stem cells to investigate promoter-centered chromatin interaction networks and calculate the presence of specific epigenomic features in the chromatin fragments constituting the nodes of the network. We estimate the association of these features with the topology of four chromatin interaction networks and identify features localized in connected areas of the network. Polycomb group proteins and associated histone marks are the features with the highest chromatin assortativity in promoter-centered networks. We then ask which features distinguish contacts amongst promoters from contacts between promoters and other genomic elements. We observe higher chromatin assortativity of the actively elongating form of RNA polymerase 2 (RNAPII) compared with inactive forms only in interactions between promoters and other elements. Contacts among promoters and between promoters and other elements have different characteristic epigenomic features. We identify a possible role for the elongating form of RNAPII in mediating interactions among promoters, enhancers, and transcribed gene bodies. Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing the comparison of chromatin interaction networks.

On B-type Open-Closed Landau-Ginzburg Theories Defined on Calabi-Yau Stein Manifolds

NASA Astrophysics Data System (ADS)

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

2018-05-01

We consider the bulk algebra and topological D-brane category arising from the differential model of the open-closed B-type topological Landau-Ginzburg theory defined by a pair (X,W), where X is a non-compact Calabi-Yau manifold and W is a complex-valued holomorphic function. When X is a Stein manifold (but not restricted to be a domain of holomorphy), we extract equivalent descriptions of the bulk algebra and of the category of topological D-branes which are constructed using only the analytic space associated to X. In particular, we show that the D-brane category is described by projective factorizations defined over the ring of holomorphic functions of X. We also discuss simplifications of the analytic models which arise when X is holomorphically parallelizable and illustrate these in a few classes of examples.

The Impact of the Network Topology on the Viral Prevalence: A Node-Based Approach

PubMed Central

Yang, Lu-Xing; Draief, Moez; Yang, Xiaofan

2015-01-01

This paper addresses the impact of the structure of the viral propagation network on the viral prevalence. For that purpose, a new epidemic model of computer virus, known as the node-based SLBS model, is proposed. Our analysis shows that the maximum eigenvalue of the underlying network is a key factor determining the viral prevalence. Specifically, the value range of the maximum eigenvalue is partitioned into three subintervals: viruses tend to extinction very quickly or approach extinction or persist depending on into which subinterval the maximum eigenvalue of the propagation network falls. Consequently, computer virus can be contained by adjusting the propagation network so that its maximum eigenvalue falls into the desired subinterval. PMID:26222539

Magnetoresistance of a nanostep junction based on topological insulators

NASA Astrophysics Data System (ADS)

Hu, Wei; Hong, Jin-Bin; Zhai, Feng

2018-06-01

We investigate ballistic transport of helical electrons in a three-dimensional topological insulator traversing a nanostep junction. We find that a magnetic field perpendicular to its side surface shrinks the phase space for transmission, leading to magnetoresistance for the Fermi energy close to the Dirac point of the top surface. We also find transmission resonances and suppression of the Fano factor due to Landau-level-related quasibound states. The transmission blockade in the off-resonance case can result in a huge magnetoresistance for Fermi energy higher than the Dirac point of the side surface.

Fits of weak annihilation and hard spectator scattering corrections in B u,d \\wideoverrightarrow VV decays

NASA Astrophysics Data System (ADS)

Chang, Qin; Li, Xiao-Nan; Sun, Jun-Feng; Yang, Yue-Ling

2016-10-01

In this paper, the contributions of weak annihilation and hard spectator scattering in B\\to ρ {K}* , {K}* {\\bar{K}}* , φ {K}* , ρ ρ and φ φ decays are investigated within the framework of quantum chromodynamics factorization. Using the experimental data available, we perform {χ }2 analyses of end-point parameters in four cases based on the topology-dependent and polarization-dependent parameterization schemes. The fitted results indicate that: (i) in the topology-dependent scheme, the relation ({ρ }Ai,{φ }Ai)\

Topology-selective jamming of fully-connected, code-division random-access networks

NASA Technical Reports Server (NTRS)

Polydoros, Andreas; Cheng, Unjeng

1990-01-01

The purpose is to introduce certain models of topology selective stochastic jamming and examine its impact on a class of fully-connected, spread-spectrum, slotted ALOHA-type random access networks. The theory covers dedicated as well as half-duplex units. The dominant role of the spatial duty factor is established, and connections with the dual concept of time selective jamming are discussed. The optimal choices of coding rate and link access parameters (from the users' side) and the jamming spatial fraction are numerically established for DS and FH spreading.

Superconducting quantum spin-Hall systems with giant orbital g-factors

NASA Astrophysics Data System (ADS)

Hankiewicz, Ewelina; Reinthaler, Rolf; Tkachov, Grigory

Topological aspects of superconductivity in quantum spin-Hall systems (QSHSs) such as thin layers of three-dimensional topological insulators (3D Tis) or two-dimensional Tis are in the focus of current research. Here, we describe a novel superconducting quantum spin-Hall effect (quantum spin Hall system in the proximity to the s-wave superconductor and in the orbital in-plane magnetic field), which is protected against elastic backscattering by combined time-reversal and particle-hole symmetry. This effect is characterized by spin-polarized edge states, which can be manipulated in weak magnetic fields due to a giant effective orbital g-factor, allowing the generation of spin currents. The phenomenon provides a novel solution to the outstanding challenge of detecting the spin-polarization of the edge states. Here we propose the detection of the edge polarization in the three-terminal junction using unusual transport properties of superconducting quantum Hall-effect: a non-monotonic excess current and a zero-bias conductance splitting. We thank for the financial support the German Science Foundation (DFG), Grants No HA 5893/4-1 within SPP 1666, HA5893/5-2 within FOR1162 and TK60/1-1 (G.T.), as well the ENB graduate school ``Topological insulators''.

Implementation of Four-Phase Interleaved Balance Charger for Series-Connected Batteries with Power Factor Correction

NASA Astrophysics Data System (ADS)

Juan, Y. L.; Lee, Y. T.; Lee, Y. L.; Chen, L. L.; Huang, M. L.

2017-11-01

A four-phase interleaved balance charger for series-connected batteries with power factor correction is proposed in this dissertation. In the two phases of two buckboost converters, the rectified ac power is firstly converted to a dc link capacitor. In the other two phases of two flyback converters, the rectified ac power is directly converted to charge the corresponding batteries. Additionally, the energy on the leakage inductance of flyback converter is bypassed to the dc link capacitor. Then, a dual-output balance charging circuit is connected to the dc link to deliver the dc link power to charge two batteries in the series-connected batteries module. The constant-current/constant-voltage charging strategy is adopted. Finally, a prototype of the proposed charger with rated power 500 W is constructed. From the experimental results, the performance and validity of the proposed topology are verified. Compared to the conventional topology with passive RCD snubber, the efficiency of the proposed topology is improved about 3% and the voltage spike on the active switch is also reduced. The efficiency of the proposed charger is at least 83.6 % within the CC/CV charging progress.

Cell Division and Evolution of Biological Tissues

NASA Astrophysics Data System (ADS)

Rivier, Nicolas; Arcenegui-Siemens, Xavier; Schliecker, Gudrun

A tissue is a geometrical, space-filling, random cellular network; it remains in this steady state while individual cells divide. Cell division (fragmentation) is a local, elementary topological transformation which establishes statistical equilibrium of the structure. Statistical equilibrium is characterized by observable relations (Lewis, Aboav) between cell shapes, sizes and those of their neighbours, obtained through maximum entropy and topological correlation extending to nearest neighbours only, i.e. maximal randomness. For a two-dimensional tissue (epithelium), the distribution of cell shapes and that of mother and daughter cells can be obtained from elementary geometrical and physical arguments, except for an exponential factor favouring division of larger cells, and exponential and combinatorial factors encouraging a most symmetric division. The resulting distributions are very narrow, and stationarity severely restricts the range of an adjustable structural parameter

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI

PubMed Central

Xu, Tingting; Cullen, Kathryn R.; Mueller, Bryon; Schreiner, Mindy W.; Lim, Kelvin O.; Schulz, S. Charles; Parhi, Keshab K.

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03–0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03–0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works. PMID:26977400

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI.

PubMed

Xu, Tingting; Cullen, Kathryn R; Mueller, Bryon; Schreiner, Mindy W; Lim, Kelvin O; Schulz, S Charles; Parhi, Keshab K

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03-0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03-0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works.

Topology of molecular interaction networks.

PubMed

Winterbach, Wynand; Van Mieghem, Piet; Reinders, Marcel; Wang, Huijuan; de Ridder, Dick

2013-09-16

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.

Topology of molecular interaction networks

PubMed Central

2013-01-01

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks. Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs. Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes. Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

Topologically dissociable patterns of development of the human cerebral cortex.

PubMed

Vandekar, Simon N; Shinohara, Russell T; Raznahan, Armin; Roalf, David R; Ross, Michelle; DeLeo, Nicholas; Ruparel, Kosha; Verma, Ragini; Wolf, Daniel H; Gur, Ruben C; Gur, Raquel E; Satterthwaite, Theodore D

2015-01-14

Over 90 years ago, anatomists noted the cortex is thinner in sulci than gyri, suggesting that development may occur on a fine scale driven by local topology. However, studies of brain development in youth have focused on describing how cortical thickness varies over large-scale functional and anatomic regions. How the relationship between thickness and local sulcal topology arises in development is still not well understood. Here, we investigated the spatial relationships between cortical thickness, folding, and underlying white matter organization to elucidate the influence of local topology on human brain development. Our approach included using both T1-weighted imaging and diffusion tensor imaging (DTI) in a cross-sectional sample of 932 youths ages 8-21 studied as part of the Philadelphia Neurodevelopmental Cohort. Principal components analysis revealed separable development-related processes of regionally specific nonlinear cortical thickening (from ages 8-14) and widespread linear cortical thinning that have dissociable relationships with cortical topology. Whereas cortical thinning was most prominent in the depths of the sulci, early cortical thickening was present on the gyri. Furthermore, decline in mean diffusivity calculated from DTI in underlying white matter was correlated with cortical thinning, suggesting that cortical thinning is spatially associated with white matter development. Spatial permutation tests were used to assess the significance of these relationships. Together, these data demonstrate that cortical remodeling during youth occurs on a local topological scale and is associated with changes in white matter beneath the cortical surface. Copyright © 2015 the authors 0270-6474/15/350599-11$15.00/0.

Structure and Topology Dynamics of Hyper-Frequency Networks during Rest and Auditory Oddball Performance.

PubMed

Müller, Viktor; Perdikis, Dionysios; von Oertzen, Timo; Sleimen-Malkoun, Rita; Jirsa, Viktor; Lindenberger, Ulman

2016-01-01

Resting-state and task-related recordings are characterized by oscillatory brain activity and widely distributed networks of synchronized oscillatory circuits. Electroencephalographic recordings (EEG) were used to assess network structure and network dynamics during resting state with eyes open and closed, and auditory oddball performance through phase synchronization between EEG channels. For this assessment, we constructed a hyper-frequency network (HFN) based on within- and cross-frequency coupling (WFC and CFC, respectively) at 10 oscillation frequencies ranging between 2 and 20 Hz. We found that CFC generally differentiates between task conditions better than WFC. CFC was the highest during resting state with eyes open. Using a graph-theoretical approach (GTA), we found that HFNs possess small-world network (SWN) topology with a slight tendency to random network characteristics. Moreover, analysis of the temporal fluctuations of HFNs revealed specific network topology dynamics (NTD), i.e., temporal changes of different graph-theoretical measures such as strength, clustering coefficient, characteristic path length (CPL), local, and global efficiency determined for HFNs at different time windows. The different topology metrics showed significant differences between conditions in the mean and standard deviation of these metrics both across time and nodes. In addition, using an artificial neural network approach, we found stimulus-related dynamics that varied across the different network topology metrics. We conclude that functional connectivity dynamics (FCD), or NTD, which was found using the HFN approach during rest and stimulus processing, reflects temporal and topological changes in the functional organization and reorganization of neuronal cell assemblies.

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

Structure and Topology Dynamics of Hyper-Frequency Networks during Rest and Auditory Oddball Performance

PubMed Central

Müller, Viktor; Perdikis, Dionysios; von Oertzen, Timo; Sleimen-Malkoun, Rita; Jirsa, Viktor; Lindenberger, Ulman

2016-01-01

Resting-state and task-related recordings are characterized by oscillatory brain activity and widely distributed networks of synchronized oscillatory circuits. Electroencephalographic recordings (EEG) were used to assess network structure and network dynamics during resting state with eyes open and closed, and auditory oddball performance through phase synchronization between EEG channels. For this assessment, we constructed a hyper-frequency network (HFN) based on within- and cross-frequency coupling (WFC and CFC, respectively) at 10 oscillation frequencies ranging between 2 and 20 Hz. We found that CFC generally differentiates between task conditions better than WFC. CFC was the highest during resting state with eyes open. Using a graph-theoretical approach (GTA), we found that HFNs possess small-world network (SWN) topology with a slight tendency to random network characteristics. Moreover, analysis of the temporal fluctuations of HFNs revealed specific network topology dynamics (NTD), i.e., temporal changes of different graph-theoretical measures such as strength, clustering coefficient, characteristic path length (CPL), local, and global efficiency determined for HFNs at different time windows. The different topology metrics showed significant differences between conditions in the mean and standard deviation of these metrics both across time and nodes. In addition, using an artificial neural network approach, we found stimulus-related dynamics that varied across the different network topology metrics. We conclude that functional connectivity dynamics (FCD), or NTD, which was found using the HFN approach during rest and stimulus processing, reflects temporal and topological changes in the functional organization and reorganization of neuronal cell assemblies. PMID:27799906

Analyzing contentious relationships and outlier genes in phylogenomics.

PubMed

Walker, Joseph F; Brown, Joseph W; Smith, Stephen A

2018-06-08

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Here, we examined two datasets where supermatrix and coalescent-based species trees conflict. We identified two highly influential "outlier" genes in each dataset. When removed from each dataset, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate dataset have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant dataset did not exhibit any obvious systematic error and therefore may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting (ILS). Here we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic datasets that does not assume a single topology for all genes. For both datasets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic datasets by asking more targeted edge-based questions.

The topology of metabolic isotope labeling networks.

PubMed

Weitzel, Michael; Wiechert, Wolfgang; Nöh, Katharina

2007-08-29

Metabolic Flux Analysis (MFA) based on isotope labeling experiments (ILEs) is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs) contain all essential information required to describe the flow of labeled material in an ILE. Whereas recent experimental progress paves the way for high-throughput MFA, large network investigations and exact statistical methods, these developments are still limited by the poor performance of computational routines used for the evaluation and design of ILEs. In this context, the global analysis of ILN topology turns out to be a clue for realizing large speedup factors in all required computational procedures. With a strong focus on the speedup of algorithms the topology of ILNs is investigated using graph theoretic concepts and algorithms. A rigorous determination of all cyclic and isomorphic subnetworks, accompanied by the global analysis of ILN connectivity is performed. Particularly, it is proven that ILNs always brake up into a large number of small strongly connected components (SCCs) and, moreover, there are natural isomorphisms between many of these SCCs. All presented techniques are universal, i.e. they do not require special assumptions on the network structure, bidirectionality of fluxes, measurement configuration, or label input. The general results are exemplified with a practically relevant metabolic network which describes the central metabolism of E. coli comprising 10390 isotopomer pools. Exploiting the topological features of ILNs leads to a significant speedup of all universal algorithms for ILE evaluation. It is proven in theory and exemplified with the E. coli example that a speedup factor of about 1000 compared to standard algorithms is achieved. This widely opens the door for new high performance algorithms suitable for high throughput applications and large ILNs. Moreover, for the first time the global topological analysis of ILNs allows to comprehensively describe and understand the general patterns of label flow in complex networks. This is an invaluable tool for the structural design of new experiments and the interpretation of measured data.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

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.

Effects of pore topology and iron oxide core on doxorubicin loading and release from mesoporous silica nanoparticles

NASA Astrophysics Data System (ADS)

Ronhovde, Cicily J.; Baer, John; Larsen, Sarah C.

2017-06-01

Mesoporous silica nanoparticles (MSNs) have a network of pores that give rise to extremely high specific surface areas, making them attractive materials for applications such as adsorption and drug delivery. The pore topology can be readily tuned to achieve a variety of structures such as the hexagonally ordered Mobil Crystalline Material 41 (MCM-41) and the disordered "wormhole" (WO) mesoporous silica (MS) structure. In this work, the effects of pore topology and iron oxide core on doxorubicin loading and release were investigated using MSNs with pore diameters of approximately 3 nm and sub-100 nm particle diameters. The nanoparticles were loaded with doxorubicin, and the drug release into phosphate-buffered saline (PBS, 10 mM, pH 7.4) at 37 °C was monitored by fluorescence spectroscopy. The release profiles were fit using the Peppas model. The results indicated diffusion-controlled release for all samples. Statistically significant differences were observed in the kinetic host-guest parameters for each sample due to the different pore topologies and the inclusion of an iron oxide core. Applying a static magnetic field to the iron oxide core WO-MS shell materials did not have a significant impact on the doxorubicin release. This is the first time that the effects of pore topology and iron oxide core have been isolated from pore diameter and particle size for these materials.

The Impact of DNA Topology and Guide Length on Target Selection by a Cytosine-Specific Cas9.

PubMed

Tsui, Tsz Kin Martin; Hand, Travis H; Duboy, Emily C; Li, Hong

2017-06-16

Cas9 is an RNA-guided DNA cleavage enzyme being actively developed for genome editing and gene regulation. To be cleaved by Cas9, a double stranded DNA, or the protospacer, must be complementary to the guide region, typically 20-nucleotides in length, of the Cas9-bound guide RNA, and adjacent to a short Cas9-specific element called Protospacer Adjacent Motif (PAM). Understanding the correct juxtaposition of the protospacer- and PAM-interaction with Cas9 will enable development of versatile and safe Cas9-based technology. We report identification and biochemical characterization of Cas9 from Acidothermus cellulolyticus (AceCas9). AceCas9 depends on a 5'-NNNCC-3' PAM and is more efficient in cleaving negative supercoils than relaxed DNA. Kinetic as well as in vivo activity assays reveal that AceCas9 achieves optimal activity when combined with a guide RNA containing a 24-nucleotide complementarity region. The cytosine-specific, DNA topology-sensitive, and extended guide-dependent properties of AceCas9 may be explored for specific genome editing applications.

On Adding Structure to Unstructured Overlay Networks

NASA Astrophysics Data System (ADS)

Leitão, João; Carvalho, Nuno A.; Pereira, José; Oliveira, Rui; Rodrigues, Luís

Unstructured peer-to-peer overlay networks are very resilient to churn and topology changes, while requiring little maintenance cost. Therefore, they are an infrastructure to build highly scalable large-scale services in dynamic networks. Typically, the overlay topology is defined by a peer sampling service that aims at maintaining, in each process, a random partial view of peers in the system. The resulting random unstructured topology is suboptimal when a specific performance metric is considered. On the other hand, structured approaches (for instance, a spanning tree) may optimize a given target performance metric but are highly fragile. In fact, the cost for maintaining structures with strong constraints may easily become prohibitive in highly dynamic networks. This chapter discusses different techniques that aim at combining the advantages of unstructured and structured networks. Namely we focus on two distinct approaches, one based on optimizing the overlay and another based on optimizing the gossip mechanism itself.

Non-Abelian Parton Fractional Quantum Hall Effect in Multilayer Graphene.

PubMed

Wu, Ying-Hai; Shi, Tao; Jain, Jainendra K

2017-08-09

The current proposals for producing non-Abelian anyons and Majorana particles, which are neither fermions nor bosons, are primarily based on the realization of topological superconductivity in two dimensions. We show theoretically that the unique Landau level structure of bilayer graphene provides a new possible avenue for achieving such exotic particles. Specifically, we demonstrate the feasibility of a "parton" fractional quantum Hall (FQH) state, which supports non-Abelian particles without the usual topological superconductivity. Furthermore, we advance this state as the fundamental explanation of the puzzling 1/2 FQH effect observed in bilayer graphene [ Kim et al. Nano Lett. 2015 , 15 , 7445 ] and predict that it will also occur in trilayer graphene. We indicate experimental signatures that differentiate the parton state from other candidate non-Abelian FQH states and predict that a transverse electric field can induce a topological quantum phase transition between two distinct non-Abelian FQH states.

Strong gravity and structure of topological solitons

NASA Astrophysics Data System (ADS)

Rybakov, Yu. P.

The unification of Skyrme and Faddeev chiral models describing baryons and leptons respectively as topological solitons is suggested within the framework of 16-spinor field ψ = ψ1 ⊕ ψ2 nonlinear model containing two 8-semispinors ψ1 and ψ2. Using Brioschi identity for 8-spinors and special structure of the Higgs potential V implying the spontaneous symmetry breaking, it is possible to realize topological soliton-like excitations of two kinds due to the choice of S2- or S3- manifolds as phase spaces. The interactions with electromagnetic, Yang--Mills and gravitational fields are exhibited through the extention of derivatives via gauge invariance principle. Specific inclusion in the Higgs potential of the Kretschmann gravitational invariant K = RμνσλRμνσλ/48 permits one to obtain the strong gravity behavior at small distances and guarantee the correspondence with Quantum Mechanics at large distances.

Dynamical generation of Floquet Majorana flat bands in s-wave superconductors

NASA Astrophysics Data System (ADS)

Poudel, A.; Ortiz, G.; Viola, L.

2015-04-01

We present quantum control techniques to engineer flat bands of symmetry-protected Majorana edge modes in s-wave superconductors. Specifically, we show how periodic control may be employed for designing time-independent effective Hamiltonians, which support Floquet Majorana flat bands, starting from equilibrium conditions that are either topologically trivial or only support a Majorana pair per edge. In the first approach, a suitable modulation of the chemical potential simultaneously induces Majorana flat bands and dynamically activates a pre-existing chiral symmetry which is responsible for their protection. In the second approach, the application of effective parity kicks dynamically generates a desired chiral symmetry by suppressing chirality-breaking terms in the static Hamiltonian. Our results demonstrate how the use of time-dependent control enlarges the range of possibilities for realizing gapless topological superconductivity, potentially enabling access to topological states of matter that have no known equilibrium counterpart.

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.

Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.

PubMed Central

Wilson, J H

1979-01-01

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed. Images PMID:291028

Early-warning signals of topological collapse in interbank networks

NASA Astrophysics Data System (ADS)

Squartini, Tiziano; van Lelyveld, Iman; Garlaschelli, Diego

2013-11-01

The financial crisis clearly illustrated the importance of characterizing the level of `systemic' risk associated with an entire credit network, rather than with single institutions. However, the interplay between financial distress and topological changes is still poorly understood. Here we analyze the quarterly interbank exposures among Dutch banks over the period 1998-2008, ending with the crisis. After controlling for the link density, many topological properties display an abrupt change in 2008, providing a clear - but unpredictable - signature of the crisis. By contrast, if the heterogeneity of banks' connectivity is controlled for, the same properties show a gradual transition to the crisis, starting in 2005 and preceded by an even earlier period during which anomalous debt loops could have led to the underestimation of counter-party risk. These early-warning signals are undetectable if the network is reconstructed from partial bank-specific data, as routinely done. We discuss important implications for bank regulatory policies.

