Weyl nodes in Andreev spectra of multiterminal Josephson junctions: Chern numbers, conductances, and supercurrents

NASA Astrophysics Data System (ADS)

Xie, Hong-Yi; Vavilov, Maxim G.; Levchenko, Alex

2018-02-01

We consider mesoscopic four-terminal Josephson junctions and study emergent topological properties of the Andreev subgap bands. We use symmetry-constrained analysis for Wigner-Dyson classes of scattering matrices to derive band dispersions. When the scattering matrix of the normal region connecting superconducting leads is energy independent, the determinant formula for Andreev spectrum can be reduced to a palindromic equation that admits a complete analytical solution. Band topology manifests with an appearance of the Weyl nodes which serve as monopoles of finite Berry curvature. The corresponding fluxes are quantified by Chern numbers that translate into a quantized nonlocal conductance that we compute explicitly for the time-reversal-symmetric scattering matrix. The topological regime can also be identified by supercurrents as Josephson current-phase relationships exhibit pronounced nonanalytic behavior and discontinuities near Weyl points that can be controllably accessed in experiments.

Topological susceptibility in finite temperature (2 +1 )-flavor QCD using gradient flow

NASA Astrophysics Data System (ADS)

Taniguchi, Yusuke; Kanaya, Kazuyuki; Suzuki, Hiroshi; Umeda, Takashi; WHOT-QCD Collaboration

2017-03-01

We compute the topological charge and its susceptibility in finite temperature (2 +1 )-flavor QCD on the lattice applying a gradient flow method. With the Iwasaki gauge action and nonperturbatively O (a ) -improved Wilson quarks, we perform simulations on a fine lattice with a ≃0.07 fm at a heavy u , d quark mass with mπ/mρ≃0.63 , but approximately physical s quark mass with mηss/mϕ≃0.74 . In a temperature range from T ≃174 MeV (Nt=16 ) to 697 MeV (Nt=4 ), we study two topics on the topological susceptibility. One is a comparison of gluonic and fermionic definitions of the topological susceptibility. Because the two definitions are related by chiral Ward-Takahashi identities, their equivalence is not trivial for lattice quarks which violate the chiral symmetry explicitly at finite lattice spacings. The gradient flow method enables us to compute them without being bothered by the chiral violation. We find a good agreement between the two definitions with Wilson quarks. The other is a comparison with a prediction of the dilute instanton gas approximation, which is relevant in a study of axions as a candidate of the dark matter in the evolution of the Universe. We find that the topological susceptibility shows a decrease in T which is consistent with the predicted χt(T )∝(T /Tpc)-8 for three-flavor QCD even at low temperature Tpc

Topological phases of topological-insulator thin films

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Instantons, quivers and noncommutative Donaldson-Thomas theory

NASA Astrophysics Data System (ADS)

Cirafici, Michele; Sinkovics, Annamaria; Szabo, Richard J.

2011-12-01

We construct noncommutative Donaldson-Thomas invariants associated with abelian orbifold singularities by analyzing the instanton contributions to a six-dimensional topological gauge theory. The noncommutative deformation of this gauge theory localizes on noncommutative instantons which can be classified in terms of three-dimensional Young diagrams with a colouring of boxes according to the orbifold group. We construct a moduli space for these gauge field configurations which allows us to compute its virtual numbers via the counting of representations of a quiver with relations. The quiver encodes the instanton dynamics of the noncommutative gauge theory, and is associated to the geometry of the singularity via the generalized McKay correspondence. The index of BPS states which compute the noncommutative Donaldson-Thomas invariants is realized via topological quantum mechanics based on the quiver data. We illustrate these constructions with several explicit examples, involving also higher rank Coulomb branch invariants and geometries with compact divisors, and connect our approach with other ones in the literature.

Robustness of Topological Superconductivity in Solid State Hybrid Structures

NASA Astrophysics Data System (ADS)

Sitthison, Piyapong

The non-Abelian statistics of Majorana fermions (MFs) makes them an ideal platform for implementing topological quantum computation. In addition to the fascinating fundamental physics underlying the emergence of MFs, this potential for applications makes the study of these quasiparticles an extremely popular subject in condensed matter physics. The commonly called `Majorana fermions' are zero-energy bound states that emerge near boundaries and defects in topological superconducting phases, which can be engineered, for example, by proximity coupling strong spin-orbit coupling semiconductor nanowires and ordinary s-wave superconductors. The stability of these bound states is determined by the stability of the underlying topological superconducting phase. Hence, understanding their stability (which is critical for quantum computation), involves studying the robustness of the engineered topological superconductors. This work addresses this important problem in the context of two types of hybrid structures that have been proposed for realizing topological superconductivity: topological insulator - superconductor (TI-SC) and semiconductor - superconductor (SM-SC) nanostructures. In both structures, electrostatic effects due to applied external potentials and interface-induced potentials are significant. This work focuses on developing a theoretical framework for understanding these effects, to facilitate the optimization of the nanostructures studied in the laboratory. The approach presented in this thesis is based on describing the low-energy physics of the hybrid structure using effective tight-binding models that explicitly incorporate the proximity effects emerging at interfaces. Generically, as a result of the proximity coupling to the superconductor, an induced gap emerges in the semiconductor (topological insulator) sub-system. The strength of the proximity-induced gap is determined by the transparency of the interface and by the amplitude of the low- energy SM (TI) states at the interface. In turn, this amplitude is strongly impacted by electrostatic effects. In addition, these effects control the value of the chemical potential in the nanowire (nanoribbon), as well as the strength of the Rashba-type spin-orbit coupling - two key parameters that determine the stability of the topological superconducting phase. To account for these critical effects, a numerically efficient Poisson-Schrodinger scheme is developed.

Inclusion of Topological Measurements into Analytic Estimates of Effective Permeability in Fractured Media

NASA Astrophysics Data System (ADS)

Sævik, P. N.; Nixon, C. W.

2017-11-01

We demonstrate how topology-based measures of connectivity can be used to improve analytical estimates of effective permeability in 2-D fracture networks, which is one of the key parameters necessary for fluid flow simulations at the reservoir scale. Existing methods in this field usually compute fracture connectivity using the average fracture length. This approach is valid for ideally shaped, randomly distributed fractures, but is not immediately applicable to natural fracture networks. In particular, natural networks tend to be more connected than randomly positioned fractures of comparable lengths, since natural fractures often terminate in each other. The proposed topological connectivity measure is based on the number of intersections and fracture terminations per sampling area, which for statistically stationary networks can be obtained directly from limited outcrop exposures. To evaluate the method, numerical permeability upscaling was performed on a large number of synthetic and natural fracture networks, with varying topology and geometry. The proposed method was seen to provide much more reliable permeability estimates than the length-based approach, across a wide range of fracture patterns. We summarize our results in a single, explicit formula for the effective permeability.

Accurate solutions for transonic viscous flow over finite wings

NASA Technical Reports Server (NTRS)

Vatsa, V. N.

1986-01-01

An explicit multistage Runge-Kutta type time-stepping scheme is used for solving the three-dimensional, compressible, thin-layer Navier-Stokes equations. A finite-volume formulation is employed to facilitate treatment of complex grid topologies encountered in three-dimensional calculations. Convergence to steady state is expedited through usage of acceleration techniques. Further numerical efficiency is achieved through vectorization of the computer code. The accuracy of the overall scheme is evaluated by comparing the computed solutions with the experimental data for a finite wing under different test conditions in the transonic regime. A grid refinement study ir conducted to estimate the grid requirements for adequate resolution of salient features of such flows.

Possible quantum algorithm for the Lipshitz-Sarkar-Steenrod square for Khovanov homology

NASA Astrophysics Data System (ADS)

Ospina, Juan

2013-05-01

Recently the celebrated Khovanov Homology was introduced as a target for Topological Quantum Computation given that the Khovanov Homology provides a generalization of the Jones polynomal and then it is possible to think about of a generalization of the Aharonov.-Jones-Landau algorithm. Recently, Lipshitz and Sarkar introduced a space-level refinement of Khovanov homology. which is called Khovanov Homotopy. This refinement induces a Steenrod square operation Sq2 on Khovanov homology which they describe explicitly and then some computations of Sq2 were presented. Particularly, examples of links with identical integral Khovanov homology but with distinct Khovanov homotopy types were showed. In the presente work we will introduce possible quantum algorithms for the Lipshitz- Sarkar-Steenrod square for Khovanov Homolog and their possible simulations using computer algebra.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Unified Generic Geometric-Decompositions for Consensus or Flocking Systems of Cooperative Agents and Fast Recalculations of Decomposed Subsystems Under Topology-Adjustments.

PubMed

Li, Wei

2016-06-01

This paper considers a unified geometric projection approach for: 1) decomposing a general system of cooperative agents coupled via Laplacian matrices or stochastic matrices and 2) deriving a centroid-subsystem and many shape-subsystems, where each shape-subsystem has the distinct properties (e.g., preservation of formation and stability of the original system, sufficiently simple structures and explicit formation evolution of agents, and decoupling from the centroid-subsystem) which will facilitate subsequent analyses. Particularly, this paper provides an additional merit of the approach: considering adjustments of coupling topologies of agents which frequently occur in system design (e.g., to add or remove an edge, to move an edge to a new place, and to change the weight of an edge), the corresponding new shape-subsystems can be derived by a few simple computations merely from the old shape-subsystems and without referring to the original system, which will provide further convenience for analysis and flexibility of choice. Finally, such fast recalculations of new subsystems under topology adjustments are provided with examples.

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

NASA Astrophysics Data System (ADS)

Aleshkin, Konstantin; Belavin, Vladimir; Rim, Chaiho

2017-11-01

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

Extended Quantum Field Theory, Index Theory, and the Parity Anomaly

NASA Astrophysics Data System (ADS)

Müller, Lukas; Szabo, Richard J.

2018-06-01

We use techniques from functorial quantum field theory to provide a geometric description of the parity anomaly in fermionic systems coupled to background gauge and gravitational fields on odd-dimensional spacetimes. We give an explicit construction of a geometric cobordism bicategory which incorporates general background fields in a stack, and together with the theory of symmetric monoidal bicategories we use it to provide the concrete forms of invertible extended quantum field theories which capture anomalies in both the path integral and Hamiltonian frameworks. Specialising this situation by using the extension of the Atiyah-Patodi-Singer index theorem to manifolds with corners due to Loya and Melrose, we obtain a new Hamiltonian perspective on the parity anomaly. We compute explicitly the 2-cocycle of the projective representation of the gauge symmetry on the quantum state space, which is defined in a parity-symmetric way by suitably augmenting the standard chiral fermionic Fock spaces with Lagrangian subspaces of zero modes of the Dirac Hamiltonian that naturally appear in the index theorem. We describe the significance of our constructions for the bulk-boundary correspondence in a large class of time-reversal invariant gauge-gravity symmetry-protected topological phases of quantum matter with gapless charged boundary fermions, including the standard topological insulator in 3 + 1 dimensions.

Twisted quantum double model of topological order with boundaries

NASA Astrophysics Data System (ADS)

Bullivant, Alex; Hu, Yuting; Wan, Yidun

2017-10-01

We generalize the twisted quantum double model of topological orders in two dimensions to the case with boundaries by systematically constructing the boundary Hamiltonians. Given the bulk Hamiltonian defined by a gauge group G and a 3-cocycle in the third cohomology group of G over U (1 ) , a boundary Hamiltonian can be defined by a subgroup K of G and a 2-cochain in the second cochain group of K over U (1 ) . The consistency between the bulk and boundary Hamiltonians is dictated by what we call the Frobenius condition that constrains the 2-cochain given the 3-cocyle. We offer a closed-form formula computing the ground-state degeneracy of the model on a cylinder in terms of the input data only, which can be naturally generalized to surfaces with more boundaries. We also explicitly write down the ground-state wave function of the model on a disk also in terms of the input data only.

Gpu Implementation of a Viscous Flow Solver on Unstructured Grids

NASA Astrophysics Data System (ADS)

Xu, Tianhao; Chen, Long

2016-06-01

Graphics processing units have gained popularities in scientific computing over past several years due to their outstanding parallel computing capability. Computational fluid dynamics applications involve large amounts of calculations, therefore a latest GPU card is preferable of which the peak computing performance and memory bandwidth are much better than a contemporary high-end CPU. We herein focus on the detailed implementation of our GPU targeting Reynolds-averaged Navier-Stokes equations solver based on finite-volume method. The solver employs a vertex-centered scheme on unstructured grids for the sake of being capable of handling complex topologies. Multiple optimizations are carried out to improve the memory accessing performance and kernel utilization. Both steady and unsteady flow simulation cases are carried out using explicit Runge-Kutta scheme. The solver with GPU acceleration in this paper is demonstrated to have competitive advantages over the CPU targeting one.

Gapped boundary phases of topological insulators via weak coupling

DOE PAGES

Seiberg, Nathan; Witten, Edward

2016-11-04

The standard boundary state of a topological insulator in 3 + 1 dimensions has gapless charged fermions. We present model systems that reproduce this standard gapless boundary state in one phase, but also have gapped phases with topological order. Our models are weakly coupled and all the dynamics is explicit. We rederive some known boundary states of topological insulators and construct new ones. Consistency with the standard spin/charge relation of condensed matter physics places a nontrivial constraint on models

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.

Combined shape and topology optimization for minimization of maximal von Mises stress

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

Lian, Haojie; Christiansen, Asger N.; Tortorelli, Daniel A.

Here, this work shows that a combined shape and topology optimization method can produce optimal 2D designs with minimal stress subject to a volume constraint. The method represents the surface explicitly and discretizes the domain into a simplicial complex which adapts both structural shape and topology. By performing repeated topology and shape optimizations and adaptive mesh updates, we can minimize the maximum von Mises stress using the p-norm stress measure with p-values as high as 30, provided that the stress is calculated with sufficient accuracy.

Combined shape and topology optimization for minimization of maximal von Mises stress

DOE PAGES

Lian, Haojie; Christiansen, Asger N.; Tortorelli, Daniel A.; ...

2017-01-27

Here, this work shows that a combined shape and topology optimization method can produce optimal 2D designs with minimal stress subject to a volume constraint. The method represents the surface explicitly and discretizes the domain into a simplicial complex which adapts both structural shape and topology. By performing repeated topology and shape optimizations and adaptive mesh updates, we can minimize the maximum von Mises stress using the p-norm stress measure with p-values as high as 30, provided that the stress is calculated with sufficient accuracy.

Multiresolution and Explicit Methods for Vector Field Analysis and Visualization

NASA Technical Reports Server (NTRS)

1996-01-01

We first report on our current progress in the area of explicit methods for tangent curve computation. The basic idea of this method is to decompose the domain into a collection of triangles (or tetrahedra) and assume linear variation of the vector field over each cell. With this assumption, the equations which define a tangent curve become a system of linear, constant coefficient ODE's which can be solved explicitly. There are five different representation of the solution depending on the eigenvalues of the Jacobian. The analysis of these five cases is somewhat similar to the phase plane analysis often associate with critical point classification within the context of topological methods, but it is not exactly the same. There are some critical differences. Moving from one cell to the next as a tangent curve is tracked, requires the computation of the exit point which is an intersection of the solution of the constant coefficient ODE and the edge of a triangle. There are two possible approaches to this root computation problem. We can express the tangent curve into parametric form and substitute into an implicit form for the edge or we can express the edge in parametric form and substitute in an implicit form of the tangent curve. Normally the solution of a system of ODE's is given in parametric form and so the first approach is the most accessible and straightforward. The second approach requires the 'implicitization' of these parametric curves. The implicitization of parametric curves can often be rather difficult, but in this case we have been successful and have been able to develop algorithms and subsequent computer programs for both approaches. We will give these details along with some comparisons in a forthcoming research paper on this topic.

A new class of N=2 topological amplitudes

NASA Astrophysics Data System (ADS)

Antoniadis, I.; Hohenegger, S.; Narain, K. S.; Sokatchev, E.