Understanding the Giant Enhancement of Exchange Interaction in Bi 2 Se 3 - EuS Heterostructures

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

Kim, Jeongwoo; Kim, Kyoung-Whan; Wang, Hui

2017-07-01

A recent experiment indicated that a ferromagnetic EuS film in contact with a topological insulator Bi 2 Se 3 might show a largely enhanced Curie temperature and perpendicular magnetic anisotropy [F. Katmis et al., Nature (London) 533, 513 (2016).]. Through systematic density functional calculations, we demonstrate that in addition to the factor that Bi 2 Se 3 has a strong spin orbit coupling, the topological surface states are crucial to make these unusual behaviors robust as they hybridize with EuS states and extend rather far into the magnetic layers. The magnetic moments of Eu atoms are nevertheless not much enhanced,more » unlike what was reported in the experiment. Our results and model analyses provide useful insights for how these quantities are linked, and pave a way for the control of properties of magnetic films via contact with topological insulators.« less

Fractionally charged skyrmions in fractional quantum Hall effect

PubMed Central

Balram, Ajit C.; Wurstbauer, U.; Wójs, A.; Pinczuk, A.; Jain, J. K.

2015-01-01

The fractional quantum Hall effect has inspired searches for exotic emergent topological particles, such as fractionally charged excitations, composite fermions, abelian and nonabelian anyons and Majorana fermions. Fractionally charged skyrmions, which support both topological charge and topological vortex-like spin structure, have also been predicted to occur in the vicinity of 1/3 filling of the lowest Landau level. The fractional skyrmions, however, are anticipated to be exceedingly fragile, suppressed by very small Zeeman energies. Here we show that, slightly away from 1/3 filling, the smallest manifestations of the fractional skyrmion exist in the excitation spectrum for a broad range of Zeeman energies, and appear in resonant inelastic light scattering experiments as well-defined resonances slightly below the long wavelength spin wave mode. The spectroscopy of these exotic bound states serves as a sensitive tool for investigating the residual interaction between composite fermions, responsible for delicate new fractional quantum Hall states in this filling factor region. PMID:26608906

Isolated desynchronization and intertwined synchronization in networks of semiconductor lasers

NASA Astrophysics Data System (ADS)

Xu, Mingfeng; Pan, Wei; Zhang, Liyue

2018-04-01

Two patterns of synchronization in networks of semiconductor lasers (SLs) induced by symmetries of inherent network topology are presented. One type is termed isolated desynchronization, in which one or more clusters lose stability while all others remain synchronized. Another type is intertwined synchronization, in which some clusters always achieve and lose their synchrony at the same time. The existence of these special synchronization patterns and their relationship with the topology of network is discussed systemically. The results show that such behaviors exist in different topologies of SL networks. We also discussed the influence of significant parameters of SL networks on the stability of cluster synchronization. It is shown that the network dynamics is sensitive to the two key internal parameters of SLs, the linewidth-enhancement factor, and gain saturation coefficient. Our work is very beneficial to the implementation of secure communication and synchronization networks based on SLs.

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host-parasite cospeciation

PubMed Central

Fabrin, Thomaz M. C.; Gasques, Luciano S.; Prioli, Sônia M. A. P.; Balbuena, Juan A.; Prioli, Alberto J.; Takemoto, Ricardo M.

2018-01-01

Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, COI and 5.8S of the parasite species were used for phylogenetic reconstruction. Maximum likelihood phylogenetic trees of the host and parasite species were built and used for analyses of topological congruence with PACo and ParaFit. The program Jane was used to estimate the nature of cospeciation events. The comparison of the two phylogenies revealed high topological congruence between them. Both PACo and ParaFit supported the hypothesis of global cospeciation. Results from Jane pointed to duplications as the most frequent coevolutionary event, followed by cospeciation, whereas duplications followed by host-switching were the least common event in Anacanthorus spp. studied. Host-sharing (spreading) was also identified but only between congeneric host species. PMID:29538463

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host-parasite cospeciation.

PubMed

da Graça, Rodrigo J; Fabrin, Thomaz M C; Gasques, Luciano S; Prioli, Sônia M A P; Balbuena, Juan A; Prioli, Alberto J; Takemoto, Ricardo M

2018-01-01

Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, COI and 5.8S of the parasite species were used for phylogenetic reconstruction. Maximum likelihood phylogenetic trees of the host and parasite species were built and used for analyses of topological congruence with PACo and ParaFit. The program Jane was used to estimate the nature of cospeciation events. The comparison of the two phylogenies revealed high topological congruence between them. Both PACo and ParaFit supported the hypothesis of global cospeciation. Results from Jane pointed to duplications as the most frequent coevolutionary event, followed by cospeciation, whereas duplications followed by host-switching were the least common event in Anacanthorus spp. studied. Host-sharing (spreading) was also identified but only between congeneric host species.

Grand unified theories, topological defects, and ultrahigh-energy cosmic rays

NASA Technical Reports Server (NTRS)

Bhattacharjee, Pijushpani; Hill, Christopher T.; Schramm, David N.

1992-01-01

The ultrahigh-energy (UHE) proton and neutrino spectra resulting from collapse or annihilations of topological defects surviving from the GUT era are calculated. Irrespective of the specific process under consideration (which determines the overall normalization of the spectrum), the UHE proton spectrum always 'recovers' at approximately 1.8 x 10 exp 11 GeV after a partial Greisen-Zatsepin-Kuz'min 'cutoff' at approximately 5 x 10 exp 10 GeV and continues to a GUT-scale energy with a universal shape determined by the physics of hadronic jet fragmentation. Implications of the results are discussed.

Distributed control topologies for deep space formation flying spacecraft

NASA Technical Reports Server (NTRS)

Hadaegh, F. Y.; Smith, R. S.

2002-01-01

A formation of satellites flying in deep space can be specified in terms of the relative satellite positions and absolute satellite orientations. The redundancy in the relative position specification generates a family of control topologies with equivalent stability and reference tracking performance, one of which can be implemented without requiring communication between the spacecraft. A relative position design formulation is inherently unobservable, and a methodology for circumventing this problem is presented. Additional redundancy in the control actuation space can be exploited for feed-forward control of the formation centroid's location in space, or for minimization of total fuel consumption.

Grand unified theories, topological defects and ultrahigh-energy cosmic rays

NASA Technical Reports Server (NTRS)

Bhattacharjee, Pijushpani; Hill, Christopher T.; Schramm, David N.

1991-01-01

The ultrahigh-energy (UHE) proton and neutrino spectra resulting from collapse or annihilations of topological defects surviving from the GUT era are calculated. Irrespective of the specific process under consideration (which determines the overall normalization of the spectrum), the UHE proton spectrum always 'recovers' at approximately 1.8 x 10 exp 11 GeV after a partial Greisen-Zatsepin-Kuz'min 'cutoff' at approximately 5 x 10 exp 10 GeV and continues to a GUT-scale energy with a universal shape determined by the physics of hadronic jet fragmentation. Implications of our results are discussed.

Exact coupling threshold for structural transition reveals diversified behaviors in interconnected networks.

PubMed

Darabi Sahneh, Faryad; Scoglio, Caterina; Van Mieghem, Piet

2015-10-01

An interconnected network features a structural transition between two regimes [F. Radicchi and A. Arenas, Nat. Phys. 9, 717 (2013)]: one where the network components are structurally distinguishable and one where the interconnected network functions as a whole. Our exact solution for the coupling threshold uncovers network topologies with unexpected behaviors. Specifically, we show conditions that superdiffusion, introduced by Gómez et al. [Phys. Rev. Lett. 110, 028701 (2013)], can occur despite the network components functioning distinctly. Moreover, we find that components of certain interconnected network topologies are indistinguishable despite very weak coupling between them.

Parallel solution of closely coupled systems

NASA Technical Reports Server (NTRS)

Utku, S.; Salama, M.

1986-01-01

The odd-even permutation and associated unitary transformations for reordering the matrix coefficient A are employed as means of breaking the strong seriality which is characteristic of closely coupled systems. The nested dissection technique is also reviewed, and the equivalence between reordering A and dissecting its network is established. The effect of transforming A with odd-even permutation on its topology and the topology of its Cholesky factors is discussed. This leads to the construction of directed graphs showing the computational steps required for factoring A, their precedence relationships and their sequential and concurrent assignment to the available processors. Expressions for the speed-up and efficiency of using N processors in parallel relative to the sequential use of a single processor are derived from the directed graph. Similar expressions are also derived when the number of available processors is fewer than required.

Fibril growth kinetics link buffer conditions and topology of 3D collagen I networks.

PubMed

Kalbitzer, Liv; Pompe, Tilo

2018-02-01

Three-dimensional fibrillar networks reconstituted from collagen I are widely used as biomimetic scaffolds for in vitro and in vivo cell studies. Various physicochemical parameters of buffer conditions for in vitro fibril formation are well known, including pH-value, ion concentrations and temperature. However, there is a lack of a detailed understanding of reconstituting well-defined 3D network topologies, which is required to mimic specific properties of the native extracellular matrix. We screened a wide range of relevant physicochemical buffer conditions and characterized the topology of the reconstituted 3D networks in terms of mean pore size and fibril diameter. A congruent analysis of fibril formation kinetics by turbidimetry revealed the adjustment of the lateral growth phase of fibrils by buffer conditions to be key in the determination of pore size and fibril diameter of the networks. Although the kinetics of nucleation and linear growth phase were affected by buffer conditions as well, network topology was independent of those two growth phases. Overall, the results of our study provide necessary insights into how to engineer 3D collagen matrices with an independent control over topology parameters, in order to mimic in vivo tissues in in vitro experiments and tissue engineering applications. The study reports a comprehensive analysis of physicochemical conditions of buffer solutions to reconstitute defined 3D collagen I matrices. By a combined analysis of network topology, i.e., pore size and fibril diameter, and the kinetics of fibril formation we can reveal the dependence of 3D network topology on buffer conditions, such as pH-value, phosphate concentration and sodium chloride content. With those results we are now able to provide engineering strategies to independently tune the topology parameters of widely used 3D collagen scaffolds based on the buffer conditions. By that, we enable the straightforward mimicking of extracellular matrices of in vivo tissues for in vitro cell culture experiments and tissue engineering applications. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Atomic layer-by-layer thermoelectric conversion in topological insulator bismuth/antimony tellurides.

PubMed

Sung, Ji Ho; Heo, Hoseok; Hwang, Inchan; Lim, Myungsoo; Lee, Donghun; Kang, Kibum; Choi, Hee Cheul; Park, Jae-Hoon; Jhi, Seung-Hoon; Jo, Moon-Ho

2014-07-09

Material design for direct heat-to-electricity conversion with substantial efficiency essentially requires cooperative control of electrical and thermal transport. Bismuth telluride (Bi2Te3) and antimony telluride (Sb2Te3), displaying the highest thermoelectric power at room temperature, are also known as topological insulators (TIs) whose electronic structures are modified by electronic confinements and strong spin-orbit interaction in a-few-monolayers thickness regime, thus possibly providing another degree of freedom for electron and phonon transport at surfaces. Here, we explore novel thermoelectric conversion in the atomic monolayer steps of a-few-layer topological insulating Bi2Te3 (n-type) and Sb2Te3 (p-type). Specifically, by scanning photoinduced thermoelectric current imaging at the monolayer steps, we show that efficient thermoelectric conversion is accomplished by optothermal motion of hot electrons (Bi2Te3) and holes (Sb2Te3) through 2D subbands and topologically protected surface states in a geometrically deterministic manner. Our discovery suggests that the thermoelectric conversion can be interiorly achieved at the atomic steps of a homogeneous medium by direct exploiting of quantum nature of TIs, thus providing a new design rule for the compact thermoelectric circuitry at the ultimate size limit.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins

PubMed Central

Debelyy, Mykhaylo O.; Waridel, Patrice; Quadroni, Manfredo; Conzelmann, Andreas

2017-01-01

Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort. Here, we report novel XL-MS-based topology data for 17 integral membrane proteins (Akr1p, Fks1p, Gas1p, Ggc1p, Gpt2p, Ifa38p, Ist2p, Lag1p, Pet9p, Pma1p, Por1p, Sct1p, Sec61p, Slc1p, Spf1p, Vph1p, Ybt1p). PMID:29073188

Cell cycle stage-specific differential expression of topoisomerase I in tobacco BY-2 cells and its ectopic overexpression and knockdown unravels its crucial role in plant morphogenesis and development.

PubMed

Singh, Badri Nath; Mudgil, Yashwanti; John, Riffat; Achary, V Mohan Murali; Tripathy, Manas Kumar; Sopory, Sudhir K; Reddy, Malireddy K; Kaul, Tanushri

2015-11-01

DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. Cell cycle coupled differential accumulation of topoisomerase I (Topo I) revealed biphasic expression maximum at S-phase and M/G1-phase of cultured synchronized tobacco BY-2 cells. This suggested its active role in resolving topological constrains during DNA replication (S-phase) and chromosome decondensation (M/G1 phase). Immuno-localization revealed high concentrations of Topo I in nucleolus. Propidium iodide staining and Br-UTP incorporation patterns revealed direct correlation between immunofluorescence intensity and rRNA transcription activity within nucleolus. Immuno-stained chromosomes during metaphase and anaphase suggested possible role of Topo I in resolving topological constrains during mitotic chromosome condensation. Inhibitor studies showed that in comparison to Topo I, Topo II was essential in resolving topological constrains during chromosome condensation. Probably, Topo II substituted Topo I functioning to certain extent during chromosome condensation, but not vice-versa. Transgenic Topo I tobacco lines revealed morphological abnormalities and highlighted its crucial role in plant morphogenesis and development. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Electromagnetic waves in a topological insulator thin film stack: helicon-like wave mode and photonic band structure.

PubMed

Inoue, Jun-ichi

2013-09-09

We theoretically explore the electromagnetic modes specific to a topological insulator superlattice in which topological and conventional insulator thin films are stacked periodically. In particular, we obtain analytic formulas for low energy mode that corresponds to a helicon wave, as well as those for photonic bands. We illustrate that the system can be modeled as a stack of quantum Hall layers whose conductivity tensors alternately change signs, and then we analyze the photonic band structures. This subject is a natural extension of a previous study by Tselis et al., which took into consideration a stack of identical quantum Hall layers but their discussion was limited into a low energy mode. Thus we provide analytic formulas for photonic bands and compare their features between the two systems. Our central findings in the topological insulator superlattice are that a low energy mode corresponding to a helicon wave has linear dispersion instead of the conventional quadratic form, and that a robust gapless photonic band appears although the system considered has spacial periodicity. In addition, we demonstrate that the photonic bands agree with the numerically calculated transmission spectra.

Solar Sail Topology Variations Due to On-Orbit Thermal Effects

NASA Technical Reports Server (NTRS)

Banik, Jeremy A.; Lively, Peter S.; Taleghani, Barmac K.; Jenkins, Chrostopher H.

2006-01-01

The objective of this research was to predict the influence of non-uniform temperature distribution on solar sail topology and the effect of such topology variations on sail performance (thrust, torque). Specifically considered were the thermal effects due to on orbit attitude control maneuvers. Such maneuvers are expected to advance the sail to a position off-normal to the sun by as much as 35 degrees; a solar sail initially deformed by typical pre-tension and solar pressure loads may suffer significant thermally induced strains due to the non-uniform heating caused by these maneuvers. This on-orbit scenario was investigated through development of an automated analytical shape model that iterates many times between sail shape and sail temperature distribution before converging on a final coupled thermal structural affected sail topology. This model utilizes a validated geometrically non-linear finite element model and a thermal radiation subroutine. It was discovered that temperature gradients were deterministic for the off-normal solar angle cases as were thermally induced strains. Performance effects were found to be moderately significant but not as large as initially suspected. A roll torque was detected, and the sail center of pressure shifted by a distance that may influence on-orbit sail control stability.

Detecting network communities beyond assortativity-related attributes

NASA Astrophysics Data System (ADS)

Liu, Xin; Murata, Tsuyoshi; Wakita, Ken

2014-07-01

In network science, assortativity refers to the tendency of links to exist between nodes with similar attributes. In social networks, for example, links tend to exist between individuals of similar age, nationality, location, race, income, educational level, religious belief, and language. Thus, various attributes jointly affect the network topology. An interesting problem is to detect community structure beyond some specific assortativity-related attributes ρ, i.e., to take out the effect of ρ on network topology and reveal the hidden community structures which are due to other attributes. An approach to this problem is to redefine the null model of the modularity measure, so as to simulate the effect of ρ on network topology. However, a challenge is that we do not know to what extent the network topology is affected by ρ and by other attributes. In this paper, we propose a distance modularity, which allows us to freely choose any suitable function to simulate the effect of ρ. Such freedom can help us probe the effect of ρ and detect the hidden communities which are due to other attributes. We test the effectiveness of distance modularity on synthetic benchmarks and two real-world networks.

Efficient Photothermoelectric Conversion in Lateral Topological Insulator Heterojunctions.

PubMed

Mashhadi, Soudabeh; Duong, Dinh Loc; Burghard, Marko; Kern, Klaus

2017-01-11

Tuning the electron and phonon transport properties of thermoelectric materials by nanostructuring has enabled improving their thermopower figure of merit. Three-dimensional topological insulators, including many bismuth chalcogenides, attract increasing attention for this purpose, as their topologically protected surface states are promising to further enhance the thermoelectric performance. While individual bismuth chalcogenide nanostructures have been studied with respect to their photothermoelectric properties, nanostructured p-n junctions of these compounds have not yet been explored. Here, we experimentally investigate the room temperature thermoelectric conversion capability of lateral heterostructures consisting of two different three-dimensional topological insulators, namely, the n-type doped Bi 2 Te 2 Se and the p-type doped Sb 2 Te 3 . Scanning photocurrent microscopy of the nanoplatelets reveals efficient thermoelectric conversion at the p-n heterojunction, exploiting hot carriers of opposite sign in the two materials. From the photocurrent data, a Seebeck coefficient difference of ΔS = 200 μV/K was extracted, in accordance with the best values reported for the corresponding bulk materials. Furthermore, it is in very good agreement with the value of ΔS = 185 μV/K obtained by DFT calculation taking into account the specific doping levels of the two nanostructured components.

Two-spectral Yang-Baxter operators in topological quantum computation

NASA Astrophysics Data System (ADS)

Sanchez, William F.

2011-05-01

One of the current trends in quantum computing is the application of algebraic topological methods in the design of new algorithms and quantum computers, giving rise to topological quantum computing. One of the tools used in it is the Yang-Baxter equation whose solutions are interpreted as universal quantum gates. Lately, more general Yang-Baxter equations have been investigated, making progress as two-spectral equations and Yang-Baxter systems. This paper intends to apply these new findings to the field of topological quantum computation, more specifically, the proposition of the two-spectral Yang-Baxter operators as universal quantum gates for 2 qubits and 2 qutrits systems, obtaining 4x4 and 9x9 matrices respectively, and further elaboration of the corresponding Hamiltonian by the use of computer algebra software Mathematica® and its Qucalc package. In addition, possible physical systems to which the Yang-Baxter operators obtained can be applied are considered. In the present work it is demonstrated the utility of the Yang-Baxter equation to generate universal quantum gates and the power of computer algebra to design them; it is expected that these mathematical studies contribute to the further development of quantum computers

Quantum oscillations in a topological insulator Bi2Te2Se with large bulk resistivity (6 Ω cm)

NASA Astrophysics Data System (ADS)

Xiong, Jun; Petersen, A. C.; Qu, Dongxia; Hor, Y. S.; Cava, R. J.; Ong, N. P.

2012-02-01

We report the observation of prominent Shubnikov-de Haas oscillations in a Topological Insulator, Bi2Te2Se, with large bulk resistivity (6 Ω cm at 4 K). By fitting the SdH oscillations, we infer a large metallicity parameter kFℓ=41, with a surface mobility (μs∼2800 cm2/V s) much larger than the bulk mobility (μb∼50 cm2/V s). The plot of the index fields Bν vs. filling factor ν shows a {1}/{2}-shift, consistent with massless, Dirac states.

A modular electric power system test bed for small spacecraft

NASA Technical Reports Server (NTRS)

Button, Robert M.; Baez, Anastacio N.

1994-01-01

In the new climate of smaller, faster, and cheaper space science satellites, a new power system topology has been developed at the NASA Lewis Research Center. This new topology is based on a series connected boost converter (SCBC) and can greatly affect the size, weight, fault tolerance, and cost of any small spacecraft using photovoltaic solar arrays. The paper presents electric power system design factors and requirements as background information. The series connected boost converter topology is discussed and several advantages over existing technologies are illustrated. Besides being small, lightweight, and efficient, this topology has the added benefit of inherent fault tolerance. A positive ground power system test bed has been developed for the TROPIX spacecraft program. Performance of the SCBC in the test bed is described in detail. SCBC efficiencies of 95 percent to 98 percent have been measured. Finally, a modular, photovoltaic regulator 'kit' concept is presented. Two SCBC's are used to regulate solar array charging of batteries and to provide 'utilitytype' power to the user loads. The kit's modularity will allow a spacecraft electric power system to be built from off-the-shelf hardware; resulting in smaller, faster, and cheaper spacecraft.

Deterministic ripple-spreading model for complex networks.

PubMed

Hu, Xiao-Bing; Wang, Ming; Leeson, Mark S; Hines, Evor L; Di Paolo, Ezequiel

2011-04-01

This paper proposes a deterministic complex network model, which is inspired by the natural ripple-spreading phenomenon. The motivations and main advantages of the model are the following: (i) The establishment of many real-world networks is a dynamic process, where it is often observed that the influence of a few local events spreads out through nodes, and then largely determines the final network topology. Obviously, this dynamic process involves many spatial and temporal factors. By simulating the natural ripple-spreading process, this paper reports a very natural way to set up a spatial and temporal model for such complex networks. (ii) Existing relevant network models are all stochastic models, i.e., with a given input, they cannot output a unique topology. Differently, the proposed ripple-spreading model can uniquely determine the final network topology, and at the same time, the stochastic feature of complex networks is captured by randomly initializing ripple-spreading related parameters. (iii) The proposed model can use an easily manageable number of ripple-spreading related parameters to precisely describe a network topology, which is more memory efficient when compared with traditional adjacency matrix or similar memory-expensive data structures. (iv) The ripple-spreading model has a very good potential for both extensions and applications.

Fermi Level Manipulation through Native Doping in the Topological Insulator Bi2Se3.

PubMed

Walsh, Lee A; Green, Avery J; Addou, Rafik; Nolting, Westly; Cormier, Christopher R; Barton, Adam T; Mowll, Tyler R; Yue, Ruoyu; Lu, Ning; Kim, Jiyoung; Kim, Moon J; LaBella, Vincent P; Ventrice, Carl A; McDonnell, Stephen; Vandenberghe, William G; Wallace, Robert M; Diebold, Alain; Hinkle, Christopher L

2018-06-08

The topologically protected surface states of three-dimensional (3D) topological insulators have the potential to be transformative for high-performance logic and memory devices by exploiting their specific properties such as spin-polarized current transport and defect tolerance due to suppressed backscattering. However, topological insulator based devices have been underwhelming to date primarily due to the presence of parasitic issues. An important example is the challenge of suppressing bulk conduction in Bi 2 Se 3 and achieving Fermi levels ( E F ) that reside in between the bulk valence and conduction bands so that the topologically protected surface states dominate the transport. The overwhelming majority of the Bi 2 Se 3 studies in the literature report strongly n-type materials with E F in the bulk conduction band due to the presence of a high concentration of selenium vacancies. In contrast, here we report the growth of near-intrinsic Bi 2 Se 3 with a minimal Se vacancy concentration providing a Fermi level near midgap with no extrinsic counter-doping required. We also demonstrate the crucial ability to tune E F from below midgap into the upper half of the gap near the conduction band edge by controlling the Se vacancy concentration using post-growth anneals. Additionally, we demonstrate the ability to maintain this Fermi level control following the careful, low-temperature removal of a protective Se cap, which allows samples to be transported in air for device fabrication. Thus, we provide detailed guidance for E F control that will finally enable researchers to fabricate high-performance devices that take advantage of transport through the topologically protected surface states of Bi 2 Se 3 .