2009-12-01

We describe a new class of N=2 topological amplitudes that compute a particular class of BPS terms in the low energy effective supergravity action. Specifically they compute the coupling F(( where F, λ and ϕ are gauge field strengths, gaugino and holomorphic vector multiplet scalars. The novel feature of these terms is that they depend both on the vector and hypermultiplet moduli. The BPS nature of these terms implies that they satisfy a holomorphicity condition with respect to vector moduli and a harmonicity condition as well as a second order differential equation with respect to hypermultiplet moduli. We study these conditions explicitly in heterotic string theory and show that they are indeed satisfied up to anomalous boundary terms in the world-sheet moduli space. We also analyze the boundary terms in the holomorphicity and harmonicity equations at a generic point in the vector and hyper moduli space. In particular we show that the obstruction to the holomorphicity arises from the one loop threshold correction to the gauge couplings and we argue that this is due to the contribution of non-holomorphic couplings to the connected graphs via elimination of the auxiliary fields.

Quantum Field Theory Approach to Condensed Matter Physics

NASA Astrophysics Data System (ADS)

Marino, Eduardo C.

2017-09-01

Preface; Part I. Condensed Matter Physics: 1. Independent electrons and static crystals; 2. Vibrating crystals; 3. Interacting electrons; 4. Interactions in action; Part II. Quantum Field Theory: 5. Functional formulation of quantum field theory; 6. Quantum fields in action; 7. Symmetries: explicit or secret; 8. Classical topological excitations; 9. Quantum topological excitations; 10. Duality, bosonization and generalized statistics; 11. Statistical transmutation; 12. Pseudo quantum electrodynamics; Part III. Quantum Field Theory Approach to Condensed Matter Systems: 13. Quantum field theory methods in condensed matter; 14. Metals, Fermi liquids, Mott and Anderson insulators; 15. The dynamics of polarons; 16. Polyacetylene; 17. The Kondo effect; 18. Quantum magnets in 1D: Fermionization, bosonization, Coulomb gases and 'all that'; 19. Quantum magnets in 2D: nonlinear sigma model, CP1 and 'all that'; 20. The spin-fermion system: a quantum field theory approach; 21. The spin glass; 22. Quantum field theory approach to superfluidity; 23. Quantum field theory approach to superconductivity; 24. The cuprate high-temperature superconductors; 25. The pnictides: iron based superconductors; 26. The quantum Hall effect; 27. Graphene; 28. Silicene and transition metal dichalcogenides; 29. Topological insulators; 30. Non-abelian statistics and quantum computation; References; Index.

Experimental Identification of Non-Abelian Topological Orders on a Quantum Simulator.

PubMed

Li, Keren; Wan, Yidun; Hung, Ling-Yan; Lan, Tian; Long, Guilu; Lu, Dawei; Zeng, Bei; Laflamme, Raymond

2017-02-24

Topological orders can be used as media for topological quantum computing-a promising quantum computation model due to its invulnerability against local errors. Conversely, a quantum simulator, often regarded as a quantum computing device for special purposes, also offers a way of characterizing topological orders. Here, we show how to identify distinct topological orders via measuring their modular S and T matrices. In particular, we employ a nuclear magnetic resonance quantum simulator to study the properties of three topologically ordered matter phases described by the string-net model with two string types, including the Z_{2} toric code, doubled semion, and doubled Fibonacci. The third one, non-Abelian Fibonacci order is notably expected to be the simplest candidate for universal topological quantum computing. Our experiment serves as the basic module, built on which one can simulate braiding of non-Abelian anyons and ultimately, topological quantum computation via the braiding, and thus provides a new approach of investigating topological orders using quantum computers.

Quark-parton model from dual topological unitarization

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

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

1979-06-01

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

Six networks on a universal neuromorphic computing substrate.

PubMed

Pfeil, Thomas; Grübl, Andreas; Jeltsch, Sebastian; Müller, Eric; Müller, Paul; Petrovici, Mihai A; Schmuker, Michael; Brüderle, Daniel; Schemmel, Johannes; Meier, Karlheinz

2013-01-01

In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks. At the heart of this system lies a mixed-signal chip, with analog implementations of neurons and synapses and digital transmission of action potentials. Major advantages of this emulation device, which has been explicitly designed as a universal neural network emulator, are its inherent parallelism and high acceleration factor compared to conventional computers. Its configurability allows the realization of almost arbitrary network topologies and the use of widely varied neuronal and synaptic parameters. Fixed-pattern noise inherent to analog circuitry is reduced by calibration routines. An integrated development environment allows neuroscientists to operate the device without any prior knowledge of neuromorphic circuit design. As a showcase for the capabilities of the system, we describe the successful emulation of six different neural networks which cover a broad spectrum of both structure and functionality.

Six Networks on a Universal Neuromorphic Computing Substrate

PubMed Central

Pfeil, Thomas; Grübl, Andreas; Jeltsch, Sebastian; Müller, Eric; Müller, Paul; Petrovici, Mihai A.; Schmuker, Michael; Brüderle, Daniel; Schemmel, Johannes; Meier, Karlheinz

2013-01-01

In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks. At the heart of this system lies a mixed-signal chip, with analog implementations of neurons and synapses and digital transmission of action potentials. Major advantages of this emulation device, which has been explicitly designed as a universal neural network emulator, are its inherent parallelism and high acceleration factor compared to conventional computers. Its configurability allows the realization of almost arbitrary network topologies and the use of widely varied neuronal and synaptic parameters. Fixed-pattern noise inherent to analog circuitry is reduced by calibration routines. An integrated development environment allows neuroscientists to operate the device without any prior knowledge of neuromorphic circuit design. As a showcase for the capabilities of the system, we describe the successful emulation of six different neural networks which cover a broad spectrum of both structure and functionality. PMID:23423583

Visual sensory networks and effective information transfer in animal groups.

PubMed

Strandburg-Peshkin, Ariana; Twomey, Colin R; Bode, Nikolai W F; Kao, Albert B; Katz, Yael; Ioannou, Christos C; Rosenthal, Sara B; Torney, Colin J; Wu, Hai Shan; Levin, Simon A; Couzin, Iain D

2013-09-09

Social transmission of information is vital for many group-living animals, allowing coordination of motion and effective response to complex environments. Revealing the interaction networks underlying information flow within these groups is a central challenge. Previous work has modeled interactions between individuals based directly on their relative spatial positions: each individual is considered to interact with all neighbors within a fixed distance (metric range), a fixed number of nearest neighbors (topological range), a 'shell' of near neighbors (Voronoi range), or some combination (Figure 1A). However, conclusive evidence to support these assumptions is lacking. Here, we employ a novel approach that considers individual movement decisions to be based explicitly on the sensory information available to the organism. In other words, we consider that while spatial relations do inform interactions between individuals, they do so indirectly, through individuals' detection of sensory cues. We reconstruct computationally the visual field of each individual throughout experiments designed to investigate information propagation within fish schools (golden shiners, Notemigonus crysoleucas). Explicitly considering visual sensing allows us to more accurately predict the propagation of behavioral change in these groups during leadership events. Furthermore, we find that structural properties of visual interaction networks differ markedly from those of metric and topological counterparts, suggesting that previous assumptions may not appropriately reflect information flow in animal groups. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bosonization of fermions coupled to topologically massive gravity

NASA Astrophysics Data System (ADS)

Fradkin, Eduardo; Moreno, Enrique F.; Schaposnik, Fidel A.

2014-03-01

We establish a duality between massive fermions coupled to topologically massive gravity (TMG) in d=3 space-time dimensions and a purely gravity theory which also will turn out to be a TMG theory but with different parameters: the original graviton mass in the TMG theory coupled to fermions picks up a contribution from fermion bosonization. We obtain explicit bosonization rules for the fermionic currents and for the energy-momentum tensor showing that the identifications do not depend explicitly on the parameters of the theory. These results are the gravitational analog of the results for 2+1 Abelian and non-Abelian bosonization in flat space-time.

Innovations in individual feature history management - The significance of feature-based temporal model

USGS Publications Warehouse

Choi, J.; Seong, J.C.; Kim, B.; Usery, E.L.

2008-01-01

A feature relies on three dimensions (space, theme, and time) for its representation. Even though spatiotemporal models have been proposed, they have principally focused on the spatial changes of a feature. In this paper, a feature-based temporal model is proposed to represent the changes of both space and theme independently. The proposed model modifies the ISO's temporal schema and adds new explicit temporal relationship structure that stores temporal topological relationship with the ISO's temporal primitives of a feature in order to keep track feature history. The explicit temporal relationship can enhance query performance on feature history by removing topological comparison during query process. Further, a prototype system has been developed to test a proposed feature-based temporal model by querying land parcel history in Athens, Georgia. The result of temporal query on individual feature history shows the efficiency of the explicit temporal relationship structure. ?? Springer Science+Business Media, LLC 2007.

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.

Z3 topological order in the face-centered-cubic quantum plaquette model

NASA Astrophysics Data System (ADS)

Devakul, Trithep

2018-04-01

We examine the topological order in the resonating singlet valence plaquette (RSVP) phase of the hard-core quantum plaquette model (QPM) on the face centered cubic (FCC) lattice. To do this, we construct a Rohksar-Kivelson type Hamiltonian of local plaquette resonances. This model is shown to exhibit a Z3 topological order, which we show by identifying a Z3 topological constant (which leads to a 33-fold topological ground state degeneracy on the 3-torus) and topological pointlike charge and looplike magnetic excitations which obey Z3 statistics. We also consider an exactly solvable generalization of this model, which makes the geometrical origin of the Z3 order explicitly clear. For other models and lattices, such generalizations produce a wide variety of topological phases, some of which are novel fracton phases.

A jellium model of a catalyst particle in carbon nanotube growth

NASA Astrophysics Data System (ADS)

Artyukhov, Vasilii I.; Liu, Mingjie; Penev, Evgeni S.; Yakobson, Boris I.

2017-06-01

We show how a jellium model can represent a catalyst particle within the density-functional theory based approaches to the growth mechanism of carbon nanotubes (CNTs). The advantage of jellium is an abridged, less computationally taxing description of the multi-atom metal particle, while at the same time in avoiding the uncertainty of selecting a particular atomic geometry of either a solid or ever-changing liquid catalyst particle. A careful choice of jellium sphere size and its electron density as a descriptive parameter allows one to calculate the CNT-metal interface energies close to explicit full atomistic models. Further, we show that using jellium permits computing and comparing the formation of topological defects (sole pentagons or heptagons, the culprits of growth termination) as well as pentagon-heptagon pairs 5|7 (known as chirality-switching dislocation).

Identifying Two-Dimensional Z 2 Antiferromagnetic Topological Insulators

NASA Astrophysics Data System (ADS)

Bègue, F.; Pujol, P.; Ramazashvili, R.

2018-01-01

We revisit the question of whether a two-dimensional topological insulator may arise in a commensurate Néel antiferromagnet, where staggered magnetization breaks the symmetry with respect to both elementary translation and time reversal, but retains their product as a symmetry. In contrast to the so-called Z 2 topological insulators, an exhaustive characterization of antiferromagnetic topological phases with the help of topological invariants has been missing. We analyze a simple model of an antiferromagnetic topological insulator and chart its phase diagram, using a recently proposed criterion for centrosymmetric systems [13]. We then adapt two methods, originally designed for paramagnetic systems, and make antiferromagnetic topological phases manifest. The proposed methods apply far beyond the particular examples treated in this work, and admit straightforward generalization. We illustrate this by two examples of non-centrosymmetric systems, where no simple criteria have been known to identify topological phases. We also present, for some cases, an explicit construction of edge states in an antiferromagnetic topological insulator.

Noise Threshold and Resource Cost of Fault-Tolerant Quantum Computing with Majorana Fermions in Hybrid Systems.

PubMed

Li, Ying

2016-09-16

Fault-tolerant quantum computing in systems composed of both Majorana fermions and topologically unprotected quantum systems, e.g., superconducting circuits or quantum dots, is studied in this Letter. Errors caused by topologically unprotected quantum systems need to be corrected with error-correction schemes, for instance, the surface code. We find that the error-correction performance of such a hybrid topological quantum computer is not superior to a normal quantum computer unless the topological charge of Majorana fermions is insusceptible to noise. If errors changing the topological charge are rare, the fault-tolerance threshold is much higher than the threshold of a normal quantum computer and a surface-code logical qubit could be encoded in only tens of topological qubits instead of about 1,000 normal qubits.

Cohesive phase-field fracture and a PDE constrained optimization approach to fracture inverse problems

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

Tupek, Michael R.

2016-06-30

In recent years there has been a proliferation of modeling techniques for forward predictions of crack propagation in brittle materials, including: phase-field/gradient damage models, peridynamics, cohesive-zone models, and G/XFEM enrichment techniques. However, progress on the corresponding inverse problems has been relatively lacking. Taking advantage of key features of existing modeling approaches, we propose a parabolic regularization of Barenblatt cohesive models which borrows extensively from previous phase-field and gradient damage formulations. An efficient explicit time integration strategy for this type of nonlocal fracture model is then proposed and justified. In addition, we present a C++ computational framework for computing in- putmore » parameter sensitivities efficiently for explicit dynamic problems using the adjoint method. This capability allows for solving inverse problems involving crack propagation to answer interesting engineering questions such as: 1) what is the optimal design topology and material placement for a heterogeneous structure to maximize fracture resistance, 2) what loads must have been applied to a structure for it to have failed in an observed way, 3) what are the existing cracks in a structure given various experimental observations, etc. In this work, we focus on the first of these engineering questions and demonstrate a capability to automatically and efficiently compute optimal designs intended to minimize crack propagation in structures.« less

Topological Band Theory for Non-Hermitian Hamiltonians

NASA Astrophysics Data System (ADS)

Shen, Huitao; Zhen, Bo; Fu, Liang

2018-04-01

We develop the topological band theory for systems described by non-Hermitian Hamiltonians, whose energy spectra are generally complex. After generalizing the notion of gapped band structures to the non-Hermitian case, we classify "gapped" bands in one and two dimensions by explicitly finding their topological invariants. We find nontrivial generalizations of the Chern number in two dimensions, and a new classification in one dimension, whose topology is determined by the energy dispersion rather than the energy eigenstates. We then study the bulk-edge correspondence and the topological phase transition in two dimensions. Different from the Hermitian case, the transition generically involves an extended intermediate phase with complex-energy band degeneracies at isolated "exceptional points" in momentum space. We also systematically classify all types of band degeneracies.

QCD topological susceptibility from the nonlocal chiral quark model

NASA Astrophysics Data System (ADS)

Nam, Seung-Il; Kao, Chung-Wen

2017-06-01

We investigate the quantum chromodynamics (QCD) topological susceptibility χ by using the semi-bosonized nonlocal chiral-quark model (SB-NLχQM) for the leading large- N c contributions. This model is based on the liquid-instanton QCD-vacuum configuration, in which SU(3) flavor symmetry is explicitly broken by the finite current-quark mass ( m u,d, m s) ≈ (5, 135) MeV. To compute χ, we derive the local topological charge-density operator Q t( x) from the effective action of SB-NLχQM. We verify that the derived expression for χ in our model satisfies the Witten- Veneziano (WV) and the Leutwyler-Smilga (LS) formulae, and the Crewther theorem in the chiral limit by construction. Once the average instanton size and the inter-instanton distance are fixed with ρ¯ = 1/3 fm and R¯ = 1 fm, respectively, all the other parameters are determined self-consistently within the model. We obtain χ = (167.67MeV)4, which is comparable with the empirical value χ = (175±5MeV)4 whereas it turns out that χ QL = (194.30MeV)4 in the quenched limit. Thus, we conclude that the value of χ will be reduced around 10 20% by the dynamical-quark contribution.

On implementation of DCTCP on three-tier and fat-tree data center network topologies.

PubMed

Zafar, Saima; Bashir, Abeer; Chaudhry, Shafique Ahmad

2016-01-01

A data center is a facility for housing computational and storage systems interconnected through a communication network called data center network (DCN). Due to a tremendous growth in the computational power, storage capacity and the number of inter-connected servers, the DCN faces challenges concerning efficiency, reliability and scalability. Although transmission control protocol (TCP) is a time-tested transport protocol in the Internet, DCN challenges such as inadequate buffer space in switches and bandwidth limitations have prompted the researchers to propose techniques to improve TCP performance or design new transport protocols for DCN. Data center TCP (DCTCP) emerge as one of the most promising solutions in this domain which employs the explicit congestion notification feature of TCP to enhance the TCP congestion control algorithm. While DCTCP has been analyzed for two-tier tree-based DCN topology for traffic between servers in the same rack which is common in cloud applications, it remains oblivious to the traffic patterns common in university and private enterprise networks which traverse the complete network interconnect spanning upper tier layers. We also recognize that DCTCP performance cannot remain unaffected by the underlying DCN architecture hence there is a need to test and compare DCTCP performance when implemented over diverse DCN architectures. Some of the most notable DCN architectures are the legacy three-tier, fat-tree, BCube, DCell, VL2, and CamCube. In this research, we simulate the two switch-centric DCN architectures; the widely deployed legacy three-tier architecture and the promising fat-tree architecture using network simulator and analyze the performance of DCTCP in terms of throughput and delay for realistic traffic patterns. We also examine how DCTCP prevents incast and outcast congestion when realistic DCN traffic patterns are employed in above mentioned topologies. Our results show that the underlying DCN architecture significantly impacts DCTCP performance. We find that DCTCP gives optimal performance in fat-tree topology and is most suitable for large networks.