Correlations between prefrontal neurons form a small-world network that optimizes the generation of multineuron sequences of activity

PubMed Central

Luongo, Francisco J.; Zimmerman, Chris A.; Horn, Meryl E.

2016-01-01

Sequential patterns of prefrontal activity are believed to mediate important behaviors, e.g., working memory, but it remains unclear exactly how they are generated. In accordance with previous studies of cortical circuits, we found that prefrontal microcircuits in young adult mice spontaneously generate many more stereotyped sequences of activity than expected by chance. However, the key question of whether these sequences depend on a specific functional organization within the cortical microcircuit, or emerge simply as a by-product of random interactions between neurons, remains unanswered. We observed that correlations between prefrontal neurons do follow a specific functional organization—they have a small-world topology. However, until now it has not been possible to directly link small-world topologies to specific circuit functions, e.g., sequence generation. Therefore, we developed a novel analysis to address this issue. Specifically, we constructed surrogate data sets that have identical levels of network activity at every point in time but nevertheless represent various network topologies. We call this method shuffling activity to rearrange correlations (SHARC). We found that only surrogate data sets based on the actual small-world functional organization of prefrontal microcircuits were able to reproduce the levels of sequences observed in actual data. As expected, small-world data sets contained many more sequences than surrogate data sets with randomly arranged correlations. Surprisingly, small-world data sets also outperformed data sets in which correlations were maximally clustered. Thus the small-world functional organization of cortical microcircuits, which effectively balances the random and maximally clustered regimes, is optimal for producing stereotyped sequential patterns of activity. PMID:26888108

An ensemble framework for clustering protein-protein interaction networks.

PubMed

Asur, Sitaram; Ucar, Duygu; Parthasarathy, Srinivasan

2007-07-01

Protein-Protein Interaction (PPI) networks are believed to be important sources of information related to biological processes and complex metabolic functions of the cell. The presence of biologically relevant functional modules in these networks has been theorized by many researchers. However, the application of traditional clustering algorithms for extracting these modules has not been successful, largely due to the presence of noisy false positive interactions as well as specific topological challenges in the network. In this article, we propose an ensemble clustering framework to address this problem. For base clustering, we introduce two topology-based distance metrics to counteract the effects of noise. We develop a PCA-based consensus clustering technique, designed to reduce the dimensionality of the consensus problem and yield informative clusters. We also develop a soft consensus clustering variant to assign multifaceted proteins to multiple functional groups. We conduct an empirical evaluation of different consensus techniques using topology-based, information theoretic and domain-specific validation metrics and show that our approaches can provide significant benefits over other state-of-the-art approaches. Our analysis of the consensus clusters obtained demonstrates that ensemble clustering can (a) produce improved biologically significant functional groupings; and (b) facilitate soft clustering by discovering multiple functional associations for proteins. Supplementary data are available at Bioinformatics online.

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.

Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta Propeller Domains

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

M Collins; W Hendrickson

2011-12-31

Folding and trafficking of low-density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, are mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD {beta} propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation, and X-ray crystallography were used to define a conserved core composed of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold withmore » two distinct {beta} sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of nonspecific hydrophobic interactions that may play a role in the chaperone activity of the Boca/Mesd family.« less

Influence of DNA sequence on the structure of minicircles under torsional stress

PubMed Central

Wang, Qian; Irobalieva, Rossitza N.; Chiu, Wah; Schmid, Michael F.; Fogg, Jonathan M.; Zechiedrich, Lynn

2017-01-01

Abstract The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence. We showed that simulations and theory are able to provide sequence-specific information about individual DNA minicircles observed by cryo-electron tomography (cryo-ET). We provided a sequence-specific cryo-ET tomogram fitting of DNA minicircles, registering the sequence within the geometric features. Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy. PMID:28609782

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of non-supercoiling type II topoisomerases

PubMed Central

Stuchinskaya, Tanya; Mitchenall, Lesley A.; Schoeffler, Allyn J.; Corbett, Kevin D.; Berger, James M.; Bates, Andrew D.; Maxwell, Anthony

2015-01-01

DNA topoisomerases control the topology of DNA (e.g. the level of supercoiling) in all cells. Type IIA topoisomerases are ATP-dependent enzymes that have been shown to simplify the topology of their DNA substrates to a level beyond that expected at equilibrium (i.e. more relaxed than the product of relaxation by ATP-independent enzymes, such as type I topoisomerases, or a lower than equilibrium level of catenation). The mechanism of this effect is currently unknown, although several models have been suggested. We have analysed the DNA relaxation reactions of type II topoisomerases to further explore this phenomenon. We find that all type IIA topoisomerases tested exhibit the effect to a similar degree and that it is not dependent on the C-terminal domains of the enzymes. As recently reported, the type IIB topoisomerase, topo VI (which is only distantly related to the type IIA enzymes), does not exhibit topology simplification. We find that topology simplification is not significantly dependent on circle size in the range ~2–9 kbp, and is not altered by reducing the free energy available from ATP hydrolysis by varying the ATP:ADP ratio. A direct test of one model (DNA tracking, i.e. sliding of a protein clamp along DNA to trap supercoils) suggests that this is unlikely to be the explanation for the effect. We conclude that geometric selection of DNA segments by the enzymes is likely to be a primary source of the effect but that it is possible that other factors contribute. We also speculate whether topology simplification might simply be an evolutionary relic, with no adaptive significance. PMID:19094994

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases.

PubMed

Stuchinskaya, Tanya; Mitchenall, Lesley A; Schoeffler, Allyn J; Corbett, Kevin D; Berger, James M; Bates, Andrew D; Maxwell, Anthony

2009-02-06

DNA topoisomerases control the topology of DNA (e.g., the level of supercoiling) in all cells. Type IIA topoisomerases are ATP-dependent enzymes that have been shown to simplify the topology of their DNA substrates to a level beyond that expected at equilibrium (i.e., more relaxed than the product of relaxation by ATP-independent enzymes, such as type I topoisomerases, or a lower-than-equilibrium level of catenation). The mechanism of this effect is currently unknown, although several models have been suggested. We have analyzed the DNA relaxation reactions of type II topoisomerases to further explore this phenomenon. We find that all type IIA topoisomerases tested exhibit the effect to a similar degree and that it is not dependent on the supercoil-sensing C-terminal domains of the enzymes. As recently reported, the type IIB topoisomerase, topoisomerase VI (which is only distantly related to type IIA enzymes), does not exhibit topology simplification. We find that topology simplification is not significantly dependent on circle size in the range approximately 2-9 kbp and is not altered by reducing the free energy available from ATP hydrolysis by varying the ADP:ATP ratio. A direct test of one model (DNA tracking; i.e., sliding of a protein clamp along DNA to trap supercoils) suggests that this is unlikely to be the explanation for the effect. We conclude that geometric selection of DNA segments by the enzymes is likely to be a primary source of the effect, but that it is possible that other kinetic factors contribute. We also speculate whether topology simplification might simply be an evolutionary relic, with no adaptive significance.

Ultrahigh lattice thermal conductivity in topological semimetal TaN caused by a large acoustic-optical gap.

PubMed

Guo, San-Dong; Liu, Bang-Gui

2018-03-14

Topological semimetals may have potential applications such as in topological qubits, spintronics and quantum computations. Efficient heat dissipation is a key factor for the reliability and stability of topological semimetal-based nano-electronics devices, which is closely related to high thermal conductivity. In this work, the elastic properties and lattice thermal conductivity of TaN are investigated using first-principles calculations and the linearized phonon Boltzmann equation within the single-mode relaxation time approximation. According to the calculated bulk modulus, shear modulus and C 44 , TaN can be regarded as a potential incompressible and hard material. The room-temperature lattice thermal conductivity is predicted to be 838.62 [Formula: see text] along the a axis and 1080.40 [Formula: see text] along the c axis, showing very strong anisotropy. It is found that the lattice thermal conductivity of TaN is several tens of times higher than other topological semimetals, such as TaAs, MoP and ZrTe, which is due to the very longer phonon lifetimes for TaN than other topological semimetals. The very different atomic masses of Ta and N atoms lead to a very large acoustic-optical band gap, and then prohibit the scattering between acoustic and optical phonon modes, which gives rise to very long phonon lifetimes. Calculated results show that isotope scattering has little effect on lattice thermal conductivity, and that phonons with mean free paths larger than 20 (80) [Formula: see text] along the c direction at 300 K have little contribution to the total lattice thermal conductivity. This work implies that TaN-based nano-electronics devices may be more stable and reliable due to efficient heat dissipation, and motivates further experimental works to study lattice thermal conductivity of TaN.

Ultrahigh lattice thermal conductivity in topological semimetal TaN caused by a large acoustic-optical gap

NASA Astrophysics Data System (ADS)

Guo, San-Dong; Liu, Bang-Gui

2018-03-01

Topological semimetals may have potential applications such as in topological qubits, spintronics and quantum computations. Efficient heat dissipation is a key factor for the reliability and stability of topological semimetal-based nano-electronics devices, which is closely related to high thermal conductivity. In this work, the elastic properties and lattice thermal conductivity of TaN are investigated using first-principles calculations and the linearized phonon Boltzmann equation within the single-mode relaxation time approximation. According to the calculated bulk modulus, shear modulus and C 44, TaN can be regarded as a potential incompressible and hard material. The room-temperature lattice thermal conductivity is predicted to be 838.62 W~m-1~K^{-1} along the a axis and 1080.40 W~m-1~K^{-1} along the c axis, showing very strong anisotropy. It is found that the lattice thermal conductivity of TaN is several tens of times higher than other topological semimetals, such as TaAs, MoP and ZrTe, which is due to the very longer phonon lifetimes for TaN than other topological semimetals. The very different atomic masses of Ta and N atoms lead to a very large acoustic-optical band gap, and then prohibit the scattering between acoustic and optical phonon modes, which gives rise to very long phonon lifetimes. Calculated results show that isotope scattering has little effect on lattice thermal conductivity, and that phonons with mean free paths larger than 20 (80) μm along the c direction at 300 K have little contribution to the total lattice thermal conductivity. This work implies that TaN-based nano-electronics devices may be more stable and reliable due to efficient heat dissipation, and motivates further experimental works to study lattice thermal conductivity of TaN.

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

Adam, C.; Klimas, P.; Sanchez-Guillen, J.

For the baby Skyrme model with a specific potential, compacton solutions, i.e., configurations with a compact support and parabolic approach to the vacuum, are derived. Specifically, in the nontopological sector, we find spinning Q-balls and Q-shells, as well as peakons. Moreover, we obtain compact baby skyrmions with nontrivial topological charge. All these solutions may form stable multisoliton configurations provided they are sufficiently separated.

Connectome sensitivity or specificity: which is more important?

PubMed

Zalesky, Andrew; Fornito, Alex; Cocchi, Luca; Gollo, Leonardo L; van den Heuvel, Martijn P; Breakspear, Michael

2016-11-15

Connectomes with high sensitivity and high specificity are unattainable with current axonal fiber reconstruction methods, particularly at the macro-scale afforded by magnetic resonance imaging. Tensor-guided deterministic tractography yields sparse connectomes that are incomplete and contain false negatives (FNs), whereas probabilistic methods steered by crossing-fiber models yield dense connectomes, often with low specificity due to false positives (FPs). Densely reconstructed probabilistic connectomes are typically thresholded to improve specificity at the cost of a reduction in sensitivity. What is the optimal tradeoff between connectome sensitivity and specificity? We show empirically and theoretically that specificity is paramount. Our evaluations of the impact of FPs and FNs on empirical connectomes indicate that specificity is at least twice as important as sensitivity when estimating key properties of brain networks, including topological measures of network clustering, network efficiency and network modularity. Our asymptotic analysis of small-world networks with idealized modular structure reveals that as the number of nodes grows, specificity becomes exactly twice as important as sensitivity to the estimation of the clustering coefficient. For the estimation of network efficiency, the relative importance of specificity grows linearly with the number of nodes. The greater importance of specificity is due to FPs occurring more prevalently between network modules rather than within them. These spurious inter-modular connections have a dramatic impact on network topology. We argue that efforts to maximize the sensitivity of connectome reconstruction should be realigned with the need to map brain networks with high specificity. Copyright © 2016 Elsevier Inc. All rights reserved.

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

PubMed Central

Apte, Advait A; Cain, John W; Bonchev, Danail G; Fong, Stephen S

2008-01-01

Background Feed-forward motifs are important functional modules in biological and other complex networks. The functionality of feed-forward motifs and other network motifs is largely dictated by the connectivity of the individual network components. While studies on the dynamics of motifs and networks are usually devoted to the temporal or spatial description of processes, this study focuses on the relationship between the specific architecture and the overall rate of the processes of the feed-forward family of motifs, including double and triple feed-forward loops. The search for the most efficient network architecture could be of particular interest for regulatory or signaling pathways in biology, as well as in computational and communication systems. Results Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling. The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate. Several basic topological patterns were identified that order the specific feed-forward constructions according to the rate of dynamics they enable. At the same number of network nodes and constant other parameters, the bi-parallel and tri-parallel motifs provide higher network efficacy than single feed-forward motifs. Additionally, a topological property of isodynamicity was identified for feed-forward motifs where different network architectures resulted in the same overall rate of the target production. Conclusion It was shown for classes of structural motifs with feed-forward architecture that network topology affects the overall rate of a process in a quantitatively predictable manner. These fundamental results can be used as a basis for simulating larger networks as combinations of smaller network modules with implications on studying synthetic gene circuits, small regulatory systems, and eventually dynamic whole-cell models. PMID:18304325

Frequency specific brain networks in Parkinson's disease and comorbid depression.

PubMed

Qian, Long; Zhang, Yi; Zheng, Li; Fu, Xuemei; Liu, Weiguo; Shang, Yuqing; Zhang, Yaoyu; Xu, Yuanyuan; Liu, Yijun; Zhu, Huaiqiu; Gao, Jia-Hong

2017-02-01

The topological organization underlying the human brain was extensively investigated using resting-state functional magnetic resonance imaging, focusing on a low frequency of signal oscillation from 0.01 to 0.1 Hz. However, the frequency specificities with regard to the topological properties of the brain networks have not been fully revealed. In this study, a novel complementary ensemble empirical mode decomposition (CEEMD) method was used to separate the fMRI time series into five characteristic oscillations with distinct frequencies. Then, the small world properties of brain networks were analyzed for each of these five oscillations in patients (n = 67) with depressed Parkinson's disease (DPD, n = 20) , non-depressed Parkinson's disease (NDPD, n = 47) and healthy controls (HC, n = 46). Compared with HC, the results showed decreased network efficiency in characteristic oscillations from 0.05 to 0.12 Hz and from 0.02 to 0.05 Hz for the DPD and NDPD patients, respectively. Furthermore, compared with HC, the most significant inter-group difference across five brain oscillations was found in the basal ganglia (0.01 to 0.05 Hz) and paralimbic-limbic network (0.02 to 0.22 Hz) for the DPD patients, and in the visual cortex (0.02 to 0.05 Hz) for the NDPD patients. Compared with NDPD, the DPD patients showed reduced efficiency of nodes in the basal ganglia network (0.01 to 0.05 Hz). Our results demonstrated that DPD is characterized by a disrupted topological organization in large-scale brain functional networks. Moreover, the CEEMD analysis suggested a prominent dissociation in the topological organization of brain networks between DPD and NDPD in both space and frequency domains. Our findings indicated that these characteristic oscillatory activities in different functional circuits may contribute to distinct motor and non-motor components of clinical impairments in Parkinson's disease.

Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series.

PubMed

Klimovskaia, Anna; Ganscha, Stefan; Claassen, Manfred

2016-12-01

Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants. We have assessed the structure learning capabilities of the reactionet lasso on synthetic data for the complete TRAIL induced apoptosis signaling cascade comprising 70 reactions. We find that the reactionet lasso is able to efficiently recover the structure of these reaction systems, ab initio, with high sensitivity and specificity. With only < 1% false discoveries, the reactionet lasso is able to recover 45% of all true reactions ab initio among > 6000 possible reactions and over 102000 network topologies. In conjunction with information rich single cell technologies such as single cell RNA sequencing or mass cytometry, the reactionet lasso will enable large-scale structure learning, particularly in areas with partial network structure knowledge, such as cancer biology, and thereby enable the detection of pathological alterations of reaction networks. We provide software to allow for wide applicability of the reactionet lasso.

Superconductivity in a Misfit Phase That Combines the Topological Crystalline Insulator Pb 1-xSn xSe with the CDW-Bearing Transition Metal Dichalcogenide TiSe 2

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

Luo, H.; Yan, K.; Pletikosic, I.

We report the characterization of the misfit compound (Pb 1-xSn xSe 2)1.16(TiSe 2) 2 for 0 ≤ x ≤ 0.6, in which a [100] rocksalt-structure bilayer of Pb1-xSnxSe, which is a topological crystalline insulator in bulk form, alternates with a double layer of the normally nonsuperconducting transition metal dichalcogenide TiSe 2. The x dependence of Tc displays a weak dome-like shape with a maximum Tc of 4.5 K at x = 0.2; there is only a subtle change in Tc at the composition where the trivial to topological transition occurs in bulk Pb1-xSnxSe. We present the characterization of the superconductormore » at x = 0.4, for which the bulk Pb1-xSnxSe phase is in the topological crystalline insulator regime. For this material, the Sommerfeld parameter γ = 11.06 mJ mol -1 K -2, the Debye temperature Θ D = 161 K, the normalized specific heat jump value ΔC/γT c = 1.38 and the electron-phonon constant value γ ep = 0.72, suggesting that (Pb 0.6Sn 0.4Se) 1.16(TiSe 2) 2 is a BCS-type weak coupling superconductor. This material may be of interest for probing the interaction of superconductivity with the surface states of a topological crystalline insulator.« less

Magnetic quantum phase transition in Cr-doped Bi2(SexTe1-x)3 driven by the Stark effect

NASA Astrophysics Data System (ADS)

Zhang, Zuocheng; Feng, Xiao; Wang, Jing; Lian, Biao; Zhang, Jinsong; Chang, Cuizu; Guo, Minghua; Ou, Yunbo; Feng, Yang; Zhang, Shou-Cheng; He, Ke; Ma, Xucun; Xue, Qi-Kun; Wang, Yayu

2017-10-01

The recent experimental observation of the quantum anomalous Hall effect has cast significant attention on magnetic topological insulators. In these magnetic counterparts of conventional topological insulators such as Bi2Te3, a long-range ferromagnetic state can be established by chemical doping with transition-metal elements. However, a much richer electronic phase diagram can emerge and, in the specific case of Cr-doped Bi2(SexTe1-x)3, a magnetic quantum phase transition tuned by the actual chemical composition has been reported. From an application-oriented perspective, the relevance of these results hinges on the possibility to manipulate magnetism and electronic band topology by external perturbations such as an electric field generated by gate electrodes—similar to what has been achieved in conventional diluted magnetic semiconductors. Here, we investigate the magneto-transport properties of Cr-doped Bi2(SexTe1-x)3 with different compositions under the effect of a gate voltage. The electric field has a negligible effect on magnetic order for all investigated compositions, with the remarkable exception of the sample close to the topological quantum critical point, where the gate voltage reversibly drives a ferromagnetic-to-paramagnetic phase transition. Theoretical calculations show that a perpendicular electric field causes a shift in the electronic energy levels due to the Stark effect, which induces a topological quantum phase transition and, in turn, a magnetic phase transition.

Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks.

PubMed

Jovanović, Stojan; Rotter, Stefan

2016-06-01

The study of processes evolving on networks has recently become a very popular research field, not only because of the rich mathematical theory that underpins it, but also because of its many possible applications, a number of them in the field of biology. Indeed, molecular signaling pathways, gene regulation, predator-prey interactions and the communication between neurons in the brain can be seen as examples of networks with complex dynamics. The properties of such dynamics depend largely on the topology of the underlying network graph. In this work, we want to answer the following question: Knowing network connectivity, what can be said about the level of third-order correlations that will characterize the network dynamics? We consider a linear point process as a model for pulse-coded, or spiking activity in a neuronal network. Using recent results from theory of such processes, we study third-order correlations between spike trains in such a system and explain which features of the network graph (i.e. which topological motifs) are responsible for their emergence. Comparing two different models of network topology-random networks of Erdős-Rényi type and networks with highly interconnected hubs-we find that, in random networks, the average measure of third-order correlations does not depend on the local connectivity properties, but rather on global parameters, such as the connection probability. This, however, ceases to be the case in networks with a geometric out-degree distribution, where topological specificities have a strong impact on average correlations.

Probing the Topological Properties of Complex Networks Modeling Short Written Texts

PubMed Central

Amancio, Diego R.

2015-01-01

In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well—many informative discoveries have been made this way—but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks. PMID:25719799

Superconductivity in a Misfit Phase That Combines the Topological Crystalline Insulator Pb 1-xSn xSe with the CDW-Bearing Transition Metal Dichalcogenide TiSe 2

DOE PAGES

Luo, H.; Yan, K.; Pletikosic, I.; ...

2016-05-13

We report the characterization of the misfit compound (Pb 1-xSn xSe 2)1.16(TiSe 2) 2 for 0 ≤ x ≤ 0.6, in which a [100] rocksalt-structure bilayer of Pb1-xSnxSe, which is a topological crystalline insulator in bulk form, alternates with a double layer of the normally nonsuperconducting transition metal dichalcogenide TiSe 2. The x dependence of Tc displays a weak dome-like shape with a maximum Tc of 4.5 K at x = 0.2; there is only a subtle change in Tc at the composition where the trivial to topological transition occurs in bulk Pb1-xSnxSe. We present the characterization of the superconductormore » at x = 0.4, for which the bulk Pb1-xSnxSe phase is in the topological crystalline insulator regime. For this material, the Sommerfeld parameter γ = 11.06 mJ mol -1 K -2, the Debye temperature Θ D = 161 K, the normalized specific heat jump value ΔC/γT c = 1.38 and the electron-phonon constant value γ ep = 0.72, suggesting that (Pb 0.6Sn 0.4Se) 1.16(TiSe 2) 2 is a BCS-type weak coupling superconductor. This material may be of interest for probing the interaction of superconductivity with the surface states of a topological crystalline insulator.« less

Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species.

PubMed

Nouripour-Sisakht, Sadegh; Ahmadi, Bahram; Makimura, Koichi; Hoog, Sybren de; Umeda, Yoshiko; Alshahni, Mohamed Mahdi; Mirhendi, Hossein

2017-04-01

We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides. The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.

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

PubMed

Brown, Jeremy M; Thomson, Robert C

2018-02-15

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

Preclinical evaluation of nuclear morphometry and tissue topology for breast carcinoma detection and margin assessment

PubMed Central

Nyirenda, Ndeke; Farkas, Daniel L.