Derivation of the Time-Reversal Anomaly for (2 +1 )-Dimensional Topological Phases

NASA Astrophysics Data System (ADS)

Tachikawa, Yuji; Yonekura, Kazuya

2017-09-01

We prove an explicit formula conjectured recently by Wang and Levin for the anomaly of time-reversal symmetry in (2 +1 )-dimensional fermionic topological quantum field theories. The crucial step is to determine the cross-cap state in terms of the modular S matrix and T2 eigenvalues, generalizing the recent analysis by Barkeshli et al. in the bosonic case.

Using heteroclinic orbits to quantify topological entropy in fluid flows

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

New displacement-based methods for optimal truss topology design

NASA Technical Reports Server (NTRS)

Bendsoe, Martin P.; Ben-Tal, Aharon; Haftka, Raphael T.

1991-01-01

Two alternate methods for maximum stiffness truss topology design are presented. The ground structure approach is used, and the problem is formulated in terms of displacements and bar areas. This large, nonconvex optimization problem can be solved by a simultaneous analysis and design approach. Alternatively, an equivalent, unconstrained, and convex problem in the displacements only can be formulated, and this problem can be solved by a nonsmooth, steepest descent algorithm. In both methods, the explicit solving of the equilibrium equations and the assembly of the global stiffness matrix are circumvented. A large number of examples have been studied, showing the attractive features of topology design as well as exposing interesting features of optimal topologies.

(d -2 ) -Dimensional Edge States of Rotation Symmetry Protected Topological States

NASA Astrophysics Data System (ADS)

Song, Zhida; Fang, Zhong; Fang, Chen

2017-12-01

We study fourfold rotation-invariant gapped topological systems with time-reversal symmetry in two and three dimensions (d =2 , 3). We show that in both cases nontrivial topology is manifested by the presence of the (d -2 )-dimensional edge states, existing at a point in 2D or along a line in 3D. For fermion systems without interaction, the bulk topological invariants are given in terms of the Wannier centers of filled bands and can be readily calculated using a Fu-Kane-like formula when inversion symmetry is also present. The theory is extended to strongly interacting systems through the explicit construction of microscopic models having robust (d -2 )-dimensional edge states.

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

Sattari, Sulimon, E-mail: ssattari2@ucmerced.edu; Chen, Qianting, E-mail: qchen2@ucmerced.edu; Mitchell, Kevin A., E-mail: kmitchell@ucmerced.edu

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

Direct experimental visualization of the global Hamiltonian progression of two-dimensional Lagrangian flow topologies from integrable to chaotic state.

PubMed

Baskan, O; Speetjens, M F M; Metcalfe, G; Clercx, H J H

2015-10-01

Countless theoretical/numerical studies on transport and mixing in two-dimensional (2D) unsteady flows lean on the assumption that Hamiltonian mechanisms govern the Lagrangian dynamics of passive tracers. However, experimental studies specifically investigating said mechanisms are rare. Moreover, they typically concern local behavior in specific states (usually far away from the integrable state) and generally expose this indirectly by dye visualization. Laboratory experiments explicitly addressing the global Hamiltonian progression of the Lagrangian flow topology entirely from integrable to chaotic state, i.e., the fundamental route to efficient transport by chaotic advection, appear non-existent. This motivates our study on experimental visualization of this progression by direct measurement of Poincaré sections of passive tracer particles in a representative 2D time-periodic flow. This admits (i) accurate replication of the experimental initial conditions, facilitating true one-to-one comparison of simulated and measured behavior, and (ii) direct experimental investigation of the ensuing Lagrangian dynamics. The analysis reveals a close agreement between computations and observations and thus experimentally validates the full global Hamiltonian progression at a great level of detail.

Distributed and cooperative task processing: Cournot oligopolies on a graph.

PubMed

Pavlic, Theodore P; Passino, Kevin M

2014-06-01

This paper introduces a novel framework for the design of distributed agents that must complete externally generated tasks but also can volunteer to process tasks encountered by other agents. To reduce the computational and communication burden of coordination between agents to perfectly balance load around the network, the agents adjust their volunteering propensity asynchronously within a fictitious trading economy. This economy provides incentives for nontrivial levels of volunteering for remote tasks, and thus load is shared. Moreover, the combined effects of diminishing marginal returns and network topology lead to competitive equilibria that have task reallocations that are qualitatively similar to what is expected in a load-balancing system with explicit coordination between nodes. In the paper, topological and algorithmic conditions are given that ensure the existence and uniqueness of a competitive equilibrium. Additionally, a decentralized distributed gradient-ascent algorithm is given that is guaranteed to converge to this equilibrium while not causing any node to over-volunteer beyond its maximum task-processing rate. The framework is applied to an autonomous-air-vehicle example, and connections are drawn to classic studies of the evolution of cooperation in nature.

Fingerprints selection for topological localization

NASA Astrophysics Data System (ADS)

Popov, Vladimir

2017-07-01

Problems of visual navigation are extensively studied in contemporary robotics. In particular, we can mention different problems of visual landmarks selection, the problem of selection of a minimal set of visual landmarks, selection of partially distinguishable guards, the problem of placement of visual landmarks. In this paper, we consider one-dimensional color panoramas. Such panoramas can be used for creating fingerprints. Fingerprints give us unique identifiers for visually distinct locations by recovering statistically significant features. Fingerprints can be used as visual landmarks for the solution of various problems of mobile robot navigation. In this paper, we consider a method for automatic generation of fingerprints. In particular, we consider the bounded Post correspondence problem and applications of the problem to consensus fingerprints and topological localization. We propose an efficient approach to solve the bounded Post correspondence problem. In particular, we use an explicit reduction from the decision version of the problem to the satisfiability problem. We present the results of computational experiments for different satisfiability algorithms. In robotic experiments, we consider the average accuracy of reaching of the target point for different lengths of routes and types of fingerprints.

Topological Phases in Graphene Nanoribbons: Junction States, Spin Centers, and Quantum Spin Chains

NASA Astrophysics Data System (ADS)

Cao, Ting; Zhao, Fangzhou; Louie, Steven G.

2017-08-01

We show that semiconducting graphene nanoribbons (GNRs) of different width, edge, and end termination (synthesizable from molecular precursors with atomic precision) belong to different electronic topological classes. The topological phase of GNRs is protected by spatial symmetries and dictated by the terminating unit cell. We have derived explicit formulas for their topological invariants and shown that localized junction states developed between two GNRs of distinct topology may be tuned by lateral junction geometry. The topology of a GNR can be further modified by dopants, such as a periodic array of boron atoms. In a superlattice consisting of segments of doped and pristine GNRs, the junction states are stable spin centers, forming a Heisenberg antiferromagnetic spin 1 /2 chain with tunable exchange interaction. The discoveries here not only are of scientific interest for studies of quasi-one-dimensional systems, but also open a new path for design principles of future GNR-based devices through their topological characters.

Topological Phases in Graphene Nanoribbons: Junction States, Spin Centers, and Quantum Spin Chains.

PubMed

Cao, Ting; Zhao, Fangzhou; Louie, Steven G

2017-08-18

We show that semiconducting graphene nanoribbons (GNRs) of different width, edge, and end termination (synthesizable from molecular precursors with atomic precision) belong to different electronic topological classes. The topological phase of GNRs is protected by spatial symmetries and dictated by the terminating unit cell. We have derived explicit formulas for their topological invariants and shown that localized junction states developed between two GNRs of distinct topology may be tuned by lateral junction geometry. The topology of a GNR can be further modified by dopants, such as a periodic array of boron atoms. In a superlattice consisting of segments of doped and pristine GNRs, the junction states are stable spin centers, forming a Heisenberg antiferromagnetic spin 1/2 chain with tunable exchange interaction. The discoveries here not only are of scientific interest for studies of quasi-one-dimensional systems, but also open a new path for design principles of future GNR-based devices through their topological characters.

United States Air Force Summer Faculty Research Program: Program Management Report

DTIC Science & Technology

1988-12-01

Laboratory 64 Realization of Sublayer Relative Dr. Lane Clark Shielding Order in Electromagnetic Topology 65 Diode Laser Probe of Vibrational Dr. David...given. In addition, all possible sublayer topologies with relative shielding order at most 5 are explicitly given. S863 Diode Laser Probe of...dioxide at 193 nm to prepare the SO radicals. High resolution diode laser absorption spectrometry will be used to obtain time-dependent concentrations

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

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

Potok, Thomas E; Schuman, Catherine D; Young, Steven R

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power. In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determinemore » network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation. The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware. This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.« less

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.

Uncertainty Aware Structural Topology Optimization Via a Stochastic Reduced Order Model Approach

NASA Technical Reports Server (NTRS)

Aguilo, Miguel A.; Warner, James E.

2017-01-01

This work presents a stochastic reduced order modeling strategy for the quantification and propagation of uncertainties in topology optimization. Uncertainty aware optimization problems can be computationally complex due to the substantial number of model evaluations that are necessary to accurately quantify and propagate uncertainties. This computational complexity is greatly magnified if a high-fidelity, physics-based numerical model is used for the topology optimization calculations. Stochastic reduced order model (SROM) methods are applied here to effectively 1) alleviate the prohibitive computational cost associated with an uncertainty aware topology optimization problem; and 2) quantify and propagate the inherent uncertainties due to design imperfections. A generic SROM framework that transforms the uncertainty aware, stochastic topology optimization problem into a deterministic optimization problem that relies only on independent calls to a deterministic numerical model is presented. This approach facilitates the use of existing optimization and modeling tools to accurately solve the uncertainty aware topology optimization problems in a fraction of the computational demand required by Monte Carlo methods. Finally, an example in structural topology optimization is presented to demonstrate the effectiveness of the proposed uncertainty aware structural topology optimization approach.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

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.

Conformal field theory construction for non-Abelian hierarchy wave functions

NASA Astrophysics Data System (ADS)

Tournois, Yoran; Hermanns, Maria

2017-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Small-inclusion asymptotic of misfit functionals for inverse problems in acoustics

NASA Astrophysics Data System (ADS)

Guzina, Bojan B.; Bonnet, Marc

2006-10-01

The aim of this study is an extension and employment of the concept of topological derivative as it pertains to the nucleation of infinitesimal inclusions in a reference (i.e. background) acoustic medium. The developments are motivated by the need to develop a preliminary indicator functional that would aid the solution of inverse scattering problems in terms of a rational initial 'guess' about the geometry and material characteristics of a hidden (finite) obstacle; an information that is often required by iterative minimization algorithms. To this end the customary definition of topological derivative, which quantifies the sensitivity of a given cost functional with respect to the creation of an infinitesimal hole, is adapted to permit the nucleation of a dissimilar acoustic medium. On employing the Green's function for the background domain, computation of topological sensitivity for the three-dimensional Helmholtz equation is reduced to the solution of a reference, Laplace transmission problem. Explicit formulae are given for the nucleating inclusions of spherical and ellipsoidal shapes. For generality the developments are also presented in an alternative, adjoint-field setting that permits nucleation of inclusions in an infinite, semi-infinite or finite background medium. Through numerical examples, it is shown that the featured topological sensitivity could be used, in the context of inverse scattering, as an effective obstacle indicator through an assembly of sampling points where it attains pronounced negative values. On varying a material characteristic (density) of the nucleating obstacle, it is also shown that the proposed methodology can be used as a preparatory tool for both geometric and material identification.

Topological phase transition and unexpected mass acquisition of Dirac fermion in TlBi(S1-xSex)2

NASA Astrophysics Data System (ADS)

Niu, Chengwang; Dai, Ying; Zhu, Yingtao; Lu, Jibao; Ma, Yandong; Huang, Baibiao

2012-10-01

Based on first-principles calculations and effective Hamiltonian analysis, we predict a topological phase transition from normal to topological insulators and the opening of a gap without breaking the time-reversal symmetry in TlBi(S1-xSex)2. The transition can be driven by modulating the Se concentration, and the rescaled spin-orbit coupling and lattice parameters are the key ingredients for the transition. For topological surface states, the Dirac cone evolves differently as the explicit breaking of inversion symmetry and the energy band can be opened under asymmetry surface. Our results present theoretical evidence for experimental observations [Xu et al., Science 332, 560 (2011); Sato et al., Nat. Phys. 7, 840 (2011)].

Classification of reflection-symmetry-protected topological semimetals and nodal superconductors

NASA Astrophysics Data System (ADS)

Chiu, Ching-Kai; Schnyder, Andreas P.

2014-11-01

While the topological classification of insulators, semimetals, and superconductors in terms of nonspatial symmetries is well understood, less is known about topological states protected by crystalline symmetries, such as mirror reflections and rotations. In this work, we systematically classify topological semimetals and nodal superconductors that are protected, not only by nonspatial (i.e., global) symmetries, but also by a crystal reflection symmetry. We find that the classification crucially depends on (i) the codimension of the Fermi surface (nodal line or point) of the semimetal (superconductor), (ii) whether the mirror symmetry commutes or anticommutes with the nonspatial symmetries, and (iii) how the Fermi surfaces (nodal lines or points) transform under the mirror reflection and nonspatial symmetries. The classification is derived by examining all possible symmetry-allowed mass terms that can be added to the Bloch or Bogoliubov-de Gennes Hamiltonian in a given symmetry class and by explicitly deriving topological invariants. We discuss several examples of reflection-symmetry-protected topological semimetals and nodal superconductors, including topological crystalline semimetals with mirror Z2 numbers and topological crystalline nodal superconductors with mirror winding numbers.

On the topological sensitivity of cellular automata

NASA Astrophysics Data System (ADS)

Baetens, Jan M.; De Baets, Bernard

2011-06-01

Ever since the conceptualization of cellular automata (CA), much attention has been paid to the dynamical properties of these discrete dynamical systems, and, more in particular, to their sensitivity to the initial condition from which they are evolved. Yet, the sensitivity of CA to the topology upon which they are based has received only minor attention, such that a clear insight in this dependence is still lacking and, furthermore, a quantification of this so-called topological sensitivity has not yet been proposed. The lack of attention for this issue is rather surprising since CA are spatially explicit, which means that their dynamics is directly affected by their topology. To overcome these shortcomings, we propose topological Lyapunov exponents that measure the divergence of two close trajectories in phase space originating from a topological perturbation, and we relate them to a measure grasping the sensitivity of CA to their topology that relies on the concept of topological derivatives, which is introduced in this paper. The validity of the proposed methodology is illustrated for the 256 elementary CA and for a family of two-state irregular totalistic CA.

Complex dynamics of memristive circuits: Analytical results and universal slow relaxation

NASA Astrophysics Data System (ADS)

Caravelli, F.; Traversa, F. L.; Di Ventra, M.

2017-02-01

Networks with memristive elements (resistors with memory) are being explored for a variety of applications ranging from unconventional computing to models of the brain. However, analytical results that highlight the role of the graph connectivity on the memory dynamics are still few, thus limiting our understanding of these important dynamical systems. In this paper, we derive an exact matrix equation of motion that takes into account all the network constraints of a purely memristive circuit, and we employ it to derive analytical results regarding its relaxation properties. We are able to describe the memory evolution in terms of orthogonal projection operators onto the subspace of fundamental loop space of the underlying circuit. This orthogonal projection explicitly reveals the coupling between the spatial and temporal sectors of the memristive circuits and compactly describes the circuit topology. For the case of disordered graphs, we are able to explain the emergence of a power-law relaxation as a superposition of exponential relaxation times with a broad range of scales using random matrices. This power law is also universal, namely independent of the topology of the underlying graph but dependent only on the density of loops. In the case of circuits subject to alternating voltage instead, we are able to obtain an approximate solution of the dynamics, which is tested against a specific network topology. These results suggest a much richer dynamics of memristive networks than previously considered.