2010-01-01

Prevention and early detection of breast cancer are the major prophylactic measures taken to reduce the breast cancer related mortality and morbidity. Clinical management of breast cancer largely relies on the efficacy of the breast-conserving surgeries and the subsequent radiation therapy. A key problem that limits the success of these surgeries is the lack of accurate, real-time knowledge about the positive tumor margins in the surgically excised tumors in the operating room. This leads to tumor recurrence and, hence, the need for repeated surgeries. Current intraoperative techniques such as frozen section pathology or touch imprint cytology severely suffer from poor sampling and non-optimal detection sensitivity. Even though histopathology analysis can provide information on positive tumor margins post-operatively (~2–3 days), this information is of no immediate utility in the operating rooms. In this article, we propose a novel image analysis method for tumor margin assessment based on nuclear morphometry and tissue topology and demonstrate its high sensitivity/specificity in preclinical animal model of breast carcinoma. The method relies on imaging nuclear-specific fluorescence in the excised surgical specimen and on extracting nuclear morphometric parameters (size, number, and area fraction) from the spatial distribution of the observed fluorescence in the tissue. We also report the utility of tissue topology in tumor margin assessment by measuring the fractal dimension in the same set of images. By a systematic analysis of multiple breast tissues specimens, we show here that the proposed method is not only accurate (~97% sensitivity and 96% specificity) in thin sections, but also in three-dimensional (3D) thick tissues that mimic the realistic lumpectomy specimens. Our data clearly precludes the utility of nuclear size as a reliable diagnostic criterion for tumor margin assessment. On the other hand, nuclear area fraction addresses this issue very effectively since it is a combination of both nuclear size and count in any given region of the analyzed image, and thus yields high sensitivity and specificity (~97%) in tumor detection. This is further substantiated by an independent parameter, fractal dimension, based on the tissue topology. Although the basic definition of cancer as an uncontrolled cell growth entails a high nuclear density in tumor regions, a simple but systematic exploration of nuclear distribution in thick tissues by nuclear morphometry and tissue topology as performed in this study has never been carried out, to the best of our knowledge. We discuss the practical aspects of implementing this imaging approach in automated tissue sampling scenario where the accuracy of tumor margin assessment can be significantly increased by scanning the entire surgical specimen rather than sampling only a few sections as in current histopathology analysis. PMID:20446030

Topological Weyl semimetals in Bi1 -xSbx alloys

NASA Astrophysics Data System (ADS)

Su, Yu-Hsin; Shi, Wujun; Felser, Claudia; Sun, Yan

2018-04-01

We investigated Weyl semimetal (WSM) phases in bismuth antimony (Bi1 -xSbx ) alloys by combination of atomic composition and arrangement. Via first-principles calculations, we found two WSM states with Sb concentrations of x =0.5 and 0.83 with specific inversion-symmetry-broken elemental arrangement. The Weyl points are close to the Fermi level in both of these two WSM states. Therefore, it is likely to obtain Weyl points in Bi-Sb alloy. The WSM phase provides a reasonable explanation for the current transport study of Bi-Sb alloy with the violation of Ohm's law [D. Shin, Y. Lee, M. Sasaki, Y. H. Jeong, F. Weickert, J. B. Betts, H.-J. Kim, K.-S. Kim, and J. Kim, Nat. Mater. 16, 1096 (2017), 10.1038/nmat4965]. This paper shows that the topological phases in Bi-Sb alloys depend on both elemental composition and their specific arrangement.

Noise propagation issues in Belle II pixel detector power cable

NASA Astrophysics Data System (ADS)

Iglesias, M.; Arteche, F.; Echeverria, I.; Pradas, A.; Rivetta, C.; Moser, H.-G.; Kiesling, C.; Rummel, S.; Arcega, F. J.

2018-04-01

The vertex detector used in the upgrade of High-Energy physics experiment Belle II includes DEPFET pixel detector (PXD) technology. In this complex topology the power supply units and the front-end electronics are connected through a PXD power cable bundle which may propagate the output noise from the power supplies to the vertex area. This paper presents a study of the propagation of noise caused by power converters in the PXD cable bundle based on Multi-conductor Transmission Line (MTL) theory. The work exposes the effect of the complex cable topology and shield connections on the noise propagation, which has an impact on the requirements of the power supplies. This analysis is part of the electromagnetic compatibility based design focused on functional safety to define the shield connections and power supply specifications required to ensure the successful integration of the detector and, specifically, to achieve the designed performance of the front-end electronics.

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

PubMed

Oosterveen, Tony; Kurdija, Sanja; Ensterö, Mats; Uhde, Christopher W; Bergsland, Maria; Sandberg, Magnus; Sandberg, Rickard; Muhr, Jonas; Ericson, Johan

2013-04-30

The reiterative deployment of a small cadre of morphogen signals underlies patterning and growth of most tissues during embyogenesis, but how such inductive events result in tissue-specific responses remains poorly understood. By characterizing cis-regulatory modules (CRMs) associated with genes regulated by Sonic hedgehog (Shh), retinoids, or bone morphogenetic proteins in the CNS, we provide evidence that the neural-specific interpretation of morphogen signaling reflects a direct integration of these pathways with SoxB1 proteins at the CRM level. Moreover, expression of SoxB1 proteins in the limb bud confers on mesodermal cells the potential to activate neural-specific target genes upon Shh, retinoid, or bone morphogenetic protein signaling, and the collocation of binding sites for SoxB1 and morphogen-mediatory transcription factors in CRMs faithfully predicts neural-specific gene activity. Thus, an unexpectedly simple transcriptional paradigm appears to conceptually explain the neural-specific interpretation of pleiotropic signaling during vertebrate development. Importantly, genes induced in a SoxB1-dependent manner appear to constitute repressive gene regulatory networks that are directly interlinked at the CRM level to constrain the regional expression of patterning genes. Accordingly, not only does the topology of SoxB1-driven gene regulatory networks provide a tissue-specific mode of gene activation, but it also determines the spatial expression pattern of target genes within the developing neural tube.

Modeling Wildfire Hazard in the Western Hindu Kush-Himalayas

NASA Astrophysics Data System (ADS)

Bylow, D.

2012-12-01

Wildfire regimes are a leading driver of global environmental change affecting a diverse array of global ecosystems. Particulates and aerosols produced by wildfires are a primary source of air pollution making the early detection and monitoring of wildfires crucial. The objectives of this study were to model regional wildfire potential and identify environmental, topological, and sociological factors that contribute to the ignition of wildfire events in the Western Hindu Kush-Himalayas of South Asia. The environmental, topological, and sociological factors were used to model regional wildfire potential through multi-criteria evaluation using a method of weighted linear combination. Moderate Resolution Imaging Spectroradiometer (MODIS) and geographic information systems (GIS) data were integrated to analyze regional wildfires and construct the model. Model validation was performed using a holdout cross validation method. The study produced a significant model of wildfire potential in the Western Hindu Kush-Himalayas.; Western Hindu Kush-Himalayas ; Western Hindu Kush-Himalayas Wildfire Potential

A New Type Hi-Speed BLDC Control System Base on Indirect Current Control Strategy

NASA Astrophysics Data System (ADS)

Wang, D. P.; Wang, Y. C.; Zhang, F. G.; Jin, S.

2017-05-01

High speed BLDC has the characteristic as larger air gap smaller armature inductance, traditional PWM modulation will produce a great number of high frequency current harmonics which led problem like large torque ripple and serious motor heat. In the meantime traditional PWM modulation use the diode rectifier which cause harmonic pollution in electric power net. To solve the problem above, proposes a new motor controller topology. Using the IGBT device to replace the diode on frequency converter rectifier side, apply the power factor correction technology, reduce the pollution on the grid. Using busbar current modulation on the inverter, driving bridge-arm use 3-phase 6-state open as driving Mode, realize the control on a 10000r/min,10kw BLDC. The results of Simulation on matlab show the topological structure as proposed can effectively improve the network side power factor and reduce the motor armature winding harmonic and motor torque ripple.

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

PubMed

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

A CityGML Extension for Handling Very Large Tins

NASA Astrophysics Data System (ADS)

Kumar, K.; Ledoux, H.; Stoter, J.

2016-10-01

In addition to buildings, the terrain forms an important part of a 3D city model. Although in GIS terrains are usually represented with 2D grids, TINs are also increasingly being used in practice. One example is 3DTOP10NL, the 3D city model covering the whole of the Netherlands, which stores the relief with a constrained TIN containing more than 1 billion triangles. Due to the massive size of such datasets, the main problem that arises is: how to efficiently store and maintain them? While CityGML supports the storage of TINs, we argue in this paper that the current solution is not adequate. For instance, the 1 billion+ triangles of 3DTOP10NL require 686 GB of storage space with CityGML. Furthermore, the current solution does not store the topological relationships of the triangles, and also there are no clear mechanisms to handle several LODs. We propose in this paper a CityGML extension for the compact representation of terrains. We describe our abstract and implementation specifications (modelled in UML), and our prototype implementation to convert TINs to our CityGML structure. It increases the topological relationships that are explicitly represented, and allows us to compress up to a factor of ∼ 25 in our experiments with massive real-world terrains (more than 1 billion triangles).

Strong interband Faraday rotation in 3D topological insulator Bi2Se3.

PubMed

Ohnoutek, L; Hakl, M; Veis, M; Piot, B A; Faugeras, C; Martinez, G; Yakushev, M V; Martin, R W; Drašar, Č; Materna, A; Strzelecka, G; Hruban, A; Potemski, M; Orlita, M

2016-01-11

The Faraday effect is a representative magneto-optical phenomenon, resulting from the transfer of angular momentum between interacting light and matter in which time-reversal symmetry has been broken by an externally applied magnetic field. Here we report on the Faraday rotation induced in the prominent 3D topological insulator Bi2Se3 due to bulk interband excitations. The origin of this non-resonant effect, extraordinarily strong among other non-magnetic materials, is traced back to the specific Dirac-type Hamiltonian for Bi2Se3, which implies that electrons and holes in this material closely resemble relativistic particles with a non-zero rest mass.

Topological Aspects of Information Retrieval.

ERIC Educational Resources Information Center

Egghe, Leo; Rousseau, Ronald

1998-01-01

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

Multinetwork of international trade: A commodity-specific analysis

NASA Astrophysics Data System (ADS)

Barigozzi, Matteo; Fagiolo, Giorgio; Garlaschelli, Diego

2010-04-01

We study the topological properties of the multinetwork of commodity-specific trade relations among world countries over the 1992-2003 period, comparing them with those of the aggregate-trade network, known in the literature as the international-trade network (ITN). We show that link-weight distributions of commodity-specific networks are extremely heterogeneous and (quasi) log normality of aggregate link-weight distribution is generated as a sheer outcome of aggregation. Commodity-specific networks also display average connectivity, clustering, and centrality levels very different from their aggregate counterpart. We also find that ITN complete connectivity is mainly achieved through the presence of many weak links that keep commodity-specific networks together and that the correlation structure existing between topological statistics within each single network is fairly robust and mimics that of the aggregate network. Finally, we employ cross-commodity correlations between link weights to build hierarchies of commodities. Our results suggest that on the top of a relatively time-invariant “intrinsic” taxonomy (based on inherent between-commodity similarities), the roles played by different commodities in the ITN have become more and more dissimilar, possibly as the result of an increased trade specialization. Our approach is general and can be used to characterize any multinetwork emerging as a nontrivial aggregation of several interdependent layers.

Hsmar1 Transposition Is Sensitive to the Topology of the Transposon Donor and the Target

PubMed Central

Claeys Bouuaert, Corentin; Chalmers, Ronald

2013-01-01

Hsmar1 is a member of the Tc1-mariner superfamily of DNA transposons. These elements mobilize within the genome of their host by a cut-and-paste mechanism. We have exploited the in vitro reaction provided by Hsmar1 to investigate the effect of DNA supercoiling on transposon integration. We found that the topology of both the transposon and the target affect integration. Relaxed transposons have an integration defect that can be partially restored in the presence of elevated levels of negatively supercoiled target DNA. Negatively supercoiled DNA is a better target than nicked or positively supercoiled DNA, suggesting that underwinding of the DNA helix promotes target interactions. Like other Tc1-mariner elements, Hsmar1 integrates into 5′-TA dinucleotides. The direct vicinity of the target TA provides little sequence specificity for target interactions. However, transposition within a plasmid substrate was not random and some TA dinucleotides were targeted preferentially. The distribution of intramolecular target sites was not affected by DNA topology. PMID:23341977

Early-warning signals of topological collapse in interbank networks

PubMed Central

Squartini, Tiziano; van Lelyveld, Iman; Garlaschelli, Diego

2013-01-01

The financial crisis clearly illustrated the importance of characterizing the level of ‘systemic’ risk associated with an entire credit network, rather than with single institutions. However, the interplay between financial distress and topological changes is still poorly understood. Here we analyze the quarterly interbank exposures among Dutch banks over the period 1998–2008, ending with the crisis. After controlling for the link density, many topological properties display an abrupt change in 2008, providing a clear – but unpredictable – signature of the crisis. By contrast, if the heterogeneity of banks' connectivity is controlled for, the same properties show a gradual transition to the crisis, starting in 2005 and preceded by an even earlier period during which anomalous debt loops could have led to the underestimation of counter-party risk. These early-warning signals are undetectable if the network is reconstructed from partial bank-specific data, as routinely done. We discuss important implications for bank regulatory policies. PMID:24285089

A Novel Paradigm for Computer-Aided Design: TRIZ-Based Hybridization of Topologically Optimized Density Distributions

NASA Astrophysics Data System (ADS)

Cardillo, A.; Cascini, G.; Frillici, F. S.; Rotini, F.

In a recent project the authors have proposed the adoption of Optimization Systems [1] as a bridging element between Computer-Aided Innovation (CAI) and PLM to identify geometrical contradictions [2], a particular case of the TRIZ physical contradiction [3]. A further development of the research [4] has revealed that the solutions obtained from several topological optimizations can be considered as elementary customized modeling features for a specific design task. The topology overcoming the arising geometrical contradiction can be obtained through a manipulation of the density distributions constituting the conflicting pair. Already two strategies of density combination have been identified as capable to solve geometrical contradictions and several others are under extended testing. The paper illustrates the most recent results of the ongoing research mainly related to the extension of the algorithms from 2D to 3D design spaces. The whole approach is clarified by means of two detailed examples, where the proposed technique is compared with classical multi-goal optimization.

Comparing the locking threshold for rings and chains of oscillators.

PubMed

Ottino-Löffler, Bertrand; Strogatz, Steven H

2016-12-01

We present a case study of how topology can affect synchronization. Specifically, we consider arrays of phase oscillators coupled in a ring or a chain topology. Each ring is perfectly matched to a chain with the same initial conditions and the same random natural frequencies. The only difference is their boundary conditions: periodic for a ring and open for a chain. For both topologies, stable phase-locked states exist if and only if the spread or "width" of the natural frequencies is smaller than a critical value called the locking threshold (which depends on the boundary conditions and the particular realization of the frequencies). The central question is whether a ring synchronizes more readily than a chain. We show that it usually does, but not always. Rigorous bounds are derived for the ratio between the locking thresholds of a ring and its matched chain, for a variant of the Kuramoto model that also includes a wider family of models.

Topological self-organization and prediction learning support both action and lexical chains in the brain.

PubMed

Chersi, Fabian; Ferro, Marcello; Pezzulo, Giovanni; Pirrelli, Vito

2014-07-01

A growing body of evidence in cognitive psychology and neuroscience suggests a deep interconnection between sensory-motor and language systems in the brain. Based on recent neurophysiological findings on the anatomo-functional organization of the fronto-parietal network, we present a computational model showing that language processing may have reused or co-developed organizing principles, functionality, and learning mechanisms typical of premotor circuit. The proposed model combines principles of Hebbian topological self-organization and prediction learning. Trained on sequences of either motor or linguistic units, the network develops independent neuronal chains, formed by dedicated nodes encoding only context-specific stimuli. Moreover, neurons responding to the same stimulus or class of stimuli tend to cluster together to form topologically connected areas similar to those observed in the brain cortex. Simulations support a unitary explanatory framework reconciling neurophysiological motor data with established behavioral evidence on lexical acquisition, access, and recall. Copyright © 2014 Cognitive Science Society, Inc.

Defects controlled wrinkling and topological design in graphene

NASA Astrophysics Data System (ADS)

Zhang, Teng; Li, Xiaoyan; Gao, Huajian

2014-07-01

Due to its atomic scale thickness, the deformation energy in a free standing graphene sheet can be easily released through out-of-plane wrinkles which, if controllable, may be used to tune the electrical and mechanical properties of graphene. Here we adopt a generalized von Karman equation for a flexible solid membrane to describe graphene wrinkling induced by a prescribed distribution of topological defects such as disclinations (heptagons or pentagons) and dislocations (heptagon-pentagon dipoles). In this framework, a given distribution of topological defects in a graphene sheet is represented as an eigenstrain field which is determined from a Poisson equation and can be conveniently implemented in finite element (FEM) simulations. Comparison with atomistic simulations indicates that the proposed model, with only three parameters (i.e., bond length, stretching modulus and bending stiffness), is capable of accurately predicting the atomic scale wrinkles near disclination/dislocation cores while also capturing the large scale graphene configurations under specific defect distributions such as those leading to a sinusoidal surface ruga2

Network Analysis of Publications on Topological Indices from the Web of Science.

PubMed

Bodlaj, Jernej; Batagelj, Vladimir

2014-08-01

In this paper we analyze a collection of bibliographic networks, constructed from the data from the Web of Science on works (papers, books, etc.) on the topic of topological indices and on relating scientific fields. We present the general outlook and more specific findings about authors, works and journals, subtopics and keywords and also important relations between them based on scientometric approaches like the strongest and main citation paths, the main themes on citation path based on keywords, results of co-authorship analysis in form of the most prominent islands of citing authors, groups of collaborating authors, two-mode cores of authors and works. We investigate the nature of citing of authors, important journals and citing of works between them, journals preferred by authors and expose hierarchy of similar collaborating authors, based on keywords they use. We perform temporal analysis on one important journal as well. We give a comprehensive scientometric insight into the field of topological indices. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparing the locking threshold for rings and chains of oscillators

NASA Astrophysics Data System (ADS)

Ottino-Löffler, Bertrand; Strogatz, Steven H.

2016-12-01

We present a case study of how topology can affect synchronization. Specifically, we consider arrays of phase oscillators coupled in a ring or a chain topology. Each ring is perfectly matched to a chain with the same initial conditions and the same random natural frequencies. The only difference is their boundary conditions: periodic for a ring and open for a chain. For both topologies, stable phase-locked states exist if and only if the spread or "width" of the natural frequencies is smaller than a critical value called the locking threshold (which depends on the boundary conditions and the particular realization of the frequencies). The central question is whether a ring synchronizes more readily than a chain. We show that it usually does, but not always. Rigorous bounds are derived for the ratio between the locking thresholds of a ring and its matched chain, for a variant of the Kuramoto model that also includes a wider family of models.

Coherent ultrafast spin-dynamics probed in three dimensional topological insulators

PubMed Central

Boschini, F.; Mansurova, M.; Mussler, G.; Kampmeier, J.; Grützmacher, D.; Braun, L.; Katmis, F.; Moodera, J. S.; Dallera, C.; Carpene, E.; Franz, C.; Czerner, M.; Heiliger, C.; Kampfrath, T.; Münzenberg, M.

2015-01-01

Topological insulators are candidates to open up a novel route in spin based electronics. Different to traditional ferromagnetic materials, where the carrier spin-polarization and magnetization are based on the exchange interaction, the spin properties in topological insulators are based on the coupling of spin- and orbit interaction connected to its momentum. Specific ways to control the spin-polarization with light have been demonstrated: the energy momentum landscape of the Dirac cone provides spin-momentum locking of the charge current and its spin. We investigate a spin-related signal present only during the laser excitation studying real and imaginary part of the complex Kerr angle by disentangling spin and lattice contributions. This coherent signal is only present at the time of the pump-pulses’ light field and can be described in terms of a Raman coherence time. The Raman transition involves states at the bottom edge of the conduction band. We demonstrate a coherent femtosecond control of spin-polarization for electronic states at around the Dirac cone. PMID:26510509

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.

Topology-changing shape optimization with the genetic algorithm

NASA Astrophysics Data System (ADS)

Lamberson, Steven E., Jr.

The goal is to take a traditional shape optimization problem statement and modify it slightly to allow for prescribed changes in topology. This modification enables greater flexibility in the choice of parameters for the topology optimization problem, while improving the direct physical relevance of the results. This modification involves changing the optimization problem statement from a nonlinear programming problem into a form of mixed-discrete nonlinear programing problem. The present work demonstrates one possible way of using the Genetic Algorithm (GA) to solve such a problem, including the use of "masking bits" and a new modification to the bit-string affinity (BSA) termination criterion specifically designed for problems with "masking bits." A simple ten-bar truss problem proves the utility of the modified BSA for this type of problem. A more complicated two dimensional bracket problem is solved using both the proposed approach and a more traditional topology optimization approach (Solid Isotropic Microstructure with Penalization or SIMP) to enable comparison. The proposed approach is able to solve problems with both local and global constraints, which is something traditional methods cannot do. The proposed approach has a significantly higher computational burden --- on the order of 100 times larger than SIMP, although the proposed approach is able to offset this with parallel computing.

Hemispheric Asymmetry of Human Brain Anatomical Network Revealed by Diffusion Tensor Tractography

PubMed Central

Liu, Yaou; Duan, Yunyun; Li, Kuncheng

2015-01-01

The topological architecture of the cerebral anatomical network reflects the structural organization of the human brain. Recently, topological measures based on graph theory have provided new approaches for quantifying large-scale anatomical networks. However, few studies have investigated the hemispheric asymmetries of the human brain from the perspective of the network model, and little is known about the asymmetries of the connection patterns of brain regions, which may reflect the functional integration and interaction between different regions. Here, we utilized diffusion tensor imaging to construct binary anatomical networks for 72 right-handed healthy adult subjects. We established the existence of structural connections between any pair of the 90 cortical and subcortical regions using deterministic tractography. To investigate the hemispheric asymmetries of the brain, statistical analyses were performed to reveal the brain regions with significant differences between bilateral topological properties, such as degree of connectivity, characteristic path length, and betweenness centrality. Furthermore, local structural connections were also investigated to examine the local asymmetries of some specific white matter tracts. From the perspective of both the global and local connection patterns, we identified the brain regions with hemispheric asymmetries. Combined with the previous studies, we suggested that the topological asymmetries in the anatomical network may reflect the functional lateralization of the human brain. PMID:26539535

Dirac topological insulator in the dz2 manifold of a honeycomb oxide

NASA Astrophysics Data System (ADS)

Lado, J. L.; Pardo, V.

2016-09-01

We show by means of ab initio calculations and tight-binding modeling that an oxide system based on a honeycomb lattice can sustain topologically nontrivial states if a single orbital dominates the spectrum close to the Fermi level. In such a situation, the low-energy spectrum is described by two Dirac equations that become nontrivially gapped when spin-orbit coupling (SOC) is switched on. We provide one specific example but the recipe is general. We discuss a realization of this starting from a conventional spin-1/2 honeycomb antiferromagnet whose states close to the Fermi energy are dz2 orbitals. Switching off magnetism by atomic substitution and ensuring that the electronic structure becomes two-dimensional is sufficient for topologicality to arise in such a system. By deriving a tight-binding Wannier Hamiltonian, we find that the gap in such a model scales linearly with SOC, opposed to other oxide-based topological insulators, where smaller gaps tend to appear by construction of the lattice. We show that the quantum spin Hall state in this system survives in the presence of off-plane magnetism and the orbital magnetic field and we discuss its Landau level spectra, showing that our recipe provides a dz2 realization of the Kane-Mele model.

Coalescent histories for caterpillar-like families.

PubMed

Rosenberg, Noah A

2013-01-01

A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree topology is important in gene tree probability computations, and more generally, in studying evolutionary possibilities for gene trees on species trees. Defining the Tr-caterpillar-like family as a sequence of n-taxon trees constructed by replacing the r-taxon subtree of n-taxon caterpillars by a specific r-taxon labeled topology Tr, we examine the number of coalescent histories for caterpillar-like families with matching gene tree and species tree labeled topologies. For each Tr with size r≤8, we compute the number of coalescent histories for n-taxon trees in the Tr-caterpillar-like family. Next, as n→∞, we find that the limiting ratio of the numbers of coalescent histories for the Tr family and caterpillars themselves is correlated with the number of labeled histories for Tr. The results support a view that large numbers of coalescent histories occur when a tree has both a relatively balanced subtree and a high tree depth, contributing to deeper understanding of the combinatorics of gene trees and species trees.