Hyperswitch Network For Hypercube Computer

NASA Technical Reports Server (NTRS)

Chow, Edward; Madan, Herbert; Peterson, John

1989-01-01

Data-driven dynamic switching enables high speed data transfer. Proposed hyperswitch network based on mixed static and dynamic topologies. Routing header modified in response to congestion or faults encountered as path established. Static topology meets requirement if nodes have switching elements that perform necessary routing header revisions dynamically. Hypercube topology now being implemented with switching element in each computer node aimed at designing very-richly-interconnected multicomputer system. Interconnection network connects great number of small computer nodes, using fixed hypercube topology, characterized by point-to-point links between nodes.

Braiding errors in interacting Majorana quantum wires

NASA Astrophysics Data System (ADS)

Sekania, Michael; Plugge, Stephan; Greiter, Martin; Thomale, Ronny; Schmitteckert, Peter

2017-09-01

Avenues of Majorana bound states (MBSs) have become one of the primary directions towards a possible realization of topological quantum computation. For a Y junction of Kitaev quantum wires, we numerically investigate the braiding of MBSs while considering the full quasiparticle background. The two central sources of braiding errors are found to be the fidelity loss due to the incomplete adiabaticity of the braiding operation as well as the finite hybridization of the MBSs. The explicit extraction of the braiding phase from the full many-particle states allows us to analyze the breakdown of the independent-particle picture of Majorana braiding. Furthermore, we find nearest-neighbor interactions to significantly affect the braiding performance for better or worse, depending on the sign and magnitude of the coupling.

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.

Postprocessing of Voxel-Based Topologies for Additive Manufacturing Using the Computational Geometry Algorithms Library (CGAL)

DTIC Science & Technology

2015-06-01

10-2014 to 00-11-2014 4. TITLE AND SUBTITLE Postprocessing of Voxel-Based Topologies for Additive Manufacturing Using the Computational Geometry...ABSTRACT Postprocessing of 3-dimensional (3-D) topologies that are defined as a set of voxels using the Computational Geometry Algorithms Library (CGAL... computational geometry algorithms, several of which are suited to the task. The work flow described in this report involves first defining a set of

Constructing a logical, regular axis topology from an irregular topology

DOEpatents

Faraj, Daniel A.

2014-07-22

Constructing a logical regular topology from an irregular topology including, for each axial dimension and recursively, for each compute node in a subcommunicator until returning to a first node: adding to a logical line of the axial dimension a neighbor specified in a nearest neighbor list; calling the added compute node; determining, by the called node, whether any neighbor in the node's nearest neighbor list is available to add to the logical line; if a neighbor in the called compute node's nearest neighbor list is available to add to the logical line, adding, by the called compute node to the logical line, any neighbor in the called compute node's nearest neighbor list for the axial dimension not already added to the logical line; and, if no neighbor in the called compute node's nearest neighbor list is available to add to the logical line, returning to the calling compute node.

Constructing a logical, regular axis topology from an irregular topology

DOEpatents

Faraj, Daniel A.

2014-07-01

Constructing a logical regular topology from an irregular topology including, for each axial dimension and recursively, for each compute node in a subcommunicator until returning to a first node: adding to a logical line of the axial dimension a neighbor specified in a nearest neighbor list; calling the added compute node; determining, by the called node, whether any neighbor in the node's nearest neighbor list is available to add to the logical line; if a neighbor in the called compute node's nearest neighbor list is available to add to the logical line, adding, by the called compute node to the logical line, any neighbor in the called compute node's nearest neighbor list for the axial dimension not already added to the logical line; and, if no neighbor in the called compute node's nearest neighbor list is available to add to the logical line, returning to the calling compute node.

Adiabatic topological quantum computing

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

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Adiabatic topological quantum computing

DOE PAGES

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave; ...

2015-07-31

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions

PubMed Central

Liu, Bo; Li, Dajun; Xia, Yuanping; Ruan, Jian; Xu, Lili; Wu, Huanyi

2015-01-01

In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models. PMID:25775452

From brain topography to brain topology: relevance of graph theory to functional neuroscience.

PubMed

Minati, Ludovico; Varotto, Giulia; D'Incerti, Ludovico; Panzica, Ferruccio; Chan, Dennis

2013-07-10

Although several brain regions show significant specialization, higher functions such as cross-modal information integration, abstract reasoning and conscious awareness are viewed as emerging from interactions across distributed functional networks. Analytical approaches capable of capturing the properties of such networks can therefore enhance our ability to make inferences from functional MRI, electroencephalography and magnetoencephalography data. Graph theory is a branch of mathematics that focuses on the formal modelling of networks and offers a wide range of theoretical tools to quantify specific features of network architecture (topology) that can provide information complementing the anatomical localization of areas responding to given stimuli or tasks (topography). Explicit modelling of the architecture of axonal connections and interactions among areas can furthermore reveal peculiar topological properties that are conserved across diverse biological networks, and highly sensitive to disease states. The field is evolving rapidly, partly fuelled by computational developments that enable the study of connectivity at fine anatomical detail and the simultaneous interactions among multiple regions. Recent publications in this area have shown that graph-based modelling can enhance our ability to draw causal inferences from functional MRI experiments, and support the early detection of disconnection and the modelling of pathology spread in neurodegenerative disease, particularly Alzheimer's disease. Furthermore, neurophysiological studies have shown that network topology has a profound link to epileptogenesis and that connectivity indices derived from graph models aid in modelling the onset and spread of seizures. Graph-based analyses may therefore significantly help understand the bases of a range of neurological conditions. This review is designed to provide an overview of graph-based analyses of brain connectivity and their relevance to disease aimed principally at general neuroscientists and clinicians.

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

PubMed

Crawford, Joseph; Milenković, Tijana

2018-01-01

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

A virtual surgical training system that simulates cutting of soft tissue using a modified pre-computed elastic model.

PubMed

Toe, Kyaw Kyar; Huang, Weimin; Yang, Tao; Duan, Yuping; Zhou, Jiayin; Su, Yi; Teo, Soo-Kng; Kumar, Selvaraj Senthil; Lim, Calvin Chi-Wan; Chui, Chee Kong; Chang, Stephen

2015-08-01

This work presents a surgical training system that incorporates cutting operation of soft tissue simulated based on a modified pre-computed linear elastic model in the Simulation Open Framework Architecture (SOFA) environment. A precomputed linear elastic model used for the simulation of soft tissue deformation involves computing the compliance matrix a priori based on the topological information of the mesh. While this process may require a few minutes to several hours, based on the number of vertices in the mesh, it needs only to be computed once and allows real-time computation of the subsequent soft tissue deformation. However, as the compliance matrix is based on the initial topology of the mesh, it does not allow any topological changes during simulation, such as cutting or tearing of the mesh. This work proposes a way to modify the pre-computed data by correcting the topological connectivity in the compliance matrix, without re-computing the compliance matrix which is computationally expensive.

Linear response and Berry curvature in two-dimensional topological phases

NASA Astrophysics Data System (ADS)

Bradlyn, Barry J.

In this thesis we examine the viscous and thermal transport properties of chiral topological phases, and their relationship to topological invariants. We start by developing a Kubo formalism for calculating the frequency dependent viscosity tensor of a general quantum system, both with and without a uniform external magnetic field. The importance of contact terms is emphasized. We apply this formalism to the study of integer and fractional quantum Hall states, as well as p + ip paired superfluids, and verify the relationship between the Hall viscosity and the mean orbital spin density. We also elucidate the connection between our Kubo formulas and prior adiabatic transport calculations of the Hall viscosity. Additionally, we derive a general relationship between the frequency dependent viscosity and conductivity tensors for Galilean-invariant systems. We comment on the implications of this relationship towards the measurement of Hall viscosity in solid-state systems. To address the question of thermal transport, we first review the standard Kubo formalism of Luttinger for computing thermoelectric coefficients. We apply this to the specific case of non-interacting electrons in the integer quantum Hall regime, paying careful attention to the roles of bulk and edge effects. In order to generalize our discussion to interacting systems, we construct a low-energy effective action for a two-dimensional non-relativistic topological phase of matter in a continuum, which completely describes all of its bulk thermoelectric and visco-elastic properties in the limit of low frequencies, long distances, and zero temperature, without assuming either Lorentz or Galilean invariance, by coupling the microscopic degrees of freedom to the background spacetime geometry. We derive the most general form of a local bulk induced action to first order in derivatives of the background fields, from which thermodynamic and transport properties can be obtained. We show that the gapped bulk cannot contribute to low-temperature thermoelectric transport other than the ordinary Hall conductivity; the other thermoelectric effects (if they occur) are thus purely edge effects. The stress response to time-dependent strains is given by the Hall viscosity, which is robust against perturbations and related to the spin current. Finally, we address the issue of calculating the topological central charge from bulk wavefunctions for a topological phase. Using the form of the topological terms in the induced action, we show that we can calculate the various coefficients of these terms as Berry curvatures associated to certain metric and electromagnetic vector potential perturbations. We carry out this computation explicitly for quantum Hall trial wavefunctions that can be represented as conformal blocks in a chiral conformal field theory (CFT). These calculations make use of the gauge and gravitational anomalies in the underlying chiral CFT.

Final Scientific/Technical Report (DE-FG02-05ER46201)

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

Car, Roberto

The research supported by this grant focused on the quantum mechanical theory of the electrons in materials and molecules. Progress was made in dealing with electronic correlation effects in the ground state energy of molecular systems, and with topological concepts to classify the electronic state of molecules and materials, including excitation and transport properties. The physical and chemical properties of molecules and materials derive from their electronic structure, but the latter cannot be calculated exactly even with the most powerful computers because the computational cost of solving the exact equations of quantum mechanics increases exponentially with the number of electrons.more » The exponential cost originates from the correlations among the electrons that repel each other via Coulombic forces. In this project we have developed a new functional approximation for the ground state electronic energy that includes explicitly, and in a controllable way, the effects of the interelectronic correlations. In addition we have further developed topological concepts for classifying the electronic states of periodic ring molecules and solids. Topological concepts are very powerful because they allow us to predict subtle properties of materials and molecules using very general geometrical properties of the electron wavefunctions that do not depend on the quantitative details of the electronic interactions, which are very difficult to calculate with high accuracy. The development of a new class of controlled functional approximations for the ground state energy of molecules and materials was the main goal of the project. It has been fulfilled with the formulation of the occupation-probabilities natural orbital functional theory (OP-NOFT). This approach introduces new theoretical concepts but practical application has proved to be harder than anticipated. So far it has been utilized only at its lowest level of approximation in the context of relatively small molecules (with up to 16 atoms). The study of topological properties of the electron wavefunctions in materials was not proposed in the original proposal but was prompted during the funding period by our interaction with leading experimental groups in materials chemistry and physics at Princeton University.« less

On the Wiener Polarity Index of Lattice Networks.

PubMed

Chen, Lin; Li, Tao; Liu, Jinfeng; Shi, Yongtang; Wang, Hua

2016-01-01

Network structures are everywhere, including but not limited to applications in biological, physical and social sciences, information technology, and optimization. Network robustness is of crucial importance in all such applications. Research on this topic relies on finding a suitable measure and use this measure to quantify network robustness. A number of distance-based graph invariants, also known as topological indices, have recently been incorporated as descriptors of complex networks. Among them the Wiener type indices are the most well known and commonly used such descriptors. As one of the fundamental variants of the original Wiener index, the Wiener polarity index has been introduced for a long time and known to be related to the cluster coefficient of networks. In this paper, we consider the value of the Wiener polarity index of lattice networks, a common network structure known for its simplicity and symmetric structure. We first present a simple general formula for computing the Wiener polarity index of any graph. Using this formula, together with the symmetric and recursive topology of lattice networks, we provide explicit formulas of the Wiener polarity index of the square lattices, the hexagonal lattices, the triangular lattices, and the 33 ⋅ 42 lattices. We also comment on potential future research topics.

Direct experimental visualization of the global Hamiltonian progression of two-dimensional Lagrangian flow topologies from integrable to chaotic state

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

Baskan, O.; Clercx, H. J. H; Speetjens, M. F. M.

Countless theoretical/numerical studies on transport and mixing in two-dimensional (2D) unsteady flows lean on the assumption that Hamiltonian mechanisms govern the Lagrangian dynamics of passive tracers. However, experimental studies specifically investigating said mechanisms are rare. Moreover, they typically concern local behavior in specific states (usually far away from the integrable state) and generally expose this indirectly by dye visualization. Laboratory experiments explicitly addressing the global Hamiltonian progression of the Lagrangian flow topology entirely from integrable to chaotic state, i.e., the fundamental route to efficient transport by chaotic advection, appear non-existent. This motivates our study on experimental visualization of this progressionmore » by direct measurement of Poincaré sections of passive tracer particles in a representative 2D time-periodic flow. This admits (i) accurate replication of the experimental initial conditions, facilitating true one-to-one comparison of simulated and measured behavior, and (ii) direct experimental investigation of the ensuing Lagrangian dynamics. The analysis reveals a close agreement between computations and observations and thus experimentally validates the full global Hamiltonian progression at a great level of detail.« less

Mean-field crack networks on desiccated films and their applications: Girl with a Pearl Earring.

PubMed

Flores, J C

2017-02-15

Usual requirements for bulk and fissure energies are considered in obtaining the interdependence among external stress, thickness and area of crack polygons in desiccated films. The average area of crack polygons increases with thickness as a power-law of 4/3. The sequential fragmentation process is characterized by a topological factor related to a scaling finite procedure. Non-sequential overly tensioned (prompt) fragmentation is briefly discussed. Vermeer's painting, Girl with a Pearl Earring, is considered explicitly by using computational image tools and simple experiments and applying the proposed theoretical analysis. In particular, concerning the source of lightened effects on the girl's face, the left/right thickness layer ratio (≈1.34) and the stress ratio (≈1.102) are evaluated. Other master paintings are briefly considered.

First principle study of heterostructure of BaBi3-stanene for topological superconductor applications

NASA Astrophysics Data System (ADS)

Kore, Ashish; Singh, Poorva

2018-05-01

We have studied the heterostructure of BaBi3 (superconductor) and stanene (topological insulator) with the aim of inducing topological superconductivity in stanene, due to proximity with superconductor BaBi3. The density functional theory calculations have been done for 2D structure of BaBi3 as well as for monolayer of stanene, separately. We find that compared to bulk BaBi3, the 2D bandstructure has contributions coming from both Ba and Bi atoms, unlike bulk where only Bi-p states are contributing to the bandstructure. Surface reconstruction of surface and sub-surface layer of 2D BaBi3 is also evident. The bandstructure of heterostructure of BaBi3-stanene is expected to bring out explicit features of topological superconductivity and indicating the presence of Majorana fermions.

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

PubMed

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

2016-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Immersed Boundary Methods for Optimization of Strongly Coupled Fluid-Structure Systems

NASA Astrophysics Data System (ADS)

Jenkins, Nicholas J.

Conventional methods for design of tightly coupled multidisciplinary systems, such as fluid-structure interaction (FSI) problems, traditionally rely on manual revisions informed by a loosely coupled linearized analysis. These approaches are both inaccurate for a multitude of applications, and they require an intimate understanding of the assumptions and limitations of the procedure in order to soundly optimize the design. Computational optimization, in particular topology optimization, has been shown to yield remarkable results for problems in solid mechanics using density interpolations schemes. In the context of FSI, however, well defined boundaries play a key role in both the design problem and the mechanical model. Density methods neither accurately represent the material boundary, nor provide a suitable platform to apply appropriate interface conditions. This thesis presents a new framework for shape and topology optimization of FSI problems that uses for the design problem the Level Set method (LSM) to describe the geometry evolution in the optimization process. The Extended Finite Element method (XFEM) is combined with a fictitiously deforming fluid domain (stationary arbitrary Lagrangian-Eulerian method) to predict the FSI response. The novelty of the proposed approach lies in the fact that the XFEM explicitly captures the material boundary defined by the level set iso-surface. Moreover, the XFEM provides a means to discretize the governing equations, and weak immersed boundary conditions are applied with Nitsche's Method to couple the fields. The flow is predicted by the incompressible Navier-Stokes equations, and a finite-deformation solid model is developed and tested for both hyperelastic and linear elastic problems. Transient and stationary numerical examples are presented to validate the FSI model and numerical solver approach. Pertaining to the optimization of FSI problems, the parameters of the discretized level set function are defined as explicit functions of the optimization variables, and the parameteric optimization problem is solved by nonlinear programming methods. The gradients of the objective and constrains are computed by the adjoint method for the global monolithic fluid-solid system. Two types of design problems are explored for optimization of the fluid-structure response: 1) the internal structural topology is varied, preserving the fluid-solid interface geometry, and 2) the fluid-solid interface is manipulated directly, which leads to simultaneously configuring both internal structural topology and outer mold shape. The numerical results show that the LSM-XFEM approach is well suited for designing practical applications, while at the same time reducing the requirement on highly refined mesh resolution compared to traditional density methods. However, these results also emphasize the need for a more robust embedded boundary condition framework. Further, the LSM can exhibit greater dependence on initial design seeding, and can impede design convergence. In particular for the strongly coupled FSI analysis developed here, the thinning and eventual removal of structural members can cause jumps in the evolution of the optimization functions.

Quadratic stabilisability of multi-agent systems under switching topologies

NASA Astrophysics Data System (ADS)

Guan, Yongqiang; Ji, Zhijian; Zhang, Lin; Wang, Long

2014-12-01

This paper addresses the stabilisability of multi-agent systems (MASs) under switching topologies. Necessary and/or sufficient conditions are presented in terms of graph topology. These conditions explicitly reveal how the intrinsic dynamics of the agents, the communication topology and the external control input affect stabilisability jointly. With the appropriate selection of some agents to which the external inputs are applied and the suitable design of neighbour-interaction rules via a switching topology, an MAS is proved to be stabilisable even if so is not for each of uncertain subsystem. In addition, a method is proposed to constructively design a switching rule for MASs with norm-bounded time-varying uncertainties. The switching rules designed via this method do not rely on uncertainties, and the switched MAS is quadratically stabilisable via decentralised external self-feedback for all uncertainties. With respect to applications of the stabilisability results, the formation control and the cooperative tracking control are addressed. Numerical simulations are presented to demonstrate the effectiveness of the proposed results.

Topologies on quantum topoi induced by quantization

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

Nakayama, Kunji

2013-07-15

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

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

PubMed Central

Romero-Severson, Ethan O.; Bulla, Ingo; Hengartner, Nick; Bártolo, Inês; Abecasis, Ana; Azevedo-Pereira, José M.; Taveira, Nuno; Leitner, Thomas

2017-01-01

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission. PMID:28912340

Towards topological quantum computer

NASA Astrophysics Data System (ADS)

Melnikov, D.; Mironov, A.; Mironov, S.; Morozov, A.; Morozov, An.

2018-01-01

Quantum R-matrices, the entangling deformations of non-entangling (classical) permutations, provide a distinguished basis in the space of unitary evolutions and, consequently, a natural choice for a minimal set of basic operations (universal gates) for quantum computation. Yet they play a special role in group theory, integrable systems and modern theory of non-perturbative calculations in quantum field and string theory. Despite recent developments in those fields the idea of topological quantum computing and use of R-matrices, in particular, practically reduce to reinterpretation of standard sets of quantum gates, and subsequently algorithms, in terms of available topological ones. In this paper we summarize a modern view on quantum R-matrix calculus and propose to look at the R-matrices acting in the space of irreducible representations, which are unitary for the real-valued couplings in Chern-Simons theory, as the fundamental set of universal gates for topological quantum computer. Such an approach calls for a more thorough investigation of the relation between topological invariants of knots and quantum algorithms.

Machine learning topological states

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Noncommutative gerbes and deformation quantization

NASA Astrophysics Data System (ADS)

Aschieri, Paolo; Baković, Igor; Jurčo, Branislav; Schupp, Peter

2010-11-01

We define noncommutative gerbes using the language of star products. Quantized twisted Poisson structures are discussed as an explicit realization in the sense of deformation quantization. Our motivation is the noncommutative description of D-branes in the presence of topologically non-trivial background fields.

Numerical experiments with a symmetric high-resolution shock-capturing scheme

NASA Technical Reports Server (NTRS)

Yee, H. C.

1986-01-01

Characteristic-based explicit and implicit total variation diminishing (TVD) schemes for the two-dimensional compressible Euler equations have recently been developed. This is a generalization of recent work of Roe and Davis to a wider class of symmetric (non-upwind) TVD schemes other than Lax-Wendroff. The Roe and Davis schemes can be viewed as a subset of the class of explicit methods. The main properties of the present class of schemes are that they can be implicit, and, when steady-state calculations are sought, the numerical solution is independent of the time step. In a recent paper, a comparison of a linearized form of the present implicit symmetric TVD scheme with an implicit upwind TVD scheme originally developed by Harten and modified by Yee was given. Results favored the symmetric method. It was found that the latter is just as accurate as the upwind method while requiring less computational effort. Currently, more numerical experiments are being conducted on time-accurate calculations and on the effect of grid topology, numerical boundary condition procedures, and different flow conditions on the behavior of the method for steady-state applications. The purpose here is to report experiences with this type of scheme and give guidelines for its use.

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 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

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.

Inferring Centrality from Network Snapshots

PubMed Central

Shao, Haibin; Mesbahi, Mehran; Li, Dewei; Xi, Yugeng

2017-01-01

The topology and dynamics of a complex network shape its functionality. However, the topologies of many large-scale networks are either unavailable or incomplete. Without the explicit knowledge of network topology, we show how the data generated from the network dynamics can be utilised to infer the tempo centrality, which is proposed to quantify the influence of nodes in a consensus network. We show that the tempo centrality can be used to construct an accurate estimate of both the propagation rate of influence exerted on consensus networks and the Kirchhoff index of the underlying graph. Moreover, the tempo centrality also encodes the disturbance rejection of nodes in a consensus network. Our findings provide an approach to infer the performance of a consensus network from its temporal data. PMID:28098166

Inferring Centrality from Network Snapshots

NASA Astrophysics Data System (ADS)

Shao, Haibin; Mesbahi, Mehran; Li, Dewei; Xi, Yugeng

2017-01-01

The topology and dynamics of a complex network shape its functionality. However, the topologies of many large-scale networks are either unavailable or incomplete. Without the explicit knowledge of network topology, we show how the data generated from the network dynamics can be utilised to infer the tempo centrality, which is proposed to quantify the influence of nodes in a consensus network. We show that the tempo centrality can be used to construct an accurate estimate of both the propagation rate of influence exerted on consensus networks and the Kirchhoff index of the underlying graph. Moreover, the tempo centrality also encodes the disturbance rejection of nodes in a consensus network. Our findings provide an approach to infer the performance of a consensus network from its temporal data.

The topological particle and Morse theory

NASA Astrophysics Data System (ADS)

Rogers, Alice

2000-09-01

Canonical BRST quantization of the topological particle defined by a Morse function h is described. Stochastic calculus, using Brownian paths which implement the WKB method in a new way providing rigorous tunnelling results even in curved space, is used to give an explicit and simple expression for the matrix elements of the evolution operator for the BRST Hamiltonian. These matrix elements lead to a representation of the manifold cohomology in terms of critical points of h along lines developed by Witten (Witten E 1982 J. Diff. Geom. 17 661-92).

Blind topological measurement-based quantum computation.

PubMed

Morimae, Tomoyuki; Fujii, Keisuke

2012-01-01

Blind quantum computation is a novel secure quantum-computing protocol that enables Alice, who does not have sufficient quantum technology at her disposal, to delegate her quantum computation to Bob, who has a fully fledged quantum computer, in such a way that Bob cannot learn anything about Alice's input, output and algorithm. A recent proof-of-principle experiment demonstrating blind quantum computation in an optical system has raised new challenges regarding the scalability of blind quantum computation in realistic noisy conditions. Here we show that fault-tolerant blind quantum computation is possible in a topologically protected manner using the Raussendorf-Harrington-Goyal scheme. The error threshold of our scheme is 4.3 × 10(-3), which is comparable to that (7.5 × 10(-3)) of non-blind topological quantum computation. As the error per gate of the order 10(-3) was already achieved in some experimental systems, our result implies that secure cloud quantum computation is within reach.

Blind topological measurement-based quantum computation

NASA Astrophysics Data System (ADS)

Morimae, Tomoyuki; Fujii, Keisuke

2012-09-01

Blind quantum computation is a novel secure quantum-computing protocol that enables Alice, who does not have sufficient quantum technology at her disposal, to delegate her quantum computation to Bob, who has a fully fledged quantum computer, in such a way that Bob cannot learn anything about Alice's input, output and algorithm. A recent proof-of-principle experiment demonstrating blind quantum computation in an optical system has raised new challenges regarding the scalability of blind quantum computation in realistic noisy conditions. Here we show that fault-tolerant blind quantum computation is possible in a topologically protected manner using the Raussendorf-Harrington-Goyal scheme. The error threshold of our scheme is 4.3×10-3, which is comparable to that (7.5×10-3) of non-blind topological quantum computation. As the error per gate of the order 10-3 was already achieved in some experimental systems, our result implies that secure cloud quantum computation is within reach.

Model criticism based on likelihood-free inference, with an application to protein network evolution.

PubMed

Ratmann, Oliver; Andrieu, Christophe; Wiuf, Carsten; Richardson, Sylvia

2009-06-30

Mathematical models are an important tool to explain and comprehend complex phenomena, and unparalleled computational advances enable us to easily explore them without any or little understanding of their global properties. In fact, the likelihood of the data under complex stochastic models is often analytically or numerically intractable in many areas of sciences. This makes it even more important to simultaneously investigate the adequacy of these models-in absolute terms, against the data, rather than relative to the performance of other models-but no such procedure has been formally discussed when the likelihood is intractable. We provide a statistical interpretation to current developments in likelihood-free Bayesian inference that explicitly accounts for discrepancies between the model and the data, termed Approximate Bayesian Computation under model uncertainty (ABCmicro). We augment the likelihood of the data with unknown error terms that correspond to freely chosen checking functions, and provide Monte Carlo strategies for sampling from the associated joint posterior distribution without the need of evaluating the likelihood. We discuss the benefit of incorporating model diagnostics within an ABC framework, and demonstrate how this method diagnoses model mismatch and guides model refinement by contrasting three qualitative models of protein network evolution to the protein interaction datasets of Helicobacter pylori and Treponema pallidum. Our results make a number of model deficiencies explicit, and suggest that the T. pallidum network topology is inconsistent with evolution dominated by link turnover or lateral gene transfer alone.

Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi.

PubMed

Li, Chuan; Petukh, Marharyta; Li, Lin; Alexov, Emil

2013-08-15

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. Copyright © 2013 Wiley Periodicals, Inc.

Topological computation based on direct magnetic logic communication.

PubMed

Zhang, Shilei; Baker, Alexander A; Komineas, Stavros; Hesjedal, Thorsten

2015-10-28

Non-uniform magnetic domains with non-trivial topology, such as vortices and skyrmions, are proposed as superior state variables for nonvolatile information storage. So far, the possibility of logic operations using topological objects has not been considered. Here, we demonstrate numerically that the topology of the system plays a significant role for its dynamics, using the example of vortex-antivortex pairs in a planar ferromagnetic film. Utilising the dynamical properties and geometrical confinement, direct logic communication between the topological memory carriers is realised. This way, no additional magnetic-to-electrical conversion is required. More importantly, the information carriers can spontaneously travel up to ~300 nm, for which no spin-polarised current is required. The derived logic scheme enables topological spintronics, which can be integrated into large-scale memory and logic networks capable of complex computations.

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

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

On the Wiener Polarity Index of Lattice Networks

PubMed Central

Chen, Lin; Li, Tao; Liu, Jinfeng; Shi, Yongtang; Wang, Hua

2016-01-01

Network structures are everywhere, including but not limited to applications in biological, physical and social sciences, information technology, and optimization. Network robustness is of crucial importance in all such applications. Research on this topic relies on finding a suitable measure and use this measure to quantify network robustness. A number of distance-based graph invariants, also known as topological indices, have recently been incorporated as descriptors of complex networks. Among them the Wiener type indices are the most well known and commonly used such descriptors. As one of the fundamental variants of the original Wiener index, the Wiener polarity index has been introduced for a long time and known to be related to the cluster coefficient of networks. In this paper, we consider the value of the Wiener polarity index of lattice networks, a common network structure known for its simplicity and symmetric structure. We first present a simple general formula for computing the Wiener polarity index of any graph. Using this formula, together with the symmetric and recursive topology of lattice networks, we provide explicit formulas of the Wiener polarity index of the square lattices, the hexagonal lattices, the triangular lattices, and the 33 ⋅ 42 lattices. We also comment on potential future research topics. PMID:27930705

Inference of Ancestral Recombination Graphs through Topological Data Analysis

PubMed Central

Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

2016-01-01

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

Algebraic K-theory, K-regularity, and -duality of -stable C ∗-algebras

NASA Astrophysics Data System (ADS)

Mahanta, Snigdhayan

2015-12-01

We develop an algebraic formalism for topological -duality. More precisely, we show that topological -duality actually induces an isomorphism between noncommutative motives that in turn implements the well-known isomorphism between twisted K-theories (up to a shift). In order to establish this result we model topological K-theory by algebraic K-theory. We also construct an E ∞ -operad starting from any strongly self-absorbing C ∗-algebra . Then we show that there is a functorial topological K-theory symmetric spectrum construction on the category of separable C ∗-algebras, such that is an algebra over this operad; moreover, is a module over this algebra. Along the way we obtain a new symmetric spectra valued functorial model for the (connective) topological K-theory of C ∗-algebras. We also show that -stable C ∗-algebras are K-regular providing evidence for a conjecture of Rosenberg. We conclude with an explicit description of the algebraic K-theory of a x+ b-semigroup C ∗-algebras coming from number theory and that of -stabilized noncommutative tori.

Aspects géométriques et intégrables des modèles de matrices aléatoires

NASA Astrophysics Data System (ADS)

Marchal, Olivier

2010-12-01

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

Z2Pack: Numerical implementation of hybrid Wannier centers for identifying topological materials

NASA Astrophysics Data System (ADS)

Gresch, Dominik; Autès, Gabriel; Yazyev, Oleg V.; Troyer, Matthias; Vanderbilt, David; Bernevig, B. Andrei; Soluyanov, Alexey A.

2017-02-01

The intense theoretical and experimental interest in topological insulators and semimetals has established band structure topology as a fundamental material property. Consequently, identifying band topologies has become an important, but often challenging, problem, with no exhaustive solution at the present time. In this work we compile a series of techniques, some previously known, that allow for a solution to this problem for a large set of the possible band topologies. The method is based on tracking hybrid Wannier charge centers computed for relevant Bloch states, and it works at all levels of materials modeling: continuous k .p models, tight-binding models, and ab initio calculations. We apply the method to compute and identify Chern, Z2, and crystalline topological insulators, as well as topological semimetal phases, using real material examples. Moreover, we provide a numerical implementation of this technique (the Z2Pack software package) that is ideally suited for high-throughput screening of materials databases for compounds with nontrivial topologies. We expect that our work will allow researchers to (a) identify topological materials optimal for experimental probes, (b) classify existing compounds, and (c) reveal materials that host novel, not yet described, topological states.

Blind topological measurement-based quantum computation

PubMed Central

Morimae, Tomoyuki; Fujii, Keisuke

2012-01-01

Blind quantum computation is a novel secure quantum-computing protocol that enables Alice, who does not have sufficient quantum technology at her disposal, to delegate her quantum computation to Bob, who has a fully fledged quantum computer, in such a way that Bob cannot learn anything about Alice's input, output and algorithm. A recent proof-of-principle experiment demonstrating blind quantum computation in an optical system has raised new challenges regarding the scalability of blind quantum computation in realistic noisy conditions. Here we show that fault-tolerant blind quantum computation is possible in a topologically protected manner using the Raussendorf–Harrington–Goyal scheme. The error threshold of our scheme is 4.3×10−3, which is comparable to that (7.5×10−3) of non-blind topological quantum computation. As the error per gate of the order 10−3 was already achieved in some experimental systems, our result implies that secure cloud quantum computation is within reach. PMID:22948818

An Invitation to the Mathematics of Topological Quantum Computation

NASA Astrophysics Data System (ADS)

Rowell, E. C.

2016-03-01

Two-dimensional topological states of matter offer a route to quantum computation that would be topologically protected against the nemesis of the quantum circuit model: decoherence. Research groups in industry, government and academic institutions are pursuing this approach. We give a mathematician's perspective on some of the advantages and challenges of this model, highlighting some recent advances. We then give a short description of how we might extend the theory to three-dimensional materials.