Visualization of Morse connection graphs for topologically rich 2D vector fields.

PubMed

Szymczak, Andrzej; Sipeki, Levente

2013-12-01

Recent advances in vector field topologymake it possible to compute its multi-scale graph representations for autonomous 2D vector fields in a robust and efficient manner. One of these representations is a Morse Connection Graph (MCG), a directed graph whose nodes correspond to Morse sets, generalizing stationary points and periodic trajectories, and arcs - to trajectories connecting them. While being useful for simple vector fields, the MCG can be hard to comprehend for topologically rich vector fields, containing a large number of features. This paper describes a visual representation of the MCG, inspired by previous work on graph visualization. Our approach aims to preserve the spatial relationships between the MCG arcs and nodes and highlight the coherent behavior of connecting trajectories. Using simulations of ocean flow, we show that it can provide useful information on the flow structure. This paper focuses specifically on MCGs computed for piecewise constant (PC) vector fields. In particular, we describe extensions of the PC framework that make it more flexible and better suited for analysis of data on complex shaped domains with a boundary. We also describe a topology simplification scheme that makes our MCG visualizations less ambiguous. Despite the focus on the PC framework, our approach could also be applied to graph representations or topological skeletons computed using different methods.

Development of Human Brain Structural Networks Through Infancy and Childhood

PubMed Central

Huang, Hao; Shu, Ni; Mishra, Virendra; Jeon, Tina; Chalak, Lina; Wang, Zhiyue J.; Rollins, Nancy; Gong, Gaolang; Cheng, Hua; Peng, Yun; Dong, Qi; He, Yong

2015-01-01

During human brain development through infancy and childhood, microstructural and macrostructural changes take place to reshape the brain's structural networks and better adapt them to sophisticated functional and cognitive requirements. However, structural topological configuration of the human brain during this specific development period is not well understood. In this study, diffusion magnetic resonance image (dMRI) of 25 neonates, 13 toddlers, and 25 preadolescents were acquired to characterize network dynamics at these 3 landmark cross-sectional ages during early childhood. dMRI tractography was used to construct human brain structural networks, and the underlying topological properties were quantified by graph-theory approaches. Modular organization and small-world attributes are evident at birth with several important topological metrics increasing monotonically during development. Most significant increases of regional nodes occur in the posterior cingulate cortex, which plays a pivotal role in the functional default mode network. Positive correlations exist between nodal efficiencies and fractional anisotropy of the white matter traced from these nodes, while correlation slopes vary among the brain regions. These results reveal substantial topological reorganization of human brain structural networks through infancy and childhood, which is likely to be the outcome of both heterogeneous strengthening of the major white matter tracts and pruning of other axonal fibers. PMID:24335033

Topology design and performance analysis of an integrated communication network

NASA Technical Reports Server (NTRS)

Li, V. O. K.; Lam, Y. F.; Hou, T. C.; Yuen, J. H.

1985-01-01

A research study on the topology design and performance analysis for the Space Station Information System (SSIS) network is conducted. It is begun with a survey of existing research efforts in network topology design. Then a new approach for topology design is presented. It uses an efficient algorithm to generate candidate network designs (consisting of subsets of the set of all network components) in increasing order of their total costs, and checks each design to see if it forms an acceptable network. This technique gives the true cost-optimal network, and is particularly useful when the network has many constraints and not too many components. The algorithm for generating subsets is described in detail, and various aspects of the overall design procedure are discussed. Two more efficient versions of this algorithm (applicable in specific situations) are also given. Next, two important aspects of network performance analysis: network reliability and message delays are discussed. A new model is introduced to study the reliability of a network with dependent failures. For message delays, a collection of formulas from existing research results is given to compute or estimate the delays of messages in a communication network without making the independence assumption. The design algorithm coded in PASCAL is included as an appendix.

Methods and approaches in the topology-based analysis of biological pathways

PubMed Central

Mitrea, Cristina; Taghavi, Zeinab; Bokanizad, Behzad; Hanoudi, Samer; Tagett, Rebecca; Donato, Michele; Voichiţa, Călin; Drăghici, Sorin

2013-01-01

The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such pathways are meant to capture. During the past few years, a plethora of methods claiming to incorporate various aspects of the pathway topology have been proposed. These topology-based methods, sometimes referred to as “third generation,” have the potential to better model the phenomena described by pathways. Although there is now a large variety of approaches used for this purpose, no review is currently available to offer guidance for potential users and developers. This review covers 22 such topology-based pathway analysis methods published in the last decade. We compare these methods based on: type of pathways analyzed (e.g., signaling or metabolic), input (subset of genes, all genes, fold changes, gene p-values, etc.), mathematical models, pathway scoring approaches, output (one or more pathway scores, p-values, etc.) and implementation (web-based, standalone, etc.). We identify and discuss challenges, arising both in methodology and in pathway representation, including inconsistent terminology, different data formats, lack of meaningful benchmarks, and the lack of tissue and condition specificity. PMID:24133454

Andreev spectrum with high spin-orbit interactions: Revealing spin splitting and topologically protected crossings

NASA Astrophysics Data System (ADS)

Murani, A.; Chepelianskii, A.; Guéron, S.; Bouchiat, H.

2017-10-01

In order to point out experimentally accessible signatures of spin-orbit interaction, we investigate numerically the Andreev spectrum of a multichannel mesoscopic quantum wire (N) with high spin-orbit interaction coupled to superconducting electrodes (S), contrasting topological and nontopological behaviors. In the nontopological case (square lattice with Rashba interactions), we find that the Kramers degeneracy of Andreev levels is lifted by a phase difference between the S reservoirs except at multiples of π , when the normal quantum wires can host several conduction channels. The level crossings at these points invariant by time-reversal symmetry are not lifted by disorder. Whereas the dc Josephson current is insensitive to these level crossings, the high-frequency admittance (susceptibility) at finite temperature reveals these level crossings and the lifting of their degeneracy at π by a small Zeeman field. We have also investigated the hexagonal lattice with intrinsic spin-orbit interaction in the range of parameters where it is a two-dimensional topological insulator with one-dimensional helical edges protected against disorder. Nontopological superconducting contacts can induce topological superconductivity in this system characterized by zero-energy level crossing of Andreev levels. Both Josephson current and finite-frequency admittance carry then very specific signatures at low temperature of this disorder-protected Andreev level crossing at π and zero energy.

Thermodynamics. [algebraic structure

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1976-01-01

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

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.

Ambipolar surface state thermoelectric power of topological insulator Bi2Se3.

PubMed

Kim, Dohun; Syers, Paul; Butch, Nicholas P; Paglione, Johnpierre; Fuhrer, Michael S

2014-01-01

We measure gate-tuned thermoelectric power of mechanically exfoliated Bi2Se3 thin films in the topological insulator regime. The sign of the thermoelectric power changes across the charge neutrality point as the majority carrier type switches from electron to hole, consistent with the ambipolar electric field effect observed in conductivity and Hall effect measurements. Near the charge neutrality point and at low temperatures, the gate-dependent thermoelectric power follows the semiclassical Mott relation using the expected surface state density of states but is larger than expected at high electron doping, possibly reflecting a large density of states in the bulk gap. The thermoelectric power factor shows significant enhancement near the electron-hole puddle carrier density ∼0.5 × 10(12) cm(-2) per surface at all temperatures. Together with the expected reduction of lattice thermal conductivity in low-dimensional structures, the results demonstrate that nanostructuring and Fermi level tuning of three-dimensional topological insulators can be promising routes to realize efficient thermoelectric devices.

Optimal topologies for maximizing network transmission capacity

NASA Astrophysics Data System (ADS)

Chen, Zhenhao; Wu, Jiajing; Rong, Zhihai; Tse, Chi K.

2018-04-01

It has been widely demonstrated that the structure of a network is a major factor that affects its traffic dynamics. In this work, we try to identify the optimal topologies for maximizing the network transmission capacity, as well as to build a clear relationship between structural features of a network and the transmission performance in terms of traffic delivery. We propose an approach for designing optimal network topologies against traffic congestion by link rewiring and apply them on the Barabási-Albert scale-free, static scale-free and Internet Autonomous System-level networks. Furthermore, we analyze the optimized networks using complex network parameters that characterize the structure of networks, and our simulation results suggest that an optimal network for traffic transmission is more likely to have a core-periphery structure. However, assortative mixing and the rich-club phenomenon may have negative impacts on network performance. Based on the observations of the optimized networks, we propose an efficient method to improve the transmission capacity of large-scale networks.

Fractionally charged skyrmions in fractional quantum Hall effect

DOE PAGES

Balram, Ajit C.; Wurstbauer, U.; Wójs, A.; ...

2015-11-26

The fractional quantum Hall effect has inspired searches for exotic emergent topological particles, such as fractionally charged excitations, composite fermions, abelian and nonabelian anyons and Majorana fermions. Fractionally charged skyrmions, which support both topological charge and topological vortex-like spin structure, have also been predicted to occur in the vicinity of 1/3 filling of the lowest Landau level. The fractional skyrmions, however, are anticipated to be exceedingly fragile, suppressed by very small Zeeman energies. Here we show that, slightly away from 1/3 filling, the smallest manifestations of the fractional skyrmion exist in the excitation spectrum for a broad range of Zeemanmore » energies, and appear in resonant inelastic light scattering experiments as well-defined resonances slightly below the long wavelength spin wave mode. The spectroscopy of these exotic bound states serves as a sensitive tool for investigating the residual interaction between composite fermions, responsible for delicate new fractional quantum Hall states in this filling factor region.« less

QSTR of the toxicity of some organophosphorus compounds by using the quantum chemical and topological descriptors.

PubMed

Senior, Samir A; Madbouly, Magdy D; El massry, Abdel-Moneim

2011-09-01

Quantum chemical and topological descriptors of some organophosphorus compounds (OP) were correlated with their toxicity LD(50) as a dermal. The quantum chemical parameters were obtained using B3LYP/LANL2DZdp-ECP optimization. Using linear regression analysis, equations were derived to calculate the theoretical LD(50) of the studied compounds. The inclusion of quantum parameters, having both charge indices and topological indices, affects the toxicity of the studied compounds resulting in high correlation coefficient factors for the obtained equations. Two of the new four firstly supposed descriptors give higher correlation coefficients namely the Heteroatom Corrected Extended Connectivity Randic index ((1)X(HCEC)) and the Density Randic index ((1)X(Den)). The obtained linear equations were applied to predict the toxicity of some related structures. It was found that the sulfur atoms in these compounds must be replaced by oxygen atoms to achieve improved toxicity. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Single-cell topological RNA-Seq analysis reveals insights into cellular differentiation and development

PubMed Central

Rizvi, Abbas H.; Camara, Pablo G.; Kandror, Elena K.; Roberts, Thomas J.; Schieren, Ira; Maniatis, Tom; Rabadan, Raul

2017-01-01

Transcriptional programs control cellular lineage commitment and differentiation during development. Understanding cell fate has been advanced by studying single-cell RNA-seq, but is limited by the assumptions of current analytic methods regarding the structure of data. We present single-cell topological data analysis (scTDA), an algorithm for topology-based computational analyses to study temporal, unbiased transcriptional regulation. Compared to other methods, scTDA is a non-linear, model-independent, unsupervised statistical framework that can characterize transient cellular states. We applied scTDA to the analysis of murine embryonic stem cell (mESC) differentiation in vitro in response to inducers of motor neuron differentiation. scTDA resolved asynchrony and continuity in cellular identity over time, and identified four transient states (pluripotent, precursor, progenitor, and fully differentiated cells) based on changes in stage-dependent combinations of transcription factors, RNA-binding proteins and long non-coding RNAs. scTDA can be applied to study asynchronous cellular responses to either developmental cues or environmental perturbations. PMID:28459448

Pierced Lasso Proteins

NASA Astrophysics Data System (ADS)

Jennings, Patricia

Entanglement and knots are naturally occurring, where, in the microscopic world, knots in DNA and homopolymers are well characterized. The most complex knots are observed in proteins which are harder to investigate, as proteins are heteropolymers composed of a combination of 20 different amino acids with different individual biophysical properties. As new-knotted topologies and new proteins containing knots continue to be discovered and characterized, the investigation of knots in proteins has gained intense interest. Thus far, the principle focus has been on the evolutionary origin of tying a knot, with questions of how a protein chain `self-ties' into a knot, what the mechanism(s) are that contribute to threading, and the biological relevance and functional implication of a knotted topology in vivo gaining the most insight. Efforts to study the fully untied and unfolded chain indicate that the knot is highly stable, remaining intact in the unfolded state orders of magnitude longer than first anticipated. The persistence of ``stable'' knots in the unfolded state, together with the challenge of defining an unfolded and untied chain from an unfolded and knotted chain, complicates the study of fully untied protein in vitro. Our discovery of a new class of knotted proteins, the Pierced Lassos (PL) loop topology, simplifies the knotting approach. While PLs are not easily recognizable by the naked eye, they have now been identified in many proteins in the PDB through the use of computation tools. PL topologies are diverse proteins found in all kingdoms of life, performing a large variety of biological responses such as cell signaling, immune responses, transporters and inhibitors (http://lassoprot.cent.uw.edu.pl/). Many of these PL topologies are secreted proteins, extracellular proteins, as well as, redox sensors, enzymes and metal and co-factor binding proteins; all of which provide a favorable environment for the formation of the disulphide bridge. In the PL topologies, the threaded topology is formed by a covalent loop where part of the polypeptide chain is threaded through, forming what we term a PL. The advantage of a PL topology for fundamental studies, compared to other knotted proteins, is that the threaded topology can easily be manipulated to yield an unknotted state. Exploiting the oxidative state of the cysteines, the building blocks that form the disulphide bridge generating the covalent loop, through altering the chemical environment, and thereby controlling the formation of the covalent loop, easily generates unknotted protein. The biological advantage, we have found, is that the PL can exert allosteric control through this on/off mechanism in a target protein. Most significantly, as the disulphide bridge acts as an on/off switch in knotting, the biophysical investigation of PL topologies can provide a new tool to steer folding and function in proteins, as disulphide bridges are commonly used in protein engineering and therapeutics.

A hybrid pulse combining topology utilizing the combination of modularized avalanche transistor Marx circuits, direct pulse adding, and transmission line transformer.

PubMed

Li, Jiangtao; Zhao, Zheng; Sun, Yi; Liu, Yuhao; Ren, Ziyuan; He, Jiaxin; Cao, Hui; Zheng, Minjun

2017-03-01

Numerous applications driven by pulsed voltage require pulses to be with high amplitude, high repetitive frequency, and narrow width, which could be satisfied by utilizing avalanche transistors. The output improvement is severely limited by power capacities of transistors. Pulse combining is an effective approach to increase the output amplitude while still adopting conventional pulse generating modules. However, there are drawbacks in traditional topologies including the saturation tendency of combining efficiency and waveform oscillation. In this paper, a hybrid pulse combining topology was adopted utilizing the combination of modularized avalanche transistor Marx circuits, direct pulse adding, and transmission line transformer. The factors affecting the combining efficiency were determined including the output time synchronization of Marx circuits, and the quantity and position of magnetic cores. The numbers of the parallel modules and the stages were determined by the output characteristics of each combining method. Experimental results illustrated the ability of generating pulses with 2-14 kV amplitude, 7-11 ns width, and a maximum 10 kHz repetitive rate on a matched 50-300 Ω resistive load. The hybrid topology would be a convinced pulse combining method for similar nanosecond pulse generators based on the solid-state switches.

A hybrid pulse combining topology utilizing the combination of modularized avalanche transistor Marx circuits, direct pulse adding, and transmission line transformer

NASA Astrophysics Data System (ADS)

Li, Jiangtao; Zhao, Zheng; Sun, Yi; Liu, Yuhao; Ren, Ziyuan; He, Jiaxin; Cao, Hui; Zheng, Minjun

2017-03-01

Numerous applications driven by pulsed voltage require pulses to be with high amplitude, high repetitive frequency, and narrow width, which could be satisfied by utilizing avalanche transistors. The output improvement is severely limited by power capacities of transistors. Pulse combining is an effective approach to increase the output amplitude while still adopting conventional pulse generating modules. However, there are drawbacks in traditional topologies including the saturation tendency of combining efficiency and waveform oscillation. In this paper, a hybrid pulse combining topology was adopted utilizing the combination of modularized avalanche transistor Marx circuits, direct pulse adding, and transmission line transformer. The factors affecting the combining efficiency were determined including the output time synchronization of Marx circuits, and the quantity and position of magnetic cores. The numbers of the parallel modules and the stages were determined by the output characteristics of each combining method. Experimental results illustrated the ability of generating pulses with 2-14 kV amplitude, 7-11 ns width, and a maximum 10 kHz repetitive rate on a matched 50-300 Ω resistive load. The hybrid topology would be a convinced pulse combining method for similar nanosecond pulse generators based on the solid-state switches.

Interbody fusion cage design using integrated global layout and local microstructure topology optimization.

PubMed

Lin, Chia-Ying; Hsiao, Chun-Ching; Chen, Po-Quan; Hollister, Scott J

2004-08-15

An approach combining global layout and local microstructure topology optimization was used to create a new interbody fusion cage design that concurrently enhanced stability, biofactor delivery, and mechanical tissue stimulation for improved arthrodesis. To develop a new interbody fusion cage design by topology optimization with porous internal architecture. To compare the performance of this new design to conventional threaded cage designs regarding early stability and long-term stress shielding effects on ingrown bone. Conventional interbody cage designs mainly fall into categories of cylindrical or rectangular shell shapes. The designs contribute to rigid stability and maintain disc height for successful arthrodesis but may also suffer mechanically mediated failures of dislocation or subsidence, as well as the possibility of bone resorption. The new optimization approach created a cage having designed microstructure that achieved desired mechanical performance while providing interconnected channels for biofactor delivery. The topology optimization algorithm determines the material layout under desirable volume fraction (50%) and displacement constraints favorable to bone formation. A local microstructural topology optimization method was used to generate periodic microstructures for porous isotropic materials. Final topology was generated by the integration of the two-scaled structures according to segmented regions and the corresponding material density. Image-base finite element analysis was used to compare the mechanical performance of the topology-optimized cage and conventional threaded cage. The final design can be fabricated by a variety of Solid Free-Form systems directly from the image output. The new design exhibited a narrower, more uniform displacement range than the threaded cage design and lower stress at the cage-vertebra interface, suggesting a reduced risk of subsidence. Strain energy density analysis also indicated that a higher portion of total strain energy density was transferred into the new bone region inside the new designed cage, indicating a reduced risk of stress shielding. The new design approach using integrated topology optimization demonstrated comparable or better stability by limited displacement and reduced localized deformation related to the risk of subsidence. Less shielding of newly formed bone was predicted inside the new designed cage. Using the present approach, it is also possible to tailor cage design for specific materials, either titanium or polymer, that can attain the desired balance between stability, reduced stress shielding, and porosity for biofactor delivery.

Queuing Time Prediction Using WiFi Positioning Data in an Indoor Scenario.

PubMed

Shu, Hua; Song, Ci; Pei, Tao; Xu, Lianming; Ou, Yang; Zhang, Libin; Li, Tao

2016-11-22

Queuing is common in urban public places. Automatically monitoring and predicting queuing time can not only help individuals to reduce their wait time and alleviate anxiety but also help managers to allocate resources more efficiently and enhance their ability to address emergencies. This paper proposes a novel method to estimate and predict queuing time in indoor environments based on WiFi positioning data. First, we use a series of parameters to identify the trajectories that can be used as representatives of queuing time. Next, we divide the day into equal time slices and estimate individuals' average queuing time during specific time slices. Finally, we build a nonstandard autoregressive (NAR) model trained using the previous day's WiFi estimation results and actual queuing time to predict the queuing time in the upcoming time slice. A case study comparing two other time series analysis models shows that the NAR model has better precision. Random topological errors caused by the drift phenomenon of WiFi positioning technology (locations determined by a WiFi positioning system may drift accidently) and systematic topological errors caused by the positioning system are the main factors that affect the estimation precision. Therefore, we optimize the deployment strategy during the positioning system deployment phase and propose a drift ratio parameter pertaining to the trajectory screening phase to alleviate the impact of topological errors and improve estimates. The WiFi positioning data from an eight-day case study conducted at the T3-C entrance of Beijing Capital International Airport show that the mean absolute estimation error is 147 s, which is approximately 26.92% of the actual queuing time. For predictions using the NAR model, the proportion is approximately 27.49%. The theoretical predictions and the empirical case study indicate that the NAR model is an effective method to estimate and predict queuing time in indoor public areas.

Queuing Time Prediction Using WiFi Positioning Data in an Indoor Scenario

PubMed Central

Shu, Hua; Song, Ci; Pei, Tao; Xu, Lianming; Ou, Yang; Zhang, Libin; Li, Tao

2016-01-01

Queuing is common in urban public places. Automatically monitoring and predicting queuing time can not only help individuals to reduce their wait time and alleviate anxiety but also help managers to allocate resources more efficiently and enhance their ability to address emergencies. This paper proposes a novel method to estimate and predict queuing time in indoor environments based on WiFi positioning data. First, we use a series of parameters to identify the trajectories that can be used as representatives of queuing time. Next, we divide the day into equal time slices and estimate individuals’ average queuing time during specific time slices. Finally, we build a nonstandard autoregressive (NAR) model trained using the previous day’s WiFi estimation results and actual queuing time to predict the queuing time in the upcoming time slice. A case study comparing two other time series analysis models shows that the NAR model has better precision. Random topological errors caused by the drift phenomenon of WiFi positioning technology (locations determined by a WiFi positioning system may drift accidently) and systematic topological errors caused by the positioning system are the main factors that affect the estimation precision. Therefore, we optimize the deployment strategy during the positioning system deployment phase and propose a drift ratio parameter pertaining to the trajectory screening phase to alleviate the impact of topological errors and improve estimates. The WiFi positioning data from an eight-day case study conducted at the T3-C entrance of Beijing Capital International Airport show that the mean absolute estimation error is 147 s, which is approximately 26.92% of the actual queuing time. For predictions using the NAR model, the proportion is approximately 27.49%. The theoretical predictions and the empirical case study indicate that the NAR model is an effective method to estimate and predict queuing time in indoor public areas. PMID:27879663

THE STRUCTURAL BIOLOGY OF THE FGF19 SUBFAMILY

PubMed Central

Beenken, Andrew; Mohammadi, Moosa

2013-01-01

The ability of the Fibroblast Growth Factor (FGF) 19 subfamily to signal in an endocrine fashion sets this subfamily apart from the remaining five FGF subfamilies known for their paracrine functions during embryonic development. Compared to the members of paracrine FGF subfamiles, the three members of the FGF 19 subfamily, namely FGF19, FGF21 and FGF23, have poor affinity for heparan sulfate (HS) and therefore can diffuse freely in the HS-rich extracellular matrix to enter into the bloodstream. In further contrast to paracrine FGFs, FGF 19 subfamily members have unusually poor affinity for their cognate FGF receptors (FGFRs) and therefore cannot bind and activate them in a solely HS-dependent fashion. As a result, the FGF 19 subfamily requires α/βklotho coreceptor proteins in order to bind, dimerize and activate their cognate FGFRs. This klotho-dependency also determines the tissue specificity of endocrine FGFs. Recent structural and biochemical studies have begun to shed light onto the molecular basis for the klotho-dependent endocrine mode of action of the FGF 19 subfamily. Crystal structures of FGF 19 and FGF23 show that the topology of the HS binding site (HBS) of FGF19 subfamily members deviates drastically from the common topology adopted by the paracrine FGFs. The distinct topologies of the HBS of FGF 19 and FGF23 prevent HS from direct hydrogen bonding with the backbone atoms of the HBS of these ligands and accordingly decrease the HS binding affinity of this subfamily. Recent biochemical data reveal that the αklotho ectodomain binds avidly to the ectodomain of FGFR1c, the main cognate FGFR of FGF23, creating a de novo high affinity binding site for the C-terminal tail of FGF23. The isolated FGF23 C-terminus can be used to effectively inhibit the formation of the FGF23-FGFR1c-αklotho complex and alleviate hypophosphatemia in renal phosphate disorders due to elevated levels of FGF23. PMID:22396159

Fine topology and locally Minkowskian manifolds

NASA Astrophysics Data System (ADS)

Agrawal, Gunjan; Sinha, Soami Pyari

2018-05-01

Fine topology is one of the several well-known topologies of physical and mathematical relevance. In the present paper, it is obtained that the nonempty open sets of different dimensional Minkowski spaces with the fine topology are not homeomorphic. This leads to the introduction of a new class of manifolds. It turns out that the technique developed here is also applicable to some other topologies, namely, the s-topology, space topology, f-topology, and A-topology.