Localization of Unitary Braid Group Representations

NASA Astrophysics Data System (ADS)

Rowell, Eric C.; Wang, Zhenghan

2012-05-01

Governed by locality, we explore a connection between unitary braid group representations associated to a unitary R-matrix and to a simple object in a unitary braided fusion category. Unitary R-matrices, namely unitary solutions to the Yang-Baxter equation, afford explicitly local unitary representations of braid groups. Inspired by topological quantum computation, we study whether or not it is possible to reassemble the irreducible summands appearing in the unitary braid group representations from a unitary braided fusion category with possibly different positive multiplicities to get representations that are uniformly equivalent to the ones from a unitary R-matrix. Such an equivalence will be called a localization of the unitary braid group representations. We show that the q = e π i/6 specialization of the unitary Jones representation of the braid groups can be localized by a unitary 9 × 9 R-matrix. Actually this Jones representation is the first one in a family of theories ( SO( N), 2) for an odd prime N > 1, which are conjectured to be localizable. We formulate several general conjectures and discuss possible connections to physics and computer science.

Artificial intelligence approach to planning the robotic assembly of large tetrahedral truss structures

NASA Technical Reports Server (NTRS)

Homemdemello, Luiz S.

1992-01-01

An assembly planner for tetrahedral truss structures is presented. To overcome the difficulties due to the large number of parts, the planner exploits the simplicity and uniformity of the shapes of the parts and the regularity of their interconnection. The planning automation is based on the computational formalism known as production system. The global data base consists of a hexagonal grid representation of the truss structure. This representation captures the regularity of tetrahedral truss structures and their multiple hierarchies. It maps into quadratic grids and can be implemented in a computer by using a two-dimensional array data structure. By maintaining the multiple hierarchies explicitly in the model, the choice of a particular hierarchy is only made when needed, thus allowing a more informed decision. Furthermore, testing the preconditions of the production rules is simple because the patterned way in which the struts are interconnected is incorporated into the topology of the hexagonal grid. A directed graph representation of assembly sequences allows the use of both graph search and backtracking control strategies.

Image model: new perspective for image processing and computer vision

NASA Astrophysics Data System (ADS)

Ziou, Djemel; Allili, Madjid

2004-05-01

We propose a new image model in which the image support and image quantities are modeled using algebraic topology concepts. The image support is viewed as a collection of chains encoding combination of pixels grouped by dimension and linking different dimensions with the boundary operators. Image quantities are encoded using the notion of cochain which associates values for pixels of given dimension that can be scalar, vector, or tensor depending on the problem that is considered. This allows obtaining algebraic equations directly from the physical laws. The coboundary and codual operators, which are generic operations on cochains allow to formulate the classical differential operators as applied for field functions and differential forms in both global and local forms. This image model makes the association between the image support and the image quantities explicit which results in several advantages: it allows the derivation of efficient algorithms that operate in any dimension and the unification of mathematics and physics to solve classical problems in image processing and computer vision. We show the effectiveness of this model by considering the isotropic diffusion.

Topological valley-chiral edge states of Lamb waves in elastic thin plates

NASA Astrophysics Data System (ADS)

Wang, Jian; Mei, Jun

2018-05-01

We investigate the nontrivial topology of the band structure of Lamb waves in a thin phononic crystal plate. When inversion symmetry is broken, a valley pseudospin degree of freedom is formed around K and K‧ valleys for the A0 Lamb mode, which is decoupled from the S0 and SH0 modes in the low-frequency regime. Chiral edge states are explicitly demonstrated, which are immune to defects and exhibit unidirectional transport behaviors when intervalley scattering is weak. The quantum valley Hall effect is thus simulated in a simple way in the context of Lamb waves.

Computing Tutte polynomials of contact networks in classrooms

NASA Astrophysics Data System (ADS)

Hincapié, Doracelly; Ospina, Juan

2013-05-01

Objective: The topological complexity of contact networks in classrooms and the potential transmission of an infectious disease were analyzed by sex and age. Methods: The Tutte polynomials, some topological properties and the number of spanning trees were used to algebraically compute the topological complexity. Computations were made with the Maple package GraphTheory. Published data of mutually reported social contacts within a classroom taken from primary school, consisting of children in the age ranges of 4-5, 7-8 and 10-11, were used. Results: The algebraic complexity of the Tutte polynomial and the probability of disease transmission increases with age. The contact networks are not bipartite graphs, gender segregation was observed especially in younger children. Conclusion: Tutte polynomials are tools to understand the topology of the contact networks and to derive numerical indexes of such topologies. It is possible to establish relationships between the Tutte polynomial of a given contact network and the potential transmission of an infectious disease within such network

An alternative low-loss stack topology for vanadium redox flow battery: Comparative assessment

NASA Astrophysics Data System (ADS)

Moro, Federico; Trovò, Andrea; Bortolin, Stefano; Del, Davide, , Col; Guarnieri, Massimo

2017-02-01

Two vanadium redox flow battery topologies have been compared. In the conventional series stack, bipolar plates connect cells electrically in series and hydraulically in parallel. The alternative topology consists of cells connected in parallel inside stacks by means of monopolar plates in order to reduce shunt currents along channels and manifolds. Channelled and flat current collectors interposed between cells were considered in both topologies. In order to compute the stack losses, an equivalent circuit model of a VRFB cell was built from a 2D FEM multiphysics numerical model based on Comsol®, accounting for coupled electrical, electrochemical, and charge and mass transport phenomena. Shunt currents were computed inside the cells with 3D FEM models and in the piping and manifolds by means of equivalent circuits solved with Matlab®. Hydraulic losses were computed with analytical models in piping and manifolds and with 3D numerical analyses based on ANSYS Fluent® in the cell porous electrodes. Total losses in the alternative topology resulted one order of magnitude lower than in an equivalent conventional battery. The alternative topology with channelled current collectors exhibits the lowest shunt currents and hydraulic losses, with round-trip efficiency higher by about 10%, as compared to the conventional topology.

Generalised Multiplicative Indices of Polycyclic Aromatic Hydrocarbons and Benzenoid Systems

NASA Astrophysics Data System (ADS)

Kulli, V. R.; Stone, Branden; Wang, Shaohui; Wei, Bing

2017-05-01

Many types of topological indices such as degree-based topological indices, distance-based topological indices, and counting-related topological indices are explored during past recent years. Among degree-based topological indices, Zagreb indices are the oldest one and studied well. In the paper, we define a generalised multiplicative version of these indices and compute exact formulas for Polycyclic Aromatic Hydrocarbons and jagged-rectangle Benzenoid systems.

Floquet topological phases with symmetry in all dimensions

NASA Astrophysics Data System (ADS)

Roy, Rahul; Harper, Fenner

2017-05-01

Dynamical systems may host a number of remarkable symmetry-protected phases that are qualitatively different from their static analogs. In this work, we consider the phase space of symmetry-respecting unitary evolutions in detail and identify several distinct classes of evolution that host dynamical order. Using ideas from group cohomology, we construct a set of interacting Floquet drives that generate dynamical symmetry-protected topological order for each nontrivial cohomology class in every dimension, illustrating our construction with explicit two-dimensional examples. We also identify a set of symmetry-protected Floquet drives that lie outside of the group cohomology construction, and a further class of symmetry-respecting topological drives which host chiral edge modes. We use these special drives to define a notion of phase (stable to a class of local perturbations in the bulk) and the concepts of relative and absolute topological order, which can be applied to many different classes of unitary evolutions. These include fully many-body localized unitary evolutions and time crystals.

Roots and decompositions of three-dimensional topological objects

NASA Astrophysics Data System (ADS)

Matveev, Sergei V.

2012-06-01

In 1942 M.H.A. Newman formulated and proved a simple lemma of great importance for various fields of mathematics, including algebra and the theory of Gröbner-Shirshov bases. Later it was called the Diamond Lemma, since its key construction was illustrated by a diamond-shaped diagram. In 2005 the author suggested a new version of this lemma suitable for topological applications. This paper gives a survey of results on the existence and uniqueness of prime decompositions of various topological objects: three-dimensional manifolds, knots in thickened surfaces, knotted graphs, three-dimensional orbifolds, and knotted theta-curves in three-dimensional manifolds. As it turned out, all these topological objects admit a prime decomposition, although it is not unique in some cases (for example, in the case of orbifolds). For theta-curves and knots of geometric degree 1 in a thickened torus, the algebraic structure of the corresponding semigroups can be completely described. In both cases the semigroups are quotients of free groups by explicit commutation relations. Bibliography: 33 titles.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems.

PubMed

Bhatia, Harsh; Gyulassy, Attila G; Lordi, Vincenzo; Pask, John E; Pascucci, Valerio; Bremer, Peer-Timo

2018-06-15

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state-of-the-art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero-de-la-Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine-grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

OPTIMAL NETWORK TOPOLOGY DESIGN

NASA Technical Reports Server (NTRS)

Yuen, J. H.

1994-01-01

This program was developed as part of a research study on the topology design and performance analysis for the Space Station Information System (SSIS) network. 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. It is intended that this new design technique consider all important performance measures explicitly and take into account the constraints due to various technical feasibilities. In the current program, technical constraints are taken care of by the user properly forming the starting set of candidate components (e.g. nonfeasible links are not included). As subsets are generated, they are tested to see if they form an acceptable network by checking that all requirements are satisfied. Thus the first acceptable subset encountered gives the cost-optimal topology satisfying all given constraints. The user must sort the set of "feasible" link elements in increasing order of their costs. The program prompts the user for the following information for each link: 1) cost, 2) connectivity (number of stations connected by the link), and 3) the stations connected by that link. Unless instructed to stop, the program generates all possible acceptable networks in increasing order of their total costs. The program is written only to generate topologies that are simply connected. Tests on reliability, delay, and other performance measures are discussed in the documentation, but have not been incorporated into the program. This program is written in PASCAL for interactive execution and has been implemented on an IBM PC series computer operating under PC DOS. The disk contains source code only. This program was developed in 1985.

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

PubMed Central

Milenković, Tijana

2018-01-01

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

Higher-Loop Amplitude Monodromy Relations in String and Gauge Theory.

PubMed

Tourkine, Piotr; Vanhove, Pierre

2016-11-18

The monodromy relations in string theory provide a powerful and elegant formalism to understand some of the deepest properties of tree-level field theory amplitudes, like the color-kinematics duality. This duality has been instrumental in tremendous progress on the computations of loop amplitudes in quantum field theory, but a higher-loop generalization of the monodromy construction was lacking. In this Letter, we extend the monodromy relations to higher loops in open string theory. Our construction, based on a contour deformation argument of the open string diagram integrands, leads to new identities that relate planar and nonplanar topologies in string theory. We write one and two-loop monodromy formulas explicitly at any multiplicity. In the field theory limit, at one-loop we obtain identities that reproduce known results. At two loops, we check our formulas by unitarity in the case of the four-point N=4 super-Yang-Mills amplitude.

SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

PubMed

Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

2015-02-10

Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

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

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

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

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

Topological transformation of fractional optical vortex beams using computer generated holograms

NASA Astrophysics Data System (ADS)

Maji, Satyajit; Brundavanam, Maruthi M.

2018-04-01

Optical vortex beams with fractional topological charges (TCs) are generated by the diffraction of a Gaussian beam using computer generated holograms embedded with mixed screw-edge dislocations. When the input Gaussian beam has a finite wave-front curvature, the generated fractional vortex beams show distinct topological transformations in comparison to the integer charge optical vortices. The topological transformations at different fractional TCs are investigated through the birth and evolution of the points of phase singularity, the azimuthal momentum transformation, occurrence of critical points in the transverse momentum and the vorticity around the singular points. This study is helpful to achieve better control in optical micro-manipulation applications.

Simulation-Based Probabilistic Seismic Hazard Assessment Using System-Level, Physics-Based Models: Assembling Virtual California

NASA Astrophysics Data System (ADS)

Rundle, P. B.; Rundle, J. B.; Morein, G.; Donnellan, A.; Turcotte, D.; Klein, W.

2004-12-01

The research community is rapidly moving towards the development of an earthquake forecast technology based on the use of complex, system-level earthquake fault system simulations. Using these topologically and dynamically realistic simulations, it is possible to develop ensemble forecasting methods similar to that used in weather and climate research. To effectively carry out such a program, one needs 1) a topologically realistic model to simulate the fault system; 2) data sets to constrain the model parameters through a systematic program of data assimilation; 3) a computational technology making use of modern paradigms of high performance and parallel computing systems; and 4) software to visualize and analyze the results. In particular, we focus attention on a new version of our code Virtual California (version 2001) in which we model all of the major strike slip faults in California, from the Mexico-California border to the Mendocino Triple Junction. Virtual California is a "backslip model", meaning that the long term rate of slip on each fault segment in the model is matched to the observed rate. We use the historic data set of earthquakes larger than magnitude M > 6 to define the frictional properties of 650 fault segments (degrees of freedom) in the model. To compute the dynamics and the associated surface deformation, we use message passing as implemented in the MPICH standard distribution on a Beowulf clusters consisting of >10 cpus. We also will report results from implementing the code on significantly larger machines so that we can begin to examine much finer spatial scales of resolution, and to assess scaling properties of the code. We present results of simulations both as static images and as mpeg movies, so that the dynamical aspects of the computation can be assessed by the viewer. We compute a variety of statistics from the simulations, including magnitude-frequency relations, and compare these with data from real fault systems. We report recent results on use of Virtual California for probabilistic earthquake forecasting for several sub-groups of major faults in California. These methods have the advantage that system-level fault interactions are explicitly included, as well as laboratory-based friction laws.

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.

Topology Optimization of Lightweight Lattice Structural Composites Inspired by Cuttlefish Bone

NASA Astrophysics Data System (ADS)

Hu, Zhong; Gadipudi, Varun Kumar; Salem, David R.

2018-03-01

Lattice structural composites are of great interest to various industries where lightweight multifunctionality is important, especially aerospace. However, strong coupling among the composition, microstructure, porous topology, and fabrication of such materials impedes conventional trial-and-error experimental development. In this work, a discontinuous carbon fiber reinforced polymer matrix composite was adopted for structural design. A reliable and robust design approach for developing lightweight multifunctional lattice structural composites was proposed, inspired by biomimetics and based on topology optimization. Three-dimensional periodic lattice blocks were initially designed, inspired by the cuttlefish bone microstructure. The topologies of the three-dimensional periodic blocks were further optimized by computer modeling, and the mechanical properties of the topology optimized lightweight lattice structures were characterized by computer modeling. The lattice structures with optimal performance were identified.

Applications of Atomic Systems in Quantum Simulation, Quantum Computation and Topological Phases of Matter

NASA Astrophysics Data System (ADS)

Wang, Shengtao

The ability to precisely and coherently control atomic systems has improved dramatically in the last two decades, driving remarkable advancements in quantum computation and simulation. In recent years, atomic and atom-like systems have also been served as a platform to study topological phases of matter and non-equilibrium many-body physics. Integrated with rapid theoretical progress, the employment of these systems is expanding the realm of our understanding on a range of physical phenomena. In this dissertation, I draw on state-of-the-art experimental technology to develop several new ideas for controlling and applying atomic systems. In the first part of this dissertation, we propose several novel schemes to realize, detect, and probe topological phases in atomic and atom-like systems. We first theoretically study the intriguing properties of Hopf insulators, a peculiar type of topological insulators beyond the standard classification paradigm of topological phases. Using a solid-state quantum simulator, we report the first experimental observation of Hopf insulators. We demonstrate the Hopf fibration with fascinating topological links in the experiment, showing clear signals of topological phase transitions for the underlying Hamiltonian. Next, we propose a feasible experimental scheme to realize the chiral topological insulator in three dimensions. They are a type of topological insulators protected by the chiral symmetry and have thus far remained unobserved in experiment. We then introduce a method to directly measure topological invariants in cold-atom experiments. This detection scheme is general and applicable to probe of different topological insulators in any spatial dimension. In another study, we theoretically discover a new type of topological gapless rings, dubbed a Weyl exceptional ring, in three-dimensional dissipative cold atomic systems. In the second part of this dissertation, we focus on the application of atomic systems in quantum computation and simulation. Trapped atomic ions are one of the leading platforms to build a scalable, universal quantum computer. The common one-dimensional setup, however, greatly limits the system's scalability. By solving the critical problem of micromotion, we propose a two-dimensional architecture for scalable trapped-ion quantum computation. Hamiltonian tomography for many-body quantum systems is essential for benchmarking quantum computation and simulation. By employing dynamical decoupling, we propose a scalable scheme for full Hamiltonian tomography. The required number of measurements increases only polynomially with the system size, in contrast to an exponential scaling in common methods. Finally, we work toward the goal of demonstrating quantum supremacy. A number of sampling tasks, such as the boson sampling problem, have been proposed to be classically intractable under mild assumptions. An intermediate quantum computer can efficiently solve the sampling problem, but the correct operation of the device is not known to be classically verifiable. Toward practical verification, we present an experimental friendly scheme to extract useful and robust information from the quantum boson samplers based on coarse-grained measurements. In a separate study, we introduce a new model built from translation-invariant Ising-interacting spins. This model possesses several advantageous properties, catalyzing the ultimate experimental demonstration of quantum supremacy.

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Unstructured Finite Elements and Dynamic Meshing for Explicit Phase Tracking in Multiphase Problems

NASA Astrophysics Data System (ADS)

Chandra, Anirban; Yang, Fan; Zhang, Yu; Shams, Ehsan; Sahni, Onkar; Oberai, Assad; Shephard, Mark

2017-11-01

Multi-phase processes involving phase change at interfaces, such as evaporation of a liquid or combustion of a solid, represent an interesting class of problems with varied applications. Large density ratio across phases, discontinuous fields at the interface and rapidly evolving geometries are some of the inherent challenges which influence the numerical modeling of multi-phase phase change problems. In this work, a mathematically consistent and robust computational approach to address these issues is presented. We use stabilized finite element methods on mixed topology unstructured grids for solving the compressible Navier-Stokes equations. Appropriate jump conditions derived from conservations laws across the interface are handled by using discontinuous interpolations, while the continuity of temperature and tangential velocity is enforced using a penalty parameter. The arbitrary Lagrangian-Eulerian (ALE) technique is utilized to explicitly track the interface motion. Mesh at the interface is constrained to move with the interface while elsewhere it is moved using the linear elasticity analogy. Repositioning is applied to the layered mesh that maintains its structure and normal resolution. In addition, mesh modification is used to preserve the quality of the volumetric mesh. This work is supported by the U.S. Army Grants W911NF1410301 and W911NF16C0117.

Topological order and memory time in marginally-self-correcting quantum memory

NASA Astrophysics Data System (ADS)

Siva, Karthik; Yoshida, Beni

2017-03-01

We examine two proposals for marginally-self-correcting quantum memory: the cubic code by Haah and the welded code by Michnicki. In particular, we prove explicitly that they are absent of topological order above zero temperature, as their Gibbs ensembles can be prepared via a short-depth quantum circuit from classical ensembles. Our proof technique naturally gives rise to the notion of free energy associated with excitations. Further, we develop a framework for an ergodic decomposition of Davies generators in CSS codes which enables formal reduction to simpler classical memory problems. We then show that memory time in the welded code is doubly exponential in inverse temperature via the Peierls argument. These results introduce further connections between thermal topological order and self-correction from the viewpoint of free energy and quantum circuit depth.

Unexpected mass acquisition of Dirac fermions at the quantum phase transition of a topological insulator

NASA Astrophysics Data System (ADS)

Sato, T.; Segawa, Kouji; Kosaka, K.; Souma, S.; Nakayama, K.; Eto, K.; Minami, T.; Ando, Yoichi; Takahashi, T.

2011-11-01

The three-dimensional (3D) topological insulator is a novel quantum state of matter where an insulating bulk hosts a linearly dispersing surface state, which can be viewed as a sea of massless Dirac fermions protected by the time-reversal symmetry (TRS). Breaking the TRS by a magnetic order leads to the opening of a gap in the surface state, and consequently the Dirac fermions become massive. It has been proposed theoretically that such a mass acquisition is necessary to realize novel topological phenomena, but achieving a sufficiently large mass is an experimental challenge. Here we report an unexpected discovery that the surface Dirac fermions in a solid-solution system TlBi(S1-xSex)2 acquire a mass without explicitly breaking the TRS. We found that this system goes through a quantum phase transition from the topological to the non-topological phase, and, by tracing the evolution of the electronic states using the angle-resolved photoemission, we observed that the massless Dirac state in TlBiSe2 switches to a massive state before it disappears in the non-topological phase. This result suggests the existence of a condensed-matter version of the `Higgs mechanism' where particles acquire a mass through spontaneous symmetry breaking.

Topology and boundary shape optimization as an integrated design tool

NASA Technical Reports Server (NTRS)

Bendsoe, Martin Philip; Rodrigues, Helder Carrico

1990-01-01

The optimal topology of a two dimensional linear elastic body can be computed by regarding the body as a domain of the plane with a high density of material. Such an optimal topology can then be used as the basis for a shape optimization method that computes the optimal form of the boundary curves of the body. This results in an efficient and reliable design tool, which can be implemented via common FEM mesh generator and CAD type input-output facilities.

Combinatorial-topological framework for the analysis of global dynamics.

PubMed

Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł

2012-12-01

We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.

Combinatorial-topological framework for the analysis of global dynamics

NASA Astrophysics Data System (ADS)

Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł

2012-12-01

We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.

The world problem: on the computability of the topology of 4-manifolds

NASA Technical Reports Server (NTRS)

vanMeter, J. R.

2005-01-01

Topological classification of the 4-manifolds bridges computation theory and physics. A proof of the undecidability of the homeomorphy problem for 4-manifolds is outlined here in a clarifying way. It is shown that an arbitrary Turing machine with an arbitrary input can be encoded into the topology of a 4-manifold, such that the 4-manifold is homeomorphic to a certain other 4-manifold if and only if the corresponding Turing machine halts on the associated input. Physical implications are briefly discussed.

Symmetry-protected topological phases with uniform computational power in one dimension

NASA Astrophysics Data System (ADS)

Raussendorf, Robert; Wang, Dong-Sheng; Prakash, Abhishodh; Wei, Tzu-Chieh; Stephen, David T.

2017-07-01

We investigate the usefulness of ground states of quantum spin chains with symmetry-protected topological order (SPTO) for measurement-based quantum computation. We show that, in spatial dimension 1, if an SPTO phase protects the identity gate, then, subject to an additional symmetry condition that is satisfied in all cases so far investigated, it can also be used for quantum computation.

EDITORIAL: Topological data analysis Topological data analysis

NASA Astrophysics Data System (ADS)

Epstein, Charles; Carlsson, Gunnar; Edelsbrunner, Herbert

2011-12-01

Inverse problems can be defined as the area of mathematics that attempts to reconstruct a physical or mathematical object from derived data. Frequently, this means the evaluation of parameters or other numerical quantities (such as eigenvalues) that characterize or provide information about the system. There are, however, other aspects of a system that are important, but are not as readily summarized by numerical quantities. If one considers observations of diabetic patients (using metabolic quantities), one will find that the data breaks up into components, or pieces, corresponding to distinct forms of the disease. The decomposition of data sets into disjoint pieces, or clustering, is an aspect of the study of the shape of the data, albeit one that has been extensively studied. A more complex notion of shape appears in observations of a predator-prey system governed by a Lotka-Volterra equation. One would find that exact observations, consisting of (prey population, predator population) pairs, appear to lie along a simple closed curve in the plane. The fact that the data lies along such a closed curve is an important piece of information, since it suggests that the system displays recurrent behavior. If one did not know, a priori, that the system is governed by a Lotka-Volterra equation, then it would not be immediately obvious that the system is undergoing recurrent motion, and this deduction would constitute a significant insight. In this case, it is again the shape of the data, namely the fact that it lies on a simple closed curve, which is the key insight. Shape is a somewhat nebulous concept, which at first blush may be too intuitive to make precise mathematically, and describe quantitatively. Within pure mathematics, the disciplines of topology and differential geometry are designed exactly to address this problem. They provide explicit signatures which, in precise senses, quantify and describe the shape of a geometric object. In addition, they provide methods for discretizing and compressing the information present in a geometric object so as to provide a useful, small representation of the object. The articles in this special issue are concerned with the applications of topology to the analysis of data sets. The adaptation of topological techniques from pure mathematics to the study of data from real systems is a project which has been undertaken during the past two decades, and the present volume contains various contributions to that project. At the current state of development, homology and persistence are two of the most popular topological techniques used in this context. Homology goes back to the beginnings of topology in Poincaré's influential papers. It is the idea that the connectivity of a space is determined by its cycles of different dimensions, and that these cycles organize themselves into abelian groups, called homology groups. Better known than these groups are their ranks, the Betti numbers of the space, which are non-negative integers that count the number of independent cycles in each dimension. To give an example, the zeroth Betti number counts the components, and the first counts the loops. A crucial feature of homology groups is that, given a reasonably explicit description of a space, their computation is an exercise in linear algebra. Even better known than the Betti numbers is the Euler characteristic, which we know from Poincaré's work, is equal to the alternating sum of the Betti numbers, which can be computed without computing the homology groups themselves. To give evidence that these numbers have relevant practical applications, we mention that integrating the Euler characteristic over a domain with sensor information can be used to count objects in the domain. This alone would not explain the popularity of homology groups, which we see rooted in the fact that they hit a sweet-spot that offers relatively strong discriminative power, and a clear intuitive meaning, all at a surprisingly low computational cost. Even these desirable qualities would not be sufficient if it were not possible to overcome a serious shortcoming, namely the high sensitivity of homology to minor mistakes in the data collection. Because of the finite nature of most data sets, the notion of shape within data sets is inevitably stochastic. To some extent this is because of the uncertainty of what a shape in nature is, but more importantly, the available data can only be used to give an estimate for the probability of a given shape. This has led to the study of persistent homology, in which the invariants are in the form of 'persistence diagrams' or 'barcodes'. These invariants quantify the stability of geometric features with respect to perturbations that, in turn, provide a basis for discriminating between artifacts caused by noise or undersampling and real phenomena. Several papers in this volume deal with questions about these diagrams, and some deal with probabilistic issues related to the occurrence of these diagrams. Our hope is that the papers in this volume will provide exposure of these techniques to both a wider audience of mathematicians and also potential users of the techniques.

EDITORIAL: Topological data analysis Topological data analysis

NASA Astrophysics Data System (ADS)

2011-12-01

Inverse problems can be defined as the area of mathematics that attempts to reconstruct a physical or mathematical object from derived data. Frequently, this means the evaluation of parameters or other numerical quantities (such as eigenvalues) that characterize or provide information about the system. There are, however, other aspects of a system that are important, but are not as readily summarized by numerical quantities. If one considers observations of diabetic patients (using metabolic quantities), one will find that the data breaks up into components, or pieces, corresponding to distinct forms of the disease. The decomposition of data sets into disjoint pieces, or clustering, is an aspect of the study of the shape of the data, albeit one that has been extensively studied. A more complex notion of shape appears in observations of a predator-prey system governed by a Lotka-Volterra equation. One would find that exact observations, consisting of (prey population, predator population) pairs, appear to lie along a simple closed curve in the plane. The fact that the data lies along such a closed curve is an important piece of information, since it suggests that the system displays recurrent behavior. If one did not know, a priori, that the system is governed by a Lotka-Volterra equation, then it would not be immediately obvious that the system is undergoing recurrent motion, and this deduction would constitute a significant insight. In this case, it is again the shape of the data, namely the fact that it lies on a simple closed curve, which is the key insight. Shape is a somewhat nebulous concept, which at first blush may be too intuitive to make precise mathematically, and describe quantitatively. Within pure mathematics, the disciplines of topology and differential geometry are designed exactly to address this problem. They provide explicit signatures which, in precise senses, quantify and describe the shape of a geometric object. In addition, they provide methods for discretizing and compressing the information present in a geometric object so as to provide a useful, small representation of the object. The articles in this special issue are concerned with the applications of topology to the analysis of data sets. The adaptation of topological techniques from pure mathematics to the study of data from real systems is a project which has been undertaken during the past two decades, and the present volume contains various contributions to that project. At the current state of development, homology and persistence are two of the most popular topological techniques used in this context. Homology goes back to the beginnings of topology in Poincaré's influential papers. It is the idea that the connectivity of a space is determined by its cycles of different dimensions, and that these cycles organize themselves into abelian groups, called homology groups. Better known than these groups are their ranks, the Betti numbers of the space, which are non-negative integers that count the number of independent cycles in each dimension. To give an example, the zeroth Betti number counts the components, and the first counts the loops. A crucial feature of homology groups is that, given a reasonably explicit description of a space, their computation is an exercise in linear algebra. Even better known than the Betti numbers is the Euler characteristic, which we know from Poincaré's work, is equal to the alternating sum of the Betti numbers, which can be computed without computing the homology groups themselves. To give evidence that these numbers have relevant practical applications, we mention that integrating the Euler characteristic over a domain with sensor information can be used to count objects in the domain. This alone would not explain the popularity of homology groups, which we see rooted in the fact that they hit a sweet-spot that offers relatively strong discriminative power, and a clear intuitive meaning, all at a surprisingly low computational cost. Even these desirable qualities would not be sufficient if it were not possible to overcome a serious shortcoming, namely the high sensitivity of homology to minor mistakes in the data collection. Because of the finite nature of most data sets, the notion of shape within data sets is inevitably stochastic. To some extent this is because of the uncertainty of what a shape in nature is, but more importantly, the available data can only be used to give an estimate for the probability of a given shape. This has led to the study of persistent homology, in which the invariants are in the form of 'persistence diagrams' or 'barcodes'. These invariants quantify the stability of geometric features with respect to perturbations that, in turn, provide a basis for discriminating between artifacts caused by noise or undersampling and real phenomena. Several papers in this volume deal with questions about these diagrams, and some deal with probabilistic issues related to the occurrence of these diagrams. Our hope is that the papers in this volume will provide exposure of these techniques to both a wider audience of mathematicians and also potential users of the techniques. Charles Epstein, Gunnar Carlsson and Herbert Edelsbrunner Guest Editors

Topological order, entanglement, and quantum memory at finite temperature

NASA Astrophysics Data System (ADS)

Mazáč, Dalimil; Hamma, Alioscia

2012-09-01

We compute the topological entropy of the toric code models in arbitrary dimension at finite temperature. We find that the critical temperatures for the existence of full quantum (classical) topological entropy correspond to the confinement-deconfinement transitions in the corresponding Z2 gauge theories. This implies that the thermal stability of topological entropy corresponds to the stability of quantum (classical) memory. The implications for the understanding of ergodicity breaking in topological phases are discussed.

Time-dependence of graph theory metrics in functional connectivity analysis

PubMed Central

Chiang, Sharon; Cassese, Alberto; Guindani, Michele; Vannucci, Marina; Yeh, Hsiang J.; Haneef, Zulfi; Stern, John M.

2016-01-01

Brain graphs provide a useful way to computationally model the network structure of the connectome, and this has led to increasing interest in the use of graph theory to quantitate and investigate the topological characteristics of the healthy brain and brain disorders on the network level. The majority of graph theory investigations of functional connectivity have relied on the assumption of temporal stationarity. However, recent evidence increasingly suggests that functional connectivity fluctuates over the length of the scan. In this study, we investigate the stationarity of brain network topology using a Bayesian hidden Markov model (HMM) approach that estimates the dynamic structure of graph theoretical measures of whole-brain functional connectivity. In addition to extracting the stationary distribution and transition probabilities of commonly employed graph theory measures, we propose two estimators of temporal stationarity: the S-index and N-index. These indexes can be used to quantify different aspects of the temporal stationarity of graph theory measures. We apply the method and proposed estimators to resting-state functional MRI data from healthy controls and patients with temporal lobe epilepsy. Our analysis shows that several graph theory measures, including small-world index, global integration measures, and betweenness centrality, may exhibit greater stationarity over time and therefore be more robust. Additionally, we demonstrate that accounting for subject-level differences in the level of temporal stationarity of network topology may increase discriminatory power in discriminating between disease states. Our results confirm and extend findings from other studies regarding the dynamic nature of functional connectivity, and suggest that using statistical models which explicitly account for the dynamic nature of functional connectivity in graph theory analyses may improve the sensitivity of investigations and consistency across investigations. PMID:26518632

Time-dependence of graph theory metrics in functional connectivity analysis.