Aging, Counterfeiting Configuration Control (AC3)

DTIC Science & Technology

2010-01-31

SARA continuously polls contributing data sources on a data specific refresh cycle. SARA supports a continuous risk topology assessment by the program...function was demonstrated at the bread -board level based on comparison of North American Industrialization Classification System (NAICS) codes. Other

Brillouin-Wigner theory for high-frequency expansion in periodically driven systems: Application to Floquet topological insulators

NASA Astrophysics Data System (ADS)

Mikami, Takahiro; Kitamura, Sota; Yasuda, Kenji; Tsuji, Naoto; Oka, Takashi; Aoki, Hideo

2016-04-01

We construct a systematic high-frequency expansion for periodically driven quantum systems based on the Brillouin-Wigner (BW) perturbation theory, which generates an effective Hamiltonian on the projected zero-photon subspace in the Floquet theory, reproducing the quasienergies and eigenstates of the original Floquet Hamiltonian up to desired order in 1 /ω , with ω being the frequency of the drive. The advantage of the BW method is that it is not only efficient in deriving higher-order terms, but even enables us to write down the whole infinite series expansion, as compared to the van Vleck degenerate perturbation theory. The expansion is also free from a spurious dependence on the driving phase, which has been an obstacle in the Floquet-Magnus expansion. We apply the BW expansion to various models of noninteracting electrons driven by circularly polarized light. As the amplitude of the light is increased, the system undergoes a series of Floquet topological-to-topological phase transitions, whose phase boundary in the high-frequency regime is well explained by the BW expansion. As the frequency is lowered, the high-frequency expansion breaks down at some point due to band touching with nonzero-photon sectors, where we find numerically even more intricate and richer Floquet topological phases spring out. We have then analyzed, with the Floquet dynamical mean-field theory, the effects of electron-electron interaction and energy dissipation. We have specifically revealed that phase transitions from Floquet-topological to Mott insulators emerge, where the phase boundaries can again be captured with the high-frequency expansion.

Transmembrane topology of the arsenite permease Acr3 from Saccharomyces cerevisiae.

PubMed

Wawrzycka, Donata; Markowska, Katarzyna; Maciaszczyk-Dziubinska, Ewa; Migocka, Magdalena; Wysocki, Robert

2017-01-01

Acr3 is a plasma membrane transporter, a member of the bile/arsenite/riboflavin transporter (BART) superfamily, which confers high-level resistance to arsenicals in the yeast Saccharomyces cerevisiae. We have previously shown that the yeast Acr3 acts as a low affinity As(III)/H + and Sb(III)/H + antiporter. We have also identified several amino acid residues that are localized in putative transmembrane helices (TM) and appeared to be critical for the Acr3 activity. In the present study, the topology of Acr3 was investigated by insertion of glycosylation and factor Xa protease cleavage sites at predicted hydrophilic regions. The analysis of the glycosylation pattern and factor Xa cleavage products of resulting Acr3 fusion constructs provide evidence supporting a topological model of Acr3 with 10 TM segments and cytoplasmically oriented N- and C-terminal domains. Next, we investigated the role of the hydrophilic loop connecting TM8 and TM9, the large size of which is unique to members of the yeast Acr3 family of metalloid transporters. We found that a 28 amino acid deletion in this region does not affect Acr3 folding, trafficking substrate binding, or transport activity. Finally, we constructed a homology-based structural model of Acr3 using the crystal structure of the Yersinia frederiksenii homologue of the human bile acid sodium symporter ASBT. Copyright © 2016 Elsevier B.V. All rights reserved.

Discrete elastic model for two-dimensional melting.

PubMed

Lansac, Yves; Glaser, Matthew A; Clark, Noel A

2006-04-01

We present a network model for the study of melting and liquid structure in two dimensions, the first in which the presence and energy of topological defects (dislocations and disclinations) and of geometrical defects (elemental voids) can be independently controlled. Interparticle interaction is via harmonic springs and control is achieved by Monte Carlo moves which springs can either be orientationally "flipped" between particles to generate topological defects, or can be "popped" in force-free shape, to generate geometrical defects. With the geometrical defects suppressed the transition to the liquid phase occurs via disclination unbinding, as described by the Kosterlitz-Thouless-Halperin-Nelson-Young model and found in soft potential two-dimensional (2D) systems, such as the dipole-dipole potential [H. H. von Grünberg, Phys. Rev. Lett. 93, 255703 (2004)]. By contrast, with topological defects suppressed, a disordering transition, the Glaser-Clark condensation of geometrical defects [M. A. Glaser and N. A. Clark, Adv. Chem. Phys. 83, 543 (1993); M. A. Glaser, (Springer-Verlag, Berlin, 1990), Vol. 52, p. 141], produces a state that accurately characterizes the local liquid structure and first-order melting observed in hard-potential 2D systems, such as hard disk and the Weeks-Chandler-Andersen (WCA) potentials (M. A. Glaser and co-workers, see above). Thus both the geometrical and topological defect systems play a role in melting. The present work introduces a system in which the relative roles of topological and geometrical defects and their interactions can be explored. We perform Monte Carlo simulations of this model in the isobaric-isothermal ensemble, and present the phase diagram as well as various thermodynamic, statistical, and structural quantities as a function of the relative populations of geometrical and topological defects. The model exhibits a rich phase behavior including hexagonal and square crystals, expanded crystal, dodecagonal quasicrystal, and isotropic liquid phases. In this system the geometrical defects effectively control the melting, reducing the solid-liquid transition temperature by a factor of relative to the topological-only case. The local structure of the dense liquid has been investigated and the results are compared to that from simulations of WCA systems.

Real-space and reciprocal-space Berry phases in the Hall effect of Mn(1-x)Fe(x)Si.

PubMed

Franz, C; Freimuth, F; Bauer, A; Ritz, R; Schnarr, C; Duvinage, C; Adams, T; Blügel, S; Rosch, A; Mokrousov, Y; Pfleiderer, C

2014-05-09

We report an experimental and computational study of the Hall effect in Mn(1-x)Fe(x)Si, as complemented by measurements in Mn(1-x)Co(x)Si, when helimagnetic order is suppressed under substitutional doping. For small x the anomalous Hall effect (AHE) and the topological Hall effect (THE) change sign. Under larger doping the AHE remains small and consistent with the magnetization, while the THE grows by over a factor of 10. Both the sign and the magnitude of the AHE and the THE are in excellent agreement with calculations based on density functional theory. Our study provides the long-sought material-specific microscopic justification that, while the AHE is due to the reciprocal-space Berry curvature, the THE originates in real-space Berry phases.

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

Berres, Anne Sabine

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

Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors.

PubMed

Chew, William; Hrmova, Maria; Lopato, Sergiy

2013-04-12

Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species.

Role of Homeodomain Leucine Zipper (HD-Zip) IV Transcription Factors in Plant Development and Plant Protection from Deleterious Environmental Factors

PubMed Central

Chew, William; Hrmova, Maria; Lopato, Sergiy

2013-01-01

Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species. PMID:23584027

Calabi-Yau structures on categories of matrix factorizations

NASA Astrophysics Data System (ADS)

Shklyarov, Dmytro

2017-09-01

Using tools of complex geometry, we construct explicit proper Calabi-Yau structures, that is, non-degenerate cyclic cocycles on differential graded categories of matrix factorizations of regular functions with isolated critical points. The formulas involve the Kapustin-Li trace and its higher corrections. From the physics perspective, our result yields explicit 'off-shell' models for categories of topological D-branes in B-twisted Landau-Ginzburg models.

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

PubMed Central

Dabaghian, Y.; Mémoli, F.; Frank, L.; Carlsson, G.

2012-01-01

An animal's ability to navigate through space rests on its ability to create a mental map of its environment. The hippocampus is the brain region centrally responsible for such maps, and it has been assumed to encode geometric information (distances, angles). Given, however, that hippocampal output consists of patterns of spiking across many neurons, and downstream regions must be able to translate those patterns into accurate information about an animal's spatial environment, we hypothesized that 1) the temporal pattern of neuronal firing, particularly co-firing, is key to decoding spatial information, and 2) since co-firing implies spatial overlap of place fields, a map encoded by co-firing will be based on connectivity and adjacency, i.e., it will be a topological map. Here we test this topological hypothesis with a simple model of hippocampal activity, varying three parameters (firing rate, place field size, and number of neurons) in computer simulations of rat trajectories in three topologically and geometrically distinct test environments. Using a computational algorithm based on recently developed tools from Persistent Homology theory in the field of algebraic topology, we find that the patterns of neuronal co-firing can, in fact, convey topological information about the environment in a biologically realistic length of time. Furthermore, our simulations reveal a “learning region” that highlights the interplay between the parameters in combining to produce hippocampal states that are more or less adept at map formation. For example, within the learning region a lower number of neurons firing can be compensated by adjustments in firing rate or place field size, but beyond a certain point map formation begins to fail. We propose that this learning region provides a coherent theoretical lens through which to view conditions that impair spatial learning by altering place cell firing rates or spatial specificity. PMID:22912564

A new logistic dynamic particle swarm optimization algorithm based on random topology.

PubMed

Ni, Qingjian; Deng, Jianming

2013-01-01

Population topology of particle swarm optimization (PSO) will directly affect the dissemination of optimal information during the evolutionary process and will have a significant impact on the performance of PSO. Classic static population topologies are usually used in PSO, such as fully connected topology, ring topology, star topology, and square topology. In this paper, the performance of PSO with the proposed random topologies is analyzed, and the relationship between population topology and the performance of PSO is also explored from the perspective of graph theory characteristics in population topologies. Further, in a relatively new PSO variant which named logistic dynamic particle optimization, an extensive simulation study is presented to discuss the effectiveness of the random topology and the design strategies of population topology. Finally, the experimental data are analyzed and discussed. And about the design and use of population topology on PSO, some useful conclusions are proposed which can provide a basis for further discussion and research.

Coexistence of type-II Dirac point and weak topological phase in Pt 3 Sn

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

Kim, Minsung; Wang, Cai -Zhuang; Ho, Kai -Ming

Intriguing topological phases may appear in both insulating and semimetallic states. Topological insulators exhibit topologically nontrivial band inversion, while topological Dirac/Weyl semimetals show “relativistic” linear band crossings. Here, we report an unusual topological state of Pt 3Sn, where the two topological features appear simultaneously. Based on first-principles calculations, we show that Pt 3Sn is a three-dimensional weak topological semimetal with topologically nontrivial band inversion between the valence and conduction bands, where the band structure also possesses type-II Dirac points at the boundary of two electron pockets. The formation of the Dirac points can be understood in terms of the representationsmore » of relevant symmetry groups and the compatibility relations. The topological surface states appear in accordance with the nontrivial bulk band topology. As a result, the unique coexistence of the two distinct topological features in Pt 3Sn enlarges the material scope in topological physics, and is potentially useful for spintronics.« less

Coexistence of type-II Dirac point and weak topological phase in Pt 3 Sn

DOE PAGES

Kim, Minsung; Wang, Cai -Zhuang; Ho, Kai -Ming

2017-11-06

Intriguing topological phases may appear in both insulating and semimetallic states. Topological insulators exhibit topologically nontrivial band inversion, while topological Dirac/Weyl semimetals show “relativistic” linear band crossings. Here, we report an unusual topological state of Pt 3Sn, where the two topological features appear simultaneously. Based on first-principles calculations, we show that Pt 3Sn is a three-dimensional weak topological semimetal with topologically nontrivial band inversion between the valence and conduction bands, where the band structure also possesses type-II Dirac points at the boundary of two electron pockets. The formation of the Dirac points can be understood in terms of the representationsmore » of relevant symmetry groups and the compatibility relations. The topological surface states appear in accordance with the nontrivial bulk band topology. As a result, the unique coexistence of the two distinct topological features in Pt 3Sn enlarges the material scope in topological physics, and is potentially useful for spintronics.« less

On genera of curves from high-loop generalized unitarity cuts

NASA Astrophysics Data System (ADS)

Huang, Rijun; Zhang, Yang

2013-04-01

Generalized unitarity cut of a Feynman diagram generates an algebraic system of polynomial equations. At high-loop levels, these equations may define a complex curve or a (hyper-)surface with complicated topology. We study the curve cases, i.e., a 4-dimensional L-loop diagram with (4 L-1) cuts. The topology of a complex curve is classified by its genus. Hence in this paper, we use computational algebraic geometry to calculate the genera of curves from two and three-loop unitarity cuts. The global structure of degenerate on-shell equations under some specific kinematic configurations is also sketched. The genus information can also be used to judge if a unitary cut solution could be rationally parameterized.

Experimental observation of anomalous topological edge modes in a slowly driven photonic lattice

PubMed Central

Mukherjee, Sebabrata; Spracklen, Alexander; Valiente, Manuel; Andersson, Erika; Öhberg, Patrik; Goldman, Nathan; Thomson, Robert R.

2017-01-01

Topological quantum matter can be realized by subjecting engineered systems to time-periodic modulations. In analogy with static systems, periodically driven quantum matter can be topologically classified by topological invariants, whose non-zero value guarantees the presence of robust edge modes. In the high-frequency limit of the drive, topology is described by standard topological invariants, such as Chern numbers. Away from this limit, these topological numbers become irrelevant, and novel topological invariants must be introduced to capture topological edge transport. The corresponding edge modes were coined anomalous topological edge modes, to highlight their intriguing origin. Here we demonstrate the experimental observation of these topological edge modes in a 2D photonic lattice, where these propagating edge states are shown to coexist with a quasi-localized bulk. Our work opens an exciting route for the exploration of topological physics in time-modulated systems operating away from the high-frequency regime. PMID:28051060

Mass-action equilibrium and non-specific interactions in protein binding networks

NASA Astrophysics Data System (ADS)

Maslov, Sergei

2009-03-01

Large-scale protein binding networks serve as a paradigm of complex properties of living cells. These networks are naturally weighted with edges characterized by binding strength and protein-nodes -- by their concentrations. However, the state-of-the-art high-throughput experimental techniques generate just a binary (yes or no) information about individual interactions. As a result, most of the previous research concentrated just on topology of these networks. In a series of recent publications [1-4] my collaborators and I went beyond purely topological studies and calculated the mass-action equilibrium of a genome-wide binding network using experimentally determined protein concentrations, localizations, and reliable binding interactions in baker's yeast. We then studied how this equilibrium responds to large perturbations [1-2] and noise [3] in concentrations of proteins. We demonstrated that the change in the equilibrium concentration of a protein exponentially decays (and sign-alternates) with its network distance away from the perturbed node. This explains why, despite a globally connected topology, individual functional modules in such networks are able to operate fairly independently. In a separate study [4] we quantified the interplay between specific and non-specific binding interactions under crowded conditions inside living cells. We show how the need to limit the waste of resources constrains the number of types and concentrations of proteins that are present at the same time and at the same place in yeast cells. [1] S Maslov, I. Ispolatov, PNAS 104:13655 (2007). [2] S. Maslov, K. Sneppen, I. Ispolatov, New J. of Phys. 9: 273 (2007). [3] K-K. Yan, D. Walker, S. Maslov, PRL accepted (2008). [4] J. Zhang, S. Maslov, and E. I. Shakhnovich, Mol Syst Biol 4, 210 (2008).

High-efficiency thermal switch based on topological Josephson junctions

NASA Astrophysics Data System (ADS)

Sothmann, Björn; Giazotto, Francesco; Hankiewicz, Ewelina M.

2017-02-01

We propose theoretically a thermal switch operating by the magnetic-flux controlled diffraction of phase-coherent heat currents in a thermally biased Josephson junction based on a two-dimensional topological insulator. For short junctions, the system shows a sharp switching behavior while for long junctions the switching is smooth. Physically, the switching arises from the Doppler shift of the superconducting condensate due to screening currents induced by a magnetic flux. We suggest a possible experimental realization that exhibits a relative temperature change of 40% between the on and off state for realistic parameters. This is a factor of two larger than in recently realized thermal modulators based on conventional superconducting tunnel junctions.

Percolation Analysis of a Wiener Reconstruction of the IRAS 1.2 Jy Redshift Catalog

NASA Astrophysics Data System (ADS)

Yess, Capp; Shandarin, Sergei F.; Fisher, Karl B.

1997-01-01

We present percolation analyses of Wiener reconstructions of the IRAS 1.2 Jy redshift survey. There are 10 reconstructions of galaxy density fields in real space spanning the range β = 0.1-1.0, where β = Ω0.6/b, Ω is the present dimensionless density, and b is the bias factor. Our method uses the growth of the largest cluster statistic to characterize the topology of a density field, where Gaussian randomized versions of the reconstructions are used as standards for analysis. For the reconstruction volume of radius R ~ 100 h-1 Mpc, percolation analysis reveals a slight ``meatball'' topology for the real space, galaxy distribution of the IRAS survey.

Community structure detection based on the neighbor node degree information

NASA Astrophysics Data System (ADS)

Tang, Li-Ying; Li, Sheng-Nan; Lin, Jian-Hong; Guo, Qiang; Liu, Jian-Guo

2016-11-01

Community structure detection is of great significance for better understanding the network topology property. By taking into account the neighbor degree information of the topological network as the link weight, we present an improved Nonnegative Matrix Factorization (NMF) method for detecting community structure. The results for empirical networks show that the largest improved ratio of the Normalized Mutual Information value could reach 63.21%. Meanwhile, for synthetic networks, the highest Normalized Mutual Information value could closely reach 1, which suggests that the improved method with the optimal λ can detect the community structure more accurately. This work is helpful for understanding the interplay between the link weight and the community structure detection.

Electrons and proton transfer in chloroplasts in silico: 1. The effect of topological factors on energy coupling in chloroplasts with a nonuniform distribution of protein complexes

NASA Astrophysics Data System (ADS)

Vershubskii, A. V.; Tikhonov, A. N.

2017-05-01

This paper presents a theoretical study of the effects of topological factors (density of thylakoid packing in grana) on the efficiency of energy coupling in chloroplasts. The study is based on a mathematical model of electron and proton transport processes coupled to ATP synthesis in chloroplasts. The model was developed by the authors earlier, and the nonuniform distribution of electron transport and ATP synthase complexes in the membranes of granal and intergranal thylakoids was taken into account in the model. The results of numerical experiments enabled the analysis of the distribution of lateral profiles of the transmembrane pH difference and the concentrations of mobile plastoquinone and plastocyanin electron transporters in granal and intergranal thylakoids and the dependence of this distribution on the metabolic state of class B chloroplasts (photosynthetic control state or the conditions of intensive ATP synthesis). Moreover, the influence of topological factors (the density of thylakoid packing in grana and the degree of thylakoid swelling) that affect the rate of diffusion of protons and mobile electron carriers in the intrathylakoid space and in the interthylakoidal gap was investigated. The results of numerical experiments that involved the variation of geometric parameters of the system revealed the influence of thylakoid thickness and the distance between the granal thylakoids on the lateral pH profiles inside the thylakoids (pHi) and in the interthylakoidal gap (pHo). Acidification of the intrathylakoid space characterized by the pHi value increased concomitantly to the increase of the width of the interthylakoidal gap l o and decreased concomitantly to the increase of the width of the intrathylakoidal space l i.

Photoinduced Topological Phase Transitions in Topological Magnon Insulators.

PubMed

Owerre, S A

2018-03-13

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

Observation of Topological Links Associated with Hopf Insulators in a Solid-State Quantum Simulator

NASA Astrophysics Data System (ADS)

Yuan, X.-X.; He, L.; Wang, S.-T.; Deng, D.-L.; Wang, F.; Lian, W.-Q.; Wang, X.; Zhang, C.-H.; Zhang, H.-L.; Chang, X.-Y.; Duan, L.-M.

2017-06-01

Hopf insulators are intriguing three-dimensional topological insulators characterized by an integer topological invariant. They originate from the mathematical theory of Hopf fibration and epitomize the deep connection between knot theory and topological phases of matter, which distinguishes them from other classes of topological insulators. Here, we implement a model Hamiltonian for Hopf insulators in a solid-state quantum simulator and report the first experimental observation of their topological properties, including fascinating topological links associated with the Hopf fibration and the integer-valued topological invariant obtained from a direct tomographic measurement. Our observation of topological links and Hopf fibration in a quantum simulator opens the door to probe rich topological properties of Hopf insulators in experiments. The quantum simulation and probing methods are also applicable to the study of other intricate three-dimensional topological model Hamiltonians.

Noise propagation issues in Belle II pixel detector power cable

DOE PAGES

Iglesias, M.; Arteche, F.; Echeverria, I.; ...

2018-04-26

The vertex detector used in the upgrade of High-Energy physics experiment Belle II includes DEPFET pixel detector (PXD) technology. In this complex topology the power supply units and the front-end electronics are connected through a PXD power cable bundle which may propagate the output noise from the power supplies to the vertex area. This article presents a study of the propagation of noise caused by power converters in the PXD cable bundle based on Multi-conductor Transmission Line (MTL) theory. The work exposes the effect of the complex cable topology and shield connections on the noise propagation, which has an impactmore » on the requirements of the power supplies. This analysis is part of the electromagnetic compatibility based design focused on functional safety to define the shield connections and power supply specifications required to ensure the successful integration of the detector and, specifically, to achieve the designed performance of the front-end electronics.« less

Noise propagation issues in Belle II pixel detector power cable

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

Iglesias, M.; Arteche, F.; Echeverria, I.

The vertex detector used in the upgrade of High-Energy physics experiment Belle II includes DEPFET pixel detector (PXD) technology. In this complex topology the power supply units and the front-end electronics are connected through a PXD power cable bundle which may propagate the output noise from the power supplies to the vertex area. This article presents a study of the propagation of noise caused by power converters in the PXD cable bundle based on Multi-conductor Transmission Line (MTL) theory. The work exposes the effect of the complex cable topology and shield connections on the noise propagation, which has an impactmore » on the requirements of the power supplies. This analysis is part of the electromagnetic compatibility based design focused on functional safety to define the shield connections and power supply specifications required to ensure the successful integration of the detector and, specifically, to achieve the designed performance of the front-end electronics.« less

Implications of Network Topology on Stability

PubMed Central

Kinkhabwala, Ali

2015-01-01

In analogy to chemical reaction networks, I demonstrate the utility of expressing the governing equations of an arbitrary dynamical system (interaction network) as sums of real functions (generalized reactions) multiplied by real scalars (generalized stoichiometries) for analysis of its stability. The reaction stoichiometries and first derivatives define the network’s “influence topology”, a signed directed bipartite graph. Parameter reduction of the influence topology permits simplified expression of the principal minors (sums of products of non-overlapping bipartite cycles) and Hurwitz determinants (sums of products of the principal minors or the bipartite cycles directly) for assessing the network’s steady state stability. Visualization of the Hurwitz determinants over the reduced parameters defines the network’s stability phase space, delimiting the range of its dynamics (specifically, the possible numbers of unstable roots at each steady state solution). Any further explicit algebraic specification of the network will project onto this stability phase space. Stability analysis via this hierarchical approach is demonstrated on classical networks from multiple fields. PMID:25826219

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.

Development of human brain structural networks through infancy and childhood.

PubMed

Huang, Hao; Shu, Ni; Mishra, Virendra; Jeon, Tina; Chalak, Lina; Wang, Zhiyue J; Rollins, Nancy; Gong, Gaolang; Cheng, Hua; Peng, Yun; Dong, Qi; He, Yong

2015-05-01

During human brain development through infancy and childhood, microstructural and macrostructural changes take place to reshape the brain's structural networks and better adapt them to sophisticated functional and cognitive requirements. However, structural topological configuration of the human brain during this specific development period is not well understood. In this study, diffusion magnetic resonance image (dMRI) of 25 neonates, 13 toddlers, and 25 preadolescents were acquired to characterize network dynamics at these 3 landmark cross-sectional ages during early childhood. dMRI tractography was used to construct human brain structural networks, and the underlying topological properties were quantified by graph-theory approaches. Modular organization and small-world attributes are evident at birth with several important topological metrics increasing monotonically during development. Most significant increases of regional nodes occur in the posterior cingulate cortex, which plays a pivotal role in the functional default mode network. Positive correlations exist between nodal efficiencies and fractional anisotropy of the white matter traced from these nodes, while correlation slopes vary among the brain regions. These results reveal substantial topological reorganization of human brain structural networks through infancy and childhood, which is likely to be the outcome of both heterogeneous strengthening of the major white matter tracts and pruning of other axonal fibers. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

Design of complex bone internal structure using topology optimization with perimeter control.

PubMed

Park, Jaejong; Sutradhar, Alok; Shah, Jami J; Paulino, Glaucio H

2018-03-01

Large facial bone loss usually requires patient-specific bone implants to restore the structural integrity and functionality that also affects the appearance of each patient. Titanium alloys (e.g., Ti-6Al-4V) are typically used in the interfacial porous coatings between the implant and the surrounding bone to promote stability. There exists a property mismatch between the two that in general leads to complications such as stress-shielding. This biomechanical discrepancy is a hurdle in the design of bone replacements. To alleviate the mismatch, the internal structure of the bone replacements should match that of the bone. Topology optimization has proven to be a good technique for designing bone replacements. However, the complex internal structure of the bone is difficult to mimic using conventional topology optimization methods without additional restrictions. In this work, the complex bone internal structure is recovered using a perimeter control based topology optimization approach. By restricting the solution space by means of the perimeter, the intricate design complexity of bones can be achieved. Three different bone regions with well-known physiological loadings are selected to illustrate the method. Additionally, we found that the target perimeter value and the pattern of the initial distribution play a vital role in obtaining the natural curvatures in the bone internal structures as well as avoiding excessive island patterns. Copyright © 2018 Elsevier Ltd. All rights reserved.

Entanglement from topology in Chern-Simons theory

NASA Astrophysics Data System (ADS)

Salton, Grant; Swingle, Brian; Walter, Michael

2017-05-01

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

Enhanced collective influence: A paradigm to optimize network disruption

NASA Astrophysics Data System (ADS)

Wu, Tao; Chen, Leiting; Zhong, Linfeng; Xian, Xingping

2017-04-01

The function of complex networks typically relies on the integrity of underlying structure. Sometimes, practical applications need to attack networks' function, namely inactivate and fragment networks' underlying structure. To effectively dismantle complex networks and regulate the function of them, a centrality measure, named CI (Morone and Makse, 2015), was proposed for node ranking. We observe that the performance of CI centrality in network disruption problem may deteriorate when it is used in networks with different topology properties. Specifically, the structural features of local network topology are overlooked in CI centrality, even though the local network topology of the nodes with a fixed CI value may have very different organization. To improve the ranking accuracy of CI, this paper proposes a variant ECI to CI by considering loop density and degree diversity of local network topology. And the proposed ECI centrality would degenerate into CI centrality with the reduction of the loop density and the degree diversity level. By comparing ECI with CI and classical centrality measures in both synthetic and real networks, the experimental results suggest that ECI can largely improve the performance of CI for network disruption. Based on the results, we analyze the correlation between the improvement and the properties of the networks. We find that the performance of ECI is positively correlated with assortative coefficient and community modularity and negatively correlated with degree inequality of networks, which can be used as guidance for practical applications.

Inhomogeneous anisotropic cosmology

DOE PAGES

Kleban, Matthew; Senatore, Leonardo

2016-10-12

In homogeneous and isotropic Friedmann-Robertson-Walker cosmology, the topology of the universe determines its ultimate fate. If the Weak Energy Condition is satisfied, open and flat universes must expand forever, while closed cosmologies can recollapse to a Big Crunch. A similar statement holds for homogeneous but anisotropic (Bianchi) universes. Here in this paper, we prove that arbitrarily inhomogeneous and anisotropic cosmologies with "flat'' (including toroidal) and "open'' (including compact hyperbolic) spatial topology that are initially expanding must continue to expand forever at least in some region at a rate bounded from below by a positive number, despite the presence of arbitrarilymore » large density fluctuations and/or the formation of black holes. Because the set of 3-manifold topologies is countable, a single integer determines the ultimate fate of the universe, and, in a specific sense, most 3-manifolds are "flat" or "open". Our result has important implications for inflation: if there is a positive cosmological constant (or suitable inflationary potential) and initial conditions for the inflaton, cosmologies with "flat'' or "open" topology must expand forever in some region at least as fast as de Sitter space, and are therefore very likely to begin inflationary expansion eventually, regardless of the scale of the inflationary energy or the spectrum and amplitude of initial inhomogeneities and gravitational waves. Our result is also significant for numerical general relativity, which often makes use of periodic (toroidal) boundary conditions.« less

Inhomogeneous anisotropic cosmology

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

Kleban, Matthew; Senatore, Leonardo

In homogeneous and isotropic Friedmann-Robertson-Walker cosmology, the topology of the universe determines its ultimate fate. If the Weak Energy Condition is satisfied, open and flat universes must expand forever, while closed cosmologies can recollapse to a Big Crunch. A similar statement holds for homogeneous but anisotropic (Bianchi) universes. Here in this paper, we prove that arbitrarily inhomogeneous and anisotropic cosmologies with "flat'' (including toroidal) and "open'' (including compact hyperbolic) spatial topology that are initially expanding must continue to expand forever at least in some region at a rate bounded from below by a positive number, despite the presence of arbitrarilymore » large density fluctuations and/or the formation of black holes. Because the set of 3-manifold topologies is countable, a single integer determines the ultimate fate of the universe, and, in a specific sense, most 3-manifolds are "flat" or "open". Our result has important implications for inflation: if there is a positive cosmological constant (or suitable inflationary potential) and initial conditions for the inflaton, cosmologies with "flat'' or "open" topology must expand forever in some region at least as fast as de Sitter space, and are therefore very likely to begin inflationary expansion eventually, regardless of the scale of the inflationary energy or the spectrum and amplitude of initial inhomogeneities and gravitational waves. Our result is also significant for numerical general relativity, which often makes use of periodic (toroidal) boundary conditions.« less

Inhomogeneous anisotropic cosmology

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

Kleban, Matthew; Senatore, Leonardo; Kavli Institute for Particle Astrophysics and Cosmology, Stanford University and SLAC,2575 Sand Hill Road, M/S 29, Menlo Park, CA 94025

In homogeneous and isotropic Friedmann-Robertson-Walker cosmology, the topology of the universe determines its ultimate fate. If the Weak Energy Condition is satisfied, open and flat universes must expand forever, while closed cosmologies can recollapse to a Big Crunch. A similar statement holds for homogeneous but anisotropic (Bianchi) universes. Here, we prove that arbitrarily inhomogeneous and anisotropic cosmologies with “flat” (including toroidal) and “open” (including compact hyperbolic) spatial topology that are initially expanding must continue to expand forever at least in some region at a rate bounded from below by a positive number, despite the presence of arbitrarily large density fluctuationsmore » and/or the formation of black holes. Because the set of 3-manifold topologies is countable, a single integer determines the ultimate fate of the universe, and, in a specific sense, most 3-manifolds are “flat” or “open”. Our result has important implications for inflation: if there is a positive cosmological constant (or suitable inflationary potential) and initial conditions for the inflaton, cosmologies with “flat” or “open” topology must expand forever in some region at least as fast as de Sitter space, and are therefore very likely to begin inflationary expansion eventually, regardless of the scale of the inflationary energy or the spectrum and amplitude of initial inhomogeneities and gravitational waves. Our result is also significant for numerical general relativity, which often makes use of periodic (toroidal) boundary conditions.« less

Topological detector: measuring continuous dosimetric quantities with few-element detector array.

PubMed

Han, Zhaohui; Brivio, Davide; Sajo, Erno; Zygmanski, Piotr

2016-08-21

A prototype topological detector was fabricated and investigated for quality assurance of radiation producing medical devices. Unlike a typical array or flat panel detector, a topological detector, while capable of achieving a very high spatial resolution, consists of only a few elements and therefore is much simpler in construction and more cost effective. The key feature allowing this advancement is a geometry-driven design that is customized for a specific dosimetric application. In the current work, a topological detector of two elements was examined for the positioning verification of the radiation collimating devices (jaws, MLCs, and blades etc). The detector was diagonally segmented from a rectangular thin film strip (2.5 cm  ×  15 cm), giving two contiguous but independent detector elements. The segmented area was the central portion of the strip measuring 5 cm in length. Under irradiation, signals from each detector element were separately digitized using a commercial multichannel data acquisition system. The center and size of an x-ray field, which were uniquely determined by the collimator positions, were shown mathematically to relate to the difference and sum of the two signals. As a proof of concept, experiments were carried out using slit x-ray fields ranging from 2 mm to 20 mm in size. It was demonstrated that, the collimator positions can be accurately measured with sub-millimeter precisions.

Topology of OxlT, the oxalate transporter of Oxalobacter formigenes, determined by site-directed fluorescence labeling.

PubMed

Ye, L; Jia, Z; Jung, T; Maloney, P C

2001-04-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His(9)-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+ linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis.

Topology of OxlT, the Oxalate Transporter of Oxalobacter formigenes, Determined by Site-Directed Fluorescence Labeling

PubMed Central

Ye, Liwen; Jia, Zhenzhen; Jung, Thomas; Maloney, Peter C.

2001-01-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His9-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+-linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis. PMID:11274108

Surface field theories of point group symmetry protected topological phases

NASA Astrophysics Data System (ADS)

Huang, Sheng-Jie; Hermele, Michael

2018-02-01

We identify field theories that describe the surfaces of three-dimensional bosonic point group symmetry protected topological (pgSPT) phases. The anomalous nature of the surface field theories is revealed via a dimensional reduction argument. Specifically, we study three different surface field theories. The first field theory is quantum electrodynamics in three space-time dimensions (QED3) with four flavors of fermions. We show this theory can describe the surfaces of a majority of bosonic pgSPT phases protected by a single mirror reflection, or by Cn v point group symmetry for n =2 ,3 ,4 ,6 . The second field theory is a variant of QED3 with charge-1 and charge-3 Dirac fermions. This field theory can describe the surface of a reflection symmetric pgSPT phase built by placing an E8 state on the mirror plane. The third field theory is an O (4 ) nonlinear sigma model with a topological theta term at θ =π , or, equivalently, a noncompact CP1 model. Using a coupled wire construction, we show this is a surface theory for bosonic pgSPT phases with U (1 ) ×Z2P symmetry. For the latter two field theories, we discuss the connection to gapped surfaces with topological order. Moreover, we conjecture that the latter two field theories can describe surfaces of more general bosonic pgSPT phases with Cn v point group symmetry.

Role of alveolar topology on acinar flows and convective mixing.

PubMed

Hofemeier, Philipp; Sznitman, Josué

2014-06-01

Due to experimental challenges, computational simulations are often sought to quantify inhaled aerosol transport in the pulmonary acinus. Commonly, these are performed using generic alveolar topologies, including spheres, toroids, and polyhedra, to mimic the complex acinar morphology. Yet, local acinar flows and ensuing particle transport are anticipated to be influenced by the specific morphological structures. We have assessed a range of acinar models under self-similar breathing conditions with respect to alveolar flow patterns, convective flow mixing, and deposition of fine particles (1.3 μm diameter). By tracking passive tracers over cumulative breathing cycles, we find that irreversible flow mixing correlates with the location and strength of the recirculating vortex inside the cavity. Such effects are strongest in proximal acinar generations where the ratio of alveolar to ductal flow rates is low and interalveolar disparities are most apparent. Our results for multi-alveolated acinar ducts highlight that fine 1 μm inhaled particles subject to alveolar flows are sensitive to the alveolar topology, underlining interalveolar disparities in particle deposition patterns. Despite the simplicity of the acinar models investigated, our findings suggest that alveolar topologies influence more significantly local flow patterns and deposition sites of fine particles for upper generations emphasizing the importance of the selected acinar model. In distal acinar generations, however, the alveolar geometry primarily needs to mimic the space-filling alveolar arrangement dictated by lung morphology.

Topological Toughening of graphene and other 2D materials

NASA Astrophysics Data System (ADS)

Gao, Huajian

It has been claimed that graphene, with the elastic modulus of 1TPa and theoretical strength as high as 130 GPa, is the strongest material. However, from an engineering point of view, it is the fracture toughness that determines the actual strength of materials, as crack-like flaws (i.e., cracks, holes, notches, corners, etc.) are inevitable in the design, fabrication, and operation of practical devices and systems. Recently, it has been demonstrated that graphene has very low fracture toughness, in fact close to that of ideally brittle solids. These findings have raised sharp questions and are calling for efforts to explore effective methods to toughen graphene. Recently, we have been exploring the potential use of topological effects to enhance the fracture toughness of graphene. For example, it has been shown that a sinusoidal graphene containing periodically distributed disclination quadrupoles can achieve a mode I fracture toughness nearly twice that of pristine graphene. Here we report working progresses on further studies of topological toughening of graphene and other 2D materials. A phase field crystal method is adopted to generate the atomic coordinates of material with specific topological patterns. We then perform molecular dynamics simulations of fracture in the designed samples, and observe a variety of toughening mechanisms, including crack tip blunting, crack trapping, ligament bridging, crack deflection and daughter crack initiation and coalescence.

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

PubMed Central

de Luis Balaguer, Maria Angels; Fisher, Adam P.; Clark, Natalie M.; Fernandez-Espinosa, Maria Guadalupe; Möller, Barbara K.; Weijers, Dolf; Williams, Cranos; Lorenzo, Oscar; Sozzani, Rosangela

2017-01-01

Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells. PMID:28827319

Structure of Radical-Induced Cell Death1 Hub Domain Reveals a Common αα-Scaffold for Disorder in Transcriptional Networks.

PubMed

Bugge, Katrine; Staby, Lasse; Kemplen, Katherine R; O'Shea, Charlotte; Bendsen, Sidsel K; Jensen, Mikael K; Olsen, Johan G; Skriver, Karen; Kragelund, Birthe B

2018-05-01

Communication within cells relies on a few protein nodes called hubs, which organize vast interactomes with many partners. Frequently, hub proteins are intrinsically disordered conferring multi-specificity and dynamic communication. Conversely, folded hub proteins may organize networks using disordered partners. In this work, the structure of the RST domain, a unique folded hub, is solved by nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, and its complex with a region of the transcription factor DREB2A is provided through data-driven HADDOCK modeling and mutagenesis analysis. The RST fold is unique, but similar structures are identified in the PAH (paired amphipathic helix), TAFH (TATA-box-associated factor homology), and NCBD (nuclear coactivator binding domain) domains. We designate them as a group the αα hubs, as they share an αα-hairpin super-secondary motif, which serves as an organizing platform for malleable helices of varying topology. This allows for partner adaptation, exclusion, and selection. Our findings provide valuable insights into structural features enabling signaling fidelity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Strongly Correlated Topological Insulators

DTIC Science & Technology

2016-02-03

Strongly Correlated Topological Insulators In the past year, the grant was used for work in the field of topological phases, with emphasis on finding...surface of topological insulators . In the past 3 years, we have started a new direction, that of fractional topological insulators . These are materials...Strongly Correlated Topological Insulators Report Title In the past year, the grant was used for work in the field of topological phases, with emphasis

Condensin-driven remodelling of X chromosome topology during dosage compensation

NASA Astrophysics Data System (ADS)

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-07-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.

Topology of AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, determined by site-directed fluorescence labeling.

PubMed

Nanatani, Kei; Fujiki, Takashi; Kanou, Kazuhiko; Takeda-Shitaka, Mayuko; Umeyama, Hideaki; Ye, Liwen; Wang, Xicheng; Nakajima, Tasuku; Uchida, Takafumi; Maloney, Peter C; Abe, Keietsu

2007-10-01

The gram-positive lactic acid bacterium Tetragenococcus halophilus catalyzes the decarboxylation of L-aspartate (Asp) with release of L-alanine (Ala) and CO(2). The decarboxylation reaction consists of two steps: electrogenic exchange of Asp for Ala catalyzed by an aspartate:alanine antiporter (AspT) and intracellular decarboxylation of the transported Asp catalyzed by an L-aspartate-beta-decarboxylase (AspD). AspT belongs to the newly classified aspartate:alanine exchanger family (transporter classification no. 2.A.81) of transporters. In this study, we were interested in the relationship between the structure and function of AspT and thus analyzed the topology by means of the substituted-cysteine accessibility method using the impermeant, fluorescent, thiol-specific probe Oregon Green 488 maleimide (OGM) and the impermeant, nonfluorescent, thiol-specific probe [2-(trimethylammonium)ethyl]methanethiosulfonate bromide. We generated 23 single-cysteine variants from a six-histidine-tagged cysteineless AspT template. A cysteine position was assigned an external location if the corresponding single-cysteine variant reacted with OGM added to intact cells, and a position was assigned an internal location if OGM labeling required cell lysis. The topology analyses revealed that AspT has a unique topology; the protein has 10 transmembrane helices (TMs), a large hydrophilic cytoplasmic loop (about 180 amino acids) between TM5 and TM6, N and C termini that face the periplasm, and a positively charged residue (arginine 76) within TM3. Moreover, the three-dimensional structure constructed by means of the full automatic modeling system indicates that the large hydrophilic cytoplasmic loop of AspT possesses a TrkA_C domain and a TrkA_C-like domain and that the three-dimensional structures of these domains are similar to each other even though their amino acid sequences show low similarity.

Topology of AspT, the Aspartate:Alanine Antiporter of Tetragenococcus halophilus, Determined by Site-Directed Fluorescence Labeling▿ †

PubMed Central

Nanatani, Kei; Fujiki, Takashi; Kanou, Kazuhiko; Takeda-Shitaka, Mayuko; Umeyama, Hideaki; Ye, Liwen; Wang, Xicheng; Nakajima, Tasuku; Uchida, Takafumi; Maloney, Peter C.; Abe, Keietsu

2007-01-01

The gram-positive lactic acid bacterium Tetragenococcus halophilus catalyzes the decarboxylation of l-aspartate (Asp) with release of l-alanine (Ala) and CO2. The decarboxylation reaction consists of two steps: electrogenic exchange of Asp for Ala catalyzed by an aspartate:alanine antiporter (AspT) and intracellular decarboxylation of the transported Asp catalyzed by an l-aspartate-β-decarboxylase (AspD). AspT belongs to the newly classified aspartate:alanine exchanger family (transporter classification no. 2.A.81) of transporters. In this study, we were interested in the relationship between the structure and function of AspT and thus analyzed the topology by means of the substituted-cysteine accessibility method using the impermeant, fluorescent, thiol-specific probe Oregon Green 488 maleimide (OGM) and the impermeant, nonfluorescent, thiol-specific probe [2-(trimethylammonium)ethyl]methanethiosulfonate bromide. We generated 23 single-cysteine variants from a six-histidine-tagged cysteineless AspT template. A cysteine position was assigned an external location if the corresponding single-cysteine variant reacted with OGM added to intact cells, and a position was assigned an internal location if OGM labeling required cell lysis. The topology analyses revealed that AspT has a unique topology; the protein has 10 transmembrane helices (TMs), a large hydrophilic cytoplasmic loop (about 180 amino acids) between TM5 and TM6, N and C termini that face the periplasm, and a positively charged residue (arginine 76) within TM3. Moreover, the three-dimensional structure constructed by means of the full automatic modeling system indicates that the large hydrophilic cytoplasmic loop of AspT possesses a TrkA_C domain and a TrkA_C-like domain and that the three-dimensional structures of these domains are similar to each other even though their amino acid sequences show low similarity. PMID:17660287

Topology of the membrane protein LamB by epitope tagging and a comparison with the X-ray model.

PubMed

Newton, S M; Klebba, P E; Michel, V; Hofnung, M; Charbit, A

1996-06-01

We previously developed a genetic approach to study, with a single antibody, the topology of the outer membrane protein LamB, an Escherichia coli porin with specificity towards maltodextrins and a receptor for bacteriophage lambda. Our initial procedure consisted of inserting at random the same reporter epitope (the C3 neutralization epitope from poliovirus) into permissive sites of LamB (i.e., sites which tolerate insertions without deleterious effects on the protein activities or the cell). A specific monoclonal antibody was then used to examine the position of the inserted epitope with respect to the protein and the membrane. In the present work, we set up a site-directed procedure to insert the C3 epitope at new sites in order to distinguish between two-dimensional folding models. This allowed us to identify two new surface loops of LamB and to predict another periplasmic exposed region. The results obtained by random and directed epitope tagging are analyzed in light of the recently published X-ray structure of the LamB protein. Study of 23 hybrid LamB-C3 proteins led to the direct identification of five of the nine external loops (L4, L5, L6, L7, and L9) and led to the prediction of four periplasmic loops (I1, I4, I5, and I8) of LamB. Nine of the hybrid proteins did not lead to topological conclusions, and none led to the wrong predictions or conclusions. The comparison indicates that parts of models based on secondary structure predictions alone are not reliable and points to the importance of experimental data in the establishment of outer membrane protein topological models. The advantages and limitations of genetic foreign epitope insertion for the study of integral membrane proteins are discussed.

Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation

PubMed Central

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-01-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X while regulating gene expression chromosome wide. PMID:26030525

Topology optimisation of micro fluidic mixers considering fluid-structure interactions with a coupled Lattice Boltzmann algorithm

NASA Astrophysics Data System (ADS)

Munk, David J.; Kipouros, Timoleon; Vio, Gareth A.; Steven, Grant P.; Parks, Geoffrey T.

2017-11-01

Recently, the study of micro fluidic devices has gained much interest in various fields from biology to engineering. In the constant development cycle, the need to optimise the topology of the interior of these devices, where there are two or more optimality criteria, is always present. In this work, twin physical situations, whereby optimal fluid mixing in the form of vorticity maximisation is accompanied by the requirement that the casing in which the mixing takes place has the best structural performance in terms of the greatest specific stiffness, are considered. In the steady state of mixing this also means that the stresses in the casing are as uniform as possible, thus giving a desired operating life with minimum weight. The ultimate aim of this research is to couple two key disciplines, fluids and structures, into a topology optimisation framework, which shows fast convergence for multidisciplinary optimisation problems. This is achieved by developing a bi-directional evolutionary structural optimisation algorithm that is directly coupled to the Lattice Boltzmann method, used for simulating the flow in the micro fluidic device, for the objectives of minimum compliance and maximum vorticity. The needs for the exploration of larger design spaces and to produce innovative designs make meta-heuristic algorithms, such as genetic algorithms, particle swarms and Tabu Searches, less efficient for this task. The multidisciplinary topology optimisation framework presented in this article is shown to increase the stiffness of the structure from the datum case and produce physically acceptable designs. Furthermore, the topology optimisation method outperforms a Tabu Search algorithm in designing the baffle to maximise the mixing of the two fluids.

Access to edge scenarios for testing a scraper element in early operation phases of Wendelstein 7-X

DOE PAGES

Holbe, H.; Pedersen, T. Sunn; Geiger, J.; ...

2016-01-29

The edge topology of magnetic fusion devices is decisive for the control of the plasma exhaust. In Wendelstein 7-X, the island divertor concept will be used, for which the edge topology can change significantly as the internal currents in a plasma discharge evolve towards steady-state. Consequently, the device has been optimized to minimize such internal currents, in particular the bootstrap current [1]. Nonetheless, there are predicted pulse scenarios where effects of the remaining internal currents could potentially lead to overload of plasma-facing components. These internal currents are predicted to evolve on long time scales (tens of seconds) so their effectsmore » on the edge topology and the divertor heat loads may not be experimentally accessible in the first years of W7-X operation, where only relatively short pulses are possible. However, we show here that for at least one important long-pulse divertor operation issue, relevant physics experiments can be performed already in short-pulse operation, through judicious adjustment of the edge topology by the use of the existing coil sets. The specific issue studied here is a potential overload of the divertor element edges. This overload might be mitigated by the installation of an extra set of plasma-facing components, so-called scraper elements, as suggested in earlier publications. It is shown here that by a targeted control of edge topology, the effectiveness of such scraper elements can be tested already with uncooled test-scraper elements in short-pulse operation. Furthermore, this will allow an early and well-informed decision on whether long-pulse-capable (actively cooled) scraper elements should be built and installed.« less

Probing topological protection using a designer surface plasmon structure

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

Gao, Fei; Gao, Zhen; Shi, Xihang

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

Disorder-induced topological phase transitions in two-dimensional spin-orbit coupled superconductors

PubMed Central

Qin, Wei; Xiao, Di; Chang, Kai; Shen, Shun-Qing; Zhang, Zhenyu

2016-01-01

Normal superconductors with Rashba spin-orbit coupling have been explored as candidate systems of topological superconductors. Here we present a comparative theoretical study of the effects of different types of disorder on the topological phases of two-dimensional Rashba spin-orbit coupled superconductors. First, we show that a topologically trivial superconductor can be driven into a chiral topological superconductor upon diluted doping of isolated magnetic disorder, which close and reopen the quasiparticle gap of the paired electrons in a nontrivial manner. Secondly, the superconducting nature of a topological superconductor is found to be robust against Anderson disorder, but the topological nature is not, converting the system into a topologically trivial state even in the weak scattering limit. These topological phase transitions are distinctly characterized by variations in the topological invariant. We discuss the central findings in connection with existing experiments, and provide new schemes towards eventual realization of topological superconductors. PMID:27991541

Probing topological protection using a designer surface plasmon structure

DOE PAGES

Gao, Fei; Gao, Zhen; Shi, Xihang; ...

2016-05-20

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

Disorder-induced topological phase transitions in two-dimensional spin-orbit coupled superconductors

NASA Astrophysics Data System (ADS)

Qin, Wei; Xiao, Di; Chang, Kai; Shen, Shun-Qing; Zhang, Zhenyu

2016-12-01

Normal superconductors with Rashba spin-orbit coupling have been explored as candidate systems of topological superconductors. Here we present a comparative theoretical study of the effects of different types of disorder on the topological phases of two-dimensional Rashba spin-orbit coupled superconductors. First, we show that a topologically trivial superconductor can be driven into a chiral topological superconductor upon diluted doping of isolated magnetic disorder, which close and reopen the quasiparticle gap of the paired electrons in a nontrivial manner. Secondly, the superconducting nature of a topological superconductor is found to be robust against Anderson disorder, but the topological nature is not, converting the system into a topologically trivial state even in the weak scattering limit. These topological phase transitions are distinctly characterized by variations in the topological invariant. We discuss the central findings in connection with existing experiments, and provide new schemes towards eventual realization of topological superconductors.

Hollow vortex Gaussian beams

NASA Astrophysics Data System (ADS)

Zhou, GuoQuan; Cai, YangJian; Dai, ChaoQing

2013-05-01

A kind of hollow vortex Gaussian beam is introduced. Based on the Collins integral, an analytical propagation formula of a hollow vortex Gaussian beam through a paraxial ABCD optical system is derived. Due to the special distribution of the optical field, which is caused by the initial vortex phase, the dark region of a hollow vortex Gaussian beam will not disappear upon propagation. The analytical expressions for the beam propagation factor, the kurtosis parameter, and the orbital angular momentum density of a hollow vortex Gaussian beam passing through a paraxial ABCD optical system are also derived, respectively. The beam propagation factor is determined by the beam order and the topological charge. The kurtosis parameter and the orbital angular momentum density depend on beam order n, topological charge m, parameter γ, and transfer matrix elements A and D. As a numerical example, the propagation properties of a hollow vortex Gaussian beam in free space are demonstrated. The hollow vortex Gaussian beam has eminent propagation stability and has crucial application prospects in optical micromanipulation.

Exploring the spiral of silence in adjustable social networks

NASA Astrophysics Data System (ADS)

Wu, Yue; Du, Ya-Jun; Li, Xian-Yong; Chen, Xiao-Liang

2015-03-01

This study extends the understanding of the spiral of silence theory by taking into account four factors, including the topology of networks, the time factor of information transmission, the node degree of individuals and the freedom of expression. Simulation experiments analyze the silencers, public opinion in steady state and relaxation time in small-world networks, scale-free networks and community-structured networks by adjusting the initial conditions. Results highlight that individuals are easier to keep silent in scale-free network, especially when the individual with big degree and minority opinion starts the discussion. Conversely, there are only a few individuals keep silent in the community-structured network when the two communities hold opposite opinions. Moreover, the number of silencers grows as the degree of coupling increases, and it decreases as the freedom of expression goes up. By analyzing the public opinion evolution, we also find some important conditions, such as the network topology, the potential public opinion distribution, and the status and sides of the first speaker, can drive the minority reversal.

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

PubMed Central

Lee, Esther J.

2018-01-01

Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks. The rapid growth of single-cell sequencing data has greatly stimulated applications of statistical and machine learning methods for inferring topologies of pluripotency regulating genetic networks. The inferred network topologies, however, often only encode Boolean information while remaining silent about the roles of dynamics and molecular stochasticity inherent in gene expression. Herein we develop a framework for systematically extending Boolean-level network topologies into higher resolution models of networks which explicitly account for the promoter architectures and gene state switching dynamics. We show the framework to be useful for disentangling the various contributions that gene switching, external signaling, and network topology make to the global heterogeneity and dynamics of transcription factor populations. We find the pluripotent state of the network to be a steady state which is robust to global variations of gene switching rates which we argue are a good proxy for epigenetic states of individual promoters. The temporal dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the rates of genetic switching which makes cells more responsive to changes in extracellular signals. PMID:29451874

Topological design of all-ceramic dental bridges for enhancing fracture resistance.

PubMed

Zhang, Zhongpu; Chen, Junning; Li, Eric; Li, Wei; Swain, Michael; Li, Qing

2016-06-01

Layered all-ceramic systems have been increasingly adopted in major dental prostheses. However, ceramics are inherently brittle, and they often subject to premature failure under high occlusion forces especially in the posterior region. This study aimed to develop mechanically sound novel topological designs for all-ceramic dental bridges by minimizing the fracture incidence under given loading conditions. A bi-directional evolutionary structural optimization (BESO) technique is implemented within the extended finite element method (XFEM) framework. Extended finite element method allows modeling crack initiation and propagation inside all-ceramic restoration systems. Following this, BESO searches the optimum distribution of two different ceramic materials, namely porcelain and zirconia, for minimizing fracture incidence. A performance index, as per a ratio of peak tensile stress to material strength, is used as a design objective. In this study, the novel XFEM based BESO topology optimization significantly improved structural strength by minimizing performance index for suppressing fracture incidence in the structures. As expected, the fracture resistance and factor of safety of fixed partial dentures structure increased upon redistributing zirconia and porcelain in the optimal topological configuration. Dental CAD/CAM systems and the emerging 3D printing technology were commercially available to facilitate implementation of such a computational design, exhibiting considerable potential for clinical application in the future. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

On-line training of recurrent neural networks with continuous topology adaptation.

PubMed

Obradovic, D

1996-01-01

This paper presents an online procedure for training dynamic neural networks with input-output recurrences whose topology is continuously adjusted to the complexity of the target system dynamics. This is accomplished by changing the number of the elements of the network hidden layer whenever the existing topology cannot capture the dynamics presented by the new data. The training mechanism is based on the suitably altered extended Kalman filter (EKF) algorithm which is simultaneously used for the network parameter adjustment and for its state estimation. The network consists of a single hidden layer with Gaussian radial basis functions (GRBF), and a linear output layer. The choice of the GRBF is induced by the requirements of the online learning. The latter implies the network architecture which permits only local influence of the new data point in order not to forget the previously learned dynamics. The continuous topology adaptation is implemented in our algorithm to avoid memory and computational problems of using a regular grid of GRBF'S which covers the network input space. Furthermore, we show that the resulting parameter increase can be handled "smoothly" without interfering with the already acquired information. If the target system dynamics are changing over time, we show that a suitable forgetting factor can be used to "unlearn" the no longer-relevant dynamics. The quality of the recurrent network training algorithm is demonstrated on the identification of nonlinear dynamic systems.

A Generic Theory of the Integer Quantum Hall Effect

NASA Astrophysics Data System (ADS)

Shen, Yu

The integer quantum Hall effect (IQHE) is usually modeled by a Galilean or rotationally invariant Hamiltonian. These are not generic symmetries for electrons moving in a crystal background and can potentially confuse non-topological quantities with topological ones and identify otherwise distinct geometrical properties. In this thesis we present a generic theory for the IQHE. First we show that a generic guiding-center coherent state, defined by a natural metric in each Landau level, has the form of an antiholomorphic function times a Gaussian factor. Then by numerically solving the eigenproblem for a quartic Hamiltonian and finding the roots of the antiholomorphic part we are able to define a topological spin sn = n + 1/2 where n is the number of central roots that are enclosed by the semiclassical orbit. We derive a generic formula for the Hall viscosity in the absence of rotational symmetry and show that the previous interpretation of the scalar Hall viscosity as the "intrinsic orbital angular momentum" breaks down since the concept of angular momentum requires the presence of rotational symmetry. We also calculate generic electromagnetic responses and differentiate between universal terms that are diagonal with respect to Landau level index and non-universal terms that depend on inter-Landau-level mixing. We conclude that the generic theory offers a fundamental definition for the topological spin and reveals finer structure in the geometrical properties of the IQHE.

Large power factor and anomalous Hall effect and their correlation with observed linear magneto resistance in Co-doped Bi2Se3 3D topological insulator

NASA Astrophysics Data System (ADS)

Singh, Rahul; Shukla, K. K.; Kumar, A.; Okram, G. S.; Singh, D.; Ganeshan, V.; Lakhani, Archana; Ghosh, A. K.; Chatterjee, Sandip

2016-09-01

Magnetoresistance (MR), thermo power, magnetization and Hall effect measurements have been performed on Co-doped Bi2Se3 topological insulators. The undoped sample shows that the maximum MR as a destructive interference due to a π-Berry phase leads to a decrease of MR. As the Co is doped, the linearity in MR is increased. The observed MR of Bi2Se3 can be explained with the classical model. The low temperature MR behavior of Co doped samples cannot be explained with the same model, but can be explained with the quantum linear MR model. Magnetization behavior indicates the establishment of ferromagnetic ordering with Co doping. Hall effect data also supports the establishment of ferromagnetic ordering in Co-doped Bi2Se3 samples by showing the anomalous Hall effect. Furthermore, when spectral weight suppression is insignificant, Bi2Se3 behaves as a dilute magnetic semiconductor. Moreover, the maximum power factor is observed when time reversal symmetry (TRS) is maintained. As the TRS is broken the power factor value is decreased, which indicates that with the rise of Dirac cone above the Fermi level the anomalous Hall effect and linearity in MR increase and the power factor decreases.

Optical force and torque on a dielectric Rayleigh particle by a circular Airy vortex beam

NASA Astrophysics Data System (ADS)

Chen, Musheng; Huang, Sujuan; Shao, Wei; Liu, Xianpeng

2018-03-01

Optical force and torque exerted on the Rayleigh particles by tightly focused circularly polarized circular Airy vortex beams (CAVB) in the far field are studied in this paper. The relation between parameters of circularly polarized CAVB and the trapping properties is numerically analyzed based on Rayleigh models and the Debye diffraction theory. The results show that both the high refractive index and low refractive index particles can be fully stably trapped in three dimensions by circularly polarized CAVB. The parameters of circularly polarized CAVB greatly affect the optical force. The longitudinal and transverse gradient force increase with the increase of decay factor and scaling factor, and decrease with the increase of the radius of the first primary ring and topological charges. The positions of the longitudinal stable equilibrium move toward the high numerical aperture lens when the scaling factor and the radius of the primary ring increase. The trapping range is broadened with the decrease of scaling factor. The optical orbital torque (OOT) of circularly polarized CAVB has circular symmetry and remains positive or negative. With the increase of topological charges, the peak value of OOT first increases and then decreases after reaches a maximum. These results are useful for optical trapping, optical levitation and particle acceleration.

Lanthanide co-ordination frameworks: Opportunities and diversity

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

Hill, Robert J.; Long, De-Liang; Hubberstey, Peter

2005-08-15

Significant successes have been made over recent years in preparing co-ordination framework polymers that show macroscopic material properties, but in the vast majority of cases this has been achieved with d-block metal-based systems. Lanthanide co-ordination frameworks also offer attractive properties in terms of their potential applications as luminescent, non-linear optical and porous materials. However, lanthanide-based systems have been far less studied to date than their d-block counterparts. One possible reason for this is that the co-ordination spheres of lanthanide cations are more difficult to control and, in the absence of design strategies for lanthanide co-ordination frameworks, it is significantly moremore » difficult to target materials with specific properties. However, this article highlights some of the exciting possibilities that have emerged from the earliest investigations in this field with new topological families of compounds being discovered from relatively simple framework components, including unusual eight, seven and five-connected framework systems. Our own research, as well as others, is leading to a much greater appreciation of the factors that control framework formation and the resultant observed topologies of these polymers. As this understanding develops targeting particular framework types will become more straightforward and the development of designed polyfunctional materials more accessible. Thus, it can be seen that lanthanide co-ordination frameworks have the potential to open up previously unexplored directions for materials chemistry. This article focuses on the underlying concepts for the construction of these enticing and potentially highly important materials.« less

Topological Quantum Phase Transition and Local Topological Order in a Strongly Interacting Light-Matter System.

PubMed

Sarkar, Sujit

2017-05-12

An attempt is made to understand the topological quantum phase transition, emergence of relativistic modes and local topological order of light in a strongly interacting light-matter system. We study this system, in a one dimensional array of nonlinear cavities. Topological quantum phase transition occurs with massless excitation only for the finite detuning process. We present a few results based on the exact analytical calculations along with the physical explanations. We observe the emergence of massive Majorana fermion mode at the topological state, massless Majorana-Weyl fermion mode during the topological quantum phase transition and Dirac fermion mode for the non-topological state. Finally, we study the quantized Berry phase (topological order) and its connection to the topological number (winding number).

Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions

PubMed Central

2014-01-01

Background Plant secondary metabolites are critical to various biological processes. However, the regulations of these metabolites are complex because of regulatory rewiring or crosstalk. To unveil how regulatory behaviors on secondary metabolism reshape biological processes, we constructed and analyzed a dynamic regulatory network of secondary metabolic pathways in Arabidopsis. Results The dynamic regulatory network was constructed through integrating co-expressed gene pairs and regulatory interactions. Regulatory interactions were either predicted by conserved transcription factor binding sites (TFBSs) or proved by experiments. We found that integrating two data (co-expression and predicted regulatory interactions) enhanced the number of highly confident regulatory interactions by over 10% compared with using single data. The dynamic changes of regulatory network systematically manifested regulatory rewiring to explain the mechanism of regulation, such as in terpenoids metabolism, the regulatory crosstalk of RAV1 (AT1G13260) and ATHB1 (AT3G01470) on HMG1 (hydroxymethylglutaryl-CoA reductase, AT1G76490); and regulation of RAV1 on epoxysqualene biosynthesis and sterol biosynthesis. Besides, we investigated regulatory rewiring with expression, network topology and upstream signaling pathways. Regulatory rewiring was revealed by the variability of genes’ expression: pathway genes and transcription factors (TFs) were significantly differentially expressed under different conditions (such as terpenoids biosynthetic genes in tissue experiments and E2F/DP family members in genotype experiments). Both network topology and signaling pathways supported regulatory rewiring. For example, we discovered correlation among the numbers of pathway genes, TFs and network topology: one-gene pathways (such as δ-carotene biosynthesis) were regulated by a fewer TFs, and were not critical to metabolic network because of their low degrees in topology. Upstream signaling pathways of 50 TFs were identified to comprehend the underlying mechanism of TFs’ regulatory rewiring. Conclusion Overall, this dynamic regulatory network largely improves the understanding of perplexed regulatory rewiring in secondary metabolism in Arabidopsis. PMID:24993737

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.

PubMed

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-07

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

NASA Astrophysics Data System (ADS)

Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

2013-05-01

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Optomechanical performance of 3D-printed mirrors with embedded cooling channels and substructures

NASA Astrophysics Data System (ADS)

Mici, Joni; Rothenberg, Bradley; Brisson, Erik; Wicks, Sunny; Stubbs, David M.

2015-09-01

Advances in 3D printing technology allow for the manufacture of topologically complex parts not otherwise feasible through conventional manufacturing methods. Maturing metal and ceramic 3D printing technologies are becoming more adept at printing complex shapes, enabling topologically intricate mirror substrates. One application area that can benefit from additive manufacturing is reflective optics used in high energy laser (HEL) systems that require materials with a low coefficient of thermal expansion (CTE), high specific stiffness, and (most importantly) high thermal conductivity to effectively dissipate heat from the optical surface. Currently, the limits of conventional manufacturing dictate the topology of HEL optics to be monolithic structures that rely on passive cooling mechanisms and high reflectivity coatings to withstand laser damage. 3D printing enables the manufacture of embedded cooling channels in metallic mirror substrates to allow for (1) active cooling and (2) tunable structures. This paper describes the engineering and analysis of an actively cooled composite optical structure to demonstrate the potential of 3D printing on the improvement of optomechanical systems.

Majorana surface modes of nodal topological pairings in spin-3/2 semimetals

NASA Astrophysics Data System (ADS)

Yang, Wang; Xiang, Tao; Wu, Congjun

2017-10-01

When solid state systems possess active orbital-band structures subject to spin-orbit coupling, their multicomponent electronic structures are often described in terms of effective large-spin fermion models. Their topological structures of superconductivity are beyond the framework of spin singlet and triplet Cooper pairings for spin-1/2 systems. Examples include the half-Heusler compound series of RPtBi, where R stands for a rare-earth element. Their spin-orbit coupled electronic structures are described by the Luttinger-Kohn model with effective spin-3/2 fermions and are characterized by band inversion. Recent experiments provide evidence to unconventional superconductivity in the YPtBi material with nodal spin-septet pairing. We systematically study topological pairing structures in spin-3/2 systems with the cubic group symmetries and calculate the surface Majorana spectra, which exhibit zero energy flat bands, or, cubic dispersion depending on the specific symmetry of the superconducting gap functions. The signatures of these surface states in the quasiparticle interference patterns of tunneling spectroscopy are studied, which can be tested in future experiments.

Topological susceptibility with a single light quark flavour

NASA Astrophysics Data System (ADS)

Frison, Julien; Kitano, Ryuichiro; Yamada, Norikazu

2018-03-01

One of the historical suggestions to tackle the strong CP problem is to take the up quark mass to zero while keeping md finite. The θ angle is then supposed to become irrelevant, i.e. the topological susceptibility vanishes. However, the definition of the quark mass is scheme-dependent and identifying the mu = 0 point is not trivial, in particular with Wilson-like fermions. More specifically, up to our knowledge there is no theoretical argument guaranteeing that the topological susceptibility exactly vanishes when the PCAC mass does. We will present our recent progresses on the empirical check of this property using Nf = 1 + 2 flavours of clover fermions, where the lightest fermion is tuned very close to muPCAC= 0 and the mass of the other two is kept of the order of magnitude of the physical ms. This choice is indeed expected to amplify any unknown non-perturbative effect caused by mu ≠ md. The simulation is repeated for several βs and those results, although preliminary, give a hint about what happens in the continuum limit.

Distinguishing topological Majorana bound states from trivial Andreev bound states: Proposed tests through differential tunneling conductance spectroscopy

NASA Astrophysics Data System (ADS)

Liu, Chun-Xiao; Sau, Jay D.; Das Sarma, S.

2018-06-01

Trivial Andreev bound states arising from chemical-potential variations could lead to zero-bias tunneling conductance peaks at finite magnetic field in class-D nanowires, precisely mimicking the predicted zero-bias conductance peaks arising from the topological Majorana bound states. This finding raises a serious question on the efficacy of using zero-bias tunneling conductance peaks, by themselves, as evidence supporting the existence of topological Majorana bound states in nanowires. In the current work, we provide specific experimental protocols for tunneling spectroscopy measurements to distinguish between Andreev and Majorana bound states without invoking more demanding nonlocal measurements which have not yet been successfully performed in nanowire systems. In particular, we discuss three distinct experimental schemes involving the response of the zero-bias peak to local perturbations of the tunnel barrier, the overlap of bound states from the wire ends, and, most compellingly, introducing a sharp localized potential in the wire itself to perturb the zero-bias tunneling peaks. We provide extensive numerical simulations clarifying and supporting our theoretical predictions.

A molecular topology approach to predicting pesticide pollution of groundwater

USGS Publications Warehouse

Worrall , Fred

2001-01-01

Various models have proposed methods for the discrimination of polluting and nonpolluting compounds on the basis of simple parameters, typically adsorption and degradation constants. However, such attempts are prone to site variability and measurement error to the extent that compounds cannot be reliably classified nor the chemistry of pollution extrapolated from them. Using observations of pesticide occurrence in U.S. groundwater it is possible to show that polluting from nonpolluting compounds can be distinguished purely on the basis of molecular topology. Topological parameters can be derived without measurement error or site-specific variability. A logistic regression model has been developed which explains 97% of the variation in the data, with 86% of the variation being explained by the rule that a compound will be found in groundwater if 6 < 0.55. Where 6χp is the sixth-order molecular path connectivity. One group of compounds cannot be classified by this rule and prediction requires reference to higher order connectivity parameters. The use of molecular approaches for understanding pollution at the molecular level and their application to agrochemical development and risk assessment is discussed.