PubMed

Chiang, Sharon; Cassese, Alberto; Guindani, Michele; Vannucci, Marina; Yeh, Hsiang J; Haneef, Zulfi; Stern, John M

2016-01-15

Brain graphs provide a useful way to computationally model the network structure of the connectome, and this has led to increasing interest in the use of graph theory to quantitate and investigate the topological characteristics of the healthy brain and brain disorders on the network level. The majority of graph theory investigations of functional connectivity have relied on the assumption of temporal stationarity. However, recent evidence increasingly suggests that functional connectivity fluctuates over the length of the scan. In this study, we investigate the stationarity of brain network topology using a Bayesian hidden Markov model (HMM) approach that estimates the dynamic structure of graph theoretical measures of whole-brain functional connectivity. In addition to extracting the stationary distribution and transition probabilities of commonly employed graph theory measures, we propose two estimators of temporal stationarity: the S-index and N-index. These indexes can be used to quantify different aspects of the temporal stationarity of graph theory measures. We apply the method and proposed estimators to resting-state functional MRI data from healthy controls and patients with temporal lobe epilepsy. Our analysis shows that several graph theory measures, including small-world index, global integration measures, and betweenness centrality, may exhibit greater stationarity over time and therefore be more robust. Additionally, we demonstrate that accounting for subject-level differences in the level of temporal stationarity of network topology may increase discriminatory power in discriminating between disease states. Our results confirm and extend findings from other studies regarding the dynamic nature of functional connectivity, and suggest that using statistical models which explicitly account for the dynamic nature of functional connectivity in graph theory analyses may improve the sensitivity of investigations and consistency across investigations. Copyright © 2015 Elsevier Inc. All rights reserved.

Aeroelastic Wingbox Stiffener Topology Optimization

NASA Technical Reports Server (NTRS)

Stanford, Bret K.

2017-01-01

This work considers an aeroelastic wingbox model seeded with run-out blade stiffeners along the skins. Topology optimization is conducted within the shell webs of the stiffeners, in order to add cutouts and holes for mass reduction. This optimization is done with a global-local approach in order to moderate the computational cost: aeroelastic loads are computed at the wing-level, but the topology and sizing optimization is conducted at the panel-level. Each panel is optimized separately under stress, buckling, and adjacency constraints, and periodically reassembled to update the trimmed aeroelastic loads. The resulting topology is baselined against a design with standard full-depth solid stiffener blades, and found to weigh 7.43% less.

Distributed Sensing and Processing: A Graphical Model Approach

DTIC Science & Technology

2005-11-30

that Ramanujan graph toplogies maximize the convergence rate of distributed detection consensus algorithms, improving over three orders of...small world type network designs. 14. SUBJECT TERMS Ramanujan graphs, sensor network topology, sensor network...that Ramanujan graphs, for which there are explicit algebraic constructions, have large eigenratios, converging much faster than structured graphs

The topology of the cosmic web in terms of persistent Betti numbers

NASA Astrophysics Data System (ADS)

Pranav, Pratyush; Edelsbrunner, Herbert; van de Weygaert, Rien; Vegter, Gert; Kerber, Michael; Jones, Bernard J. T.; Wintraecken, Mathijs

2017-03-01

We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira-Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys.

Twisted sigma-model solitons on the quantum projective line

NASA Astrophysics Data System (ADS)

Landi, Giovanni

2018-04-01

On the configuration space of projections in a noncommutative algebra, and for an automorphism of the algebra, we use a twisted Hochschild cocycle for an action functional and a twisted cyclic cocycle for a topological term. The latter is Hochschild-cohomologous to the former and positivity in twisted Hochschild cohomology results into a lower bound for the action functional. While the equations for the critical points are rather involved, the use of the positivity and the bound by the topological term lead to self-duality equations (thus yielding twisted noncommutative sigma-model solitons, or instantons). We present explicit nontrivial solutions on the quantum projective line.

Entangling qubits by Heisenberg spin exchange and anyon braiding

NASA Astrophysics Data System (ADS)

Zeuch, Daniel

As the discovery of quantum mechanics signified a revolution in the world of physics more than one century ago, the notion of a quantum computer in 1981 marked the beginning of a drastic change of our understanding of information and computability. In a quantum computer, information is stored using quantum bits, or qubits, which are described by a quantum-mechanical superposition of the quantum states 0 and 1. Computation then proceeds by acting with unitary operations on these qubits. These operations are referred to as quantum logic gates, in analogy to classical computation where bits are acted on by classical logic gates. In order to perform universal quantum computation it is, in principle, sufficient to carry out single-qubit gates and two-qubit gates, where the former act on individual qubits and the latter, acting on two qubits, are used to entangle qubits with each other. The present thesis is divided into two main parts. In the first, we are concerned with spin-based quantum computation. In a spin-based quantum computer, qubits are encoded into the Hilbert space spanned by spin-1/2 particles, such as electron spins trapped in semiconductor quantum dots. For a suitable qubit encoding, turning on-and-off, or "pulsing,'' the isotropic Heisenberg exchange Hamiltonian JSi · Sj allows for universal quantum computation and it is this scheme, known as exchange-only quantum computation, which we focus on. In the second part of this thesis, we consider a topological quantum computer in which qubits are encoded using so-called Fibonacci anyons, exotic quasiparticle excitations that obey non-Abelian statistics, and which may emerge in certain two-dimensional topological systems such as fractional quantum-Hall states. Quantum gates can then be carried out by moving these particles around one another, a process that can be viewed as braiding their 2+1 dimensional worldlines. The subject of the present thesis is the development and theoretical understanding of procedures used for entangling qubits. We begin by presenting analytical constructions of pulse sequences which can be used to carry out two-qubit gates that are locally equivalent to a controlled-PHASE gate. The corresponding phase can be arbitrarily chosen, and for one particular choice this gate is equivalent to controlled-NOT. While the constructions of these sequences are relatively lengthy and cumbersome, we further provide a straightforward and intuitive derivation of the shortest known two-qubit pulse sequence for carrying out a controlled-NOT gate. This derivation is carried out completely analytically through a novel "elevation'' of a simple three-spin pulse sequence to a more complicated five-spin pulse sequence. In the case of topological quantum computation with Fibonacci anyons, we present a new method for constructing entangling two-qubit braids. Our construction is based on an iterative procedure, established by Reichardt, which can be used to systematically generate braids whose corresponding operations quickly converge towards an operation that has a diagonal matrix representation in a particular natural basis. After describing this iteration procedure we show how the resulting braids can be used in two explicit constructions for two-qubit braids. Compared to two-qubit braids that can be found using other methods, the braids generated here are among the most efficient and can be obtained straightforwardly without computational overhead.

Efficiently computing and deriving topological relation matrices between complex regions with broad boundaries

NASA Astrophysics Data System (ADS)

Du, Shihong; Guo, Luo; Wang, Qiao; Qin, Qimin

The extended 9-intersection matrix is used to formalize topological relations between uncertain regions while it is designed to satisfy the requirements at a concept level, and to deal with the complex regions with broad boundaries (CBBRs) as a whole without considering their hierarchical structures. In contrast to simple regions with broad boundaries, CBBRs have complex hierarchical structures. Therefore, it is necessary to take into account the complex hierarchical structure and to represent the topological relations between all regions in CBBRs as a relation matrix, rather than using the extended 9-intersection matrix to determine topological relations. In this study, a tree model is first used to represent the intrinsic configuration of CBBRs hierarchically. Then, the reasoning tables are presented for deriving topological relations between child, parent and sibling regions from the relations between two given regions in CBBRs. Finally, based on the reasoning, efficient methods are proposed to compute and derive the topological relation matrix. The proposed methods can be incorporated into spatial databases to facilitate geometric-oriented applications.

On Certain Topological Indices of Boron Triangular Nanotubes

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Ahmad, Safyan; Gao, Wei

2017-08-01

The topological index gives information about the whole structure of a chemical graph, especially degree-based topological indices that are very useful. Boron triangular nanotubes are now replacing usual carbon nanotubes due to their excellent properties. We have computed general Randić (Rα), first Zagreb (M1) and second Zagreb (M2), atom-bond connectivity (ABC), and geometric-arithmetic (GA) indices of boron triangular nanotubes. Also, we have computed the fourth version of atom-bond connectivity (ABC4) and the fifth version of geometric-arithmetic (GA5) indices of boron triangular nanotubes.

A fast finite-difference algorithm for topology optimization of permanent magnets

NASA Astrophysics Data System (ADS)

Abert, Claas; Huber, Christian; Bruckner, Florian; Vogler, Christoph; Wautischer, Gregor; Suess, Dieter

2017-09-01

We present a finite-difference method for the topology optimization of permanent magnets that is based on the fast-Fourier-transform (FFT) accelerated computation of the stray-field. The presented method employs the density approach for topology optimization and uses an adjoint method for the gradient computation. Comparison to various state-of-the-art finite-element implementations shows a superior performance and accuracy. Moreover, the presented method is very flexible and easy to implement due to various preexisting FFT stray-field implementations that can be used.

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

NASA Astrophysics Data System (ADS)

Khuri, Marcus; Weinstein, Gilbert; Yamada, Sumio

2018-05-01

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

Surface to bulk Fermi arcs via Weyl nodes as topological defects

PubMed Central

Kim, Kun Woo; Lee, Woo-Ram; Kim, Yong Baek; Park, Kwon

2016-01-01

A hallmark of Weyl semimetal is the existence of surface Fermi arcs. An intriguing question is what determines the connectivity of surface Fermi arcs, when multiple pairs of Weyl nodes are present. To answer this question, we show that the locations of surface Fermi arcs are predominantly determined by the condition that the Zak phase integrated along the normal-to-surface direction is . The Zak phase can reveal the peculiar topological structure of Weyl semimetal directly in the bulk. Here, we show that the winding of the Zak phase around each projected Weyl node manifests itself as a topological defect of the Wannier–Stark ladder, energy eigenstates under an electric field. Remarkably, this leads to bulk Fermi arcs, open-line segments in the bulk spectra. Bulk Fermi arcs should exist in conjunction with surface counterparts to conserve the Weyl fermion number under an electric field, which is supported by explicit numerical evidence. PMID:27845342

Topological quantum distillation.

PubMed

Bombin, H; Martin-Delgado, M A

2006-11-03

We construct a class of topological quantum codes to perform quantum entanglement distillation. These codes implement the whole Clifford group of unitary operations in a fully topological manner and without selective addressing of qubits. This allows us to extend their application also to quantum teleportation, dense coding, and computation with magic states.

Topological phases in the Haldane model with spin–spin on-site interactions

NASA Astrophysics Data System (ADS)

Rubio-García, A.; García-Ripoll, J. J.

2018-04-01

Ultracold atom experiments allow the study of topological insulators, such as the non-interacting Haldane model. In this work we study a generalization of the Haldane model with spin–spin on-site interactions that can be implemented on such experiments. We focus on measuring the winding number, a topological invariant, of the ground state, which we compute using a mean-field calculation that effectively captures long-range correlations and a matrix product state computation in a lattice with 64 sites. Our main result is that we show how the topological phases present in the non-interacting model survive until the interactions are comparable to the kinetic energy. We also demonstrate the accuracy of our mean-field approach in efficiently capturing long-range correlations. Based on state-of-the-art ultracold atom experiments, we propose an implementation of our model that can give information about the topological phases.

Element-topology-independent preconditioners for parallel finite element computations

NASA Technical Reports Server (NTRS)

Park, K. C.; Alexander, Scott

1992-01-01

A family of preconditioners for the solution of finite element equations are presented, which are element-topology independent and thus can be applicable to element order-free parallel computations. A key feature of the present preconditioners is the repeated use of element connectivity matrices and their left and right inverses. The properties and performance of the present preconditioners are demonstrated via beam and two-dimensional finite element matrices for implicit time integration computations.

Analytic topologically nontrivial solutions of the (3 +1 )-dimensional U (1 ) gauged Skyrme model and extended duality

NASA Astrophysics Data System (ADS)

Avilés, L.; Canfora, F.; Dimakis, N.; Hidalgo, D.

2017-12-01

We construct the first analytic examples of topologically nontrivial solutions of the (3 +1 )-dimensional U (1 ) gauged Skyrme model within a finite box in (3 +1 )-dimensional flat space-time. There are two types of gauged solitons. The first type corresponds to gauged Skyrmions living within a finite volume. The second corresponds to gauged time crystals (smooth solutions of the U (1 ) gauged Skyrme model whose periodic time dependence is protected by a winding number). The notion of electromagnetic duality can be extended for these two types of configurations in the sense that the electric and one of the magnetic components can be interchanged. These analytic solutions show very explicitly the Callan-Witten mechanism (according to which magnetic monopoles may "swallow" part of the topological charge of the Skyrmion) since the electromagnetic field contributes directly to the conserved topological charge of the gauged Skyrmions. As it happens in superconductors, the magnetic field is suppressed in the core of the gauged Skyrmions. On the other hand, the electric field is strongly suppresed in the core of gauged time crystals.

Nonpolynomial vector fields under the Lotka-Volterra normal form

NASA Astrophysics Data System (ADS)

Hernández-Bermejo, Benito; Fairén, Víctor

1995-02-01

We carry out the generalization of the Lotka-Volterra embedding to flows not explicitly recognizable under the generalized Lotka-Volterra format. The procedure introduces appropriate auxiliary variables, and it is shown how, to a great extent, the final Lotka-Volterra system is independent of their specific definition. Conservation of the topological equivalence during the process is also demonstrated.

How Far Is "Near"? Inferring Distance from Spatial Descriptions

ERIC Educational Resources Information Center

Carlson, Laura A.; Covey, Eric S.

2005-01-01

A word may mean different things in different contexts. The current study explored the changing denotations of spatial terms, focusing on how the distance inferred from a spatial description varied as a function of the size of the objects being spatially related. We examined both terms that explicitly convey distance (i.e., topological terms such…

Hg-Based Epitaxial Materials for Topological Insulators

DTIC Science & Technology

2014-07-01

Research Laboratory for investigation of properties. 15. SUBJECT TERMS EOARD, topological insulator , diluted magnetic ...topological superconductors and spintronics to quantum computation (e.g. see C.L.Kane and J.E.Moore "Topological Insulators " Physics World (2011) 24...tetradymite semiconductors Bi2Te3, Bi2Se3, and Sb2Te3 which form magnetically ordered insulators when doped with transition metal elements Cr or Fe (Rui Yu et

Computational Power of Symmetry-Protected Topological Phases.

PubMed

Stephen, David T; Wang, Dong-Sheng; Prakash, Abhishodh; Wei, Tzu-Chieh; Raussendorf, Robert

2017-07-07

We consider ground states of quantum spin chains with symmetry-protected topological (SPT) order as resources for measurement-based quantum computation (MBQC). We show that, for a wide range of SPT phases, the computational power of ground states is uniform throughout each phase. This computational power, defined as the Lie group of executable gates in MBQC, is determined by the same algebraic information that labels the SPT phase itself. We prove that these Lie groups always contain a full set of single-qubit gates, thereby affirming the long-standing conjecture that general SPT phases can serve as computationally useful phases of matter.

Computational Power of Symmetry-Protected Topological Phases

NASA Astrophysics Data System (ADS)

Stephen, David T.; Wang, Dong-Sheng; Prakash, Abhishodh; Wei, Tzu-Chieh; Raussendorf, Robert

2017-07-01

We consider ground states of quantum spin chains with symmetry-protected topological (SPT) order as resources for measurement-based quantum computation (MBQC). We show that, for a wide range of SPT phases, the computational power of ground states is uniform throughout each phase. This computational power, defined as the Lie group of executable gates in MBQC, is determined by the same algebraic information that labels the SPT phase itself. We prove that these Lie groups always contain a full set of single-qubit gates, thereby affirming the long-standing conjecture that general SPT phases can serve as computationally useful phases of matter.

Universal quantum computing using (Zd) 3 symmetry-protected topologically ordered states

NASA Astrophysics Data System (ADS)

Chen, Yanzhu; Prakash, Abhishodh; Wei, Tzu-Chieh

2018-02-01

Measurement-based quantum computation describes a scheme where entanglement of resource states is utilized to simulate arbitrary quantum gates via local measurements. Recent works suggest that symmetry-protected topologically nontrivial, short-ranged entangled states are promising candidates for such a resource. Miller and Miyake [npj Quantum Inf. 2, 16036 (2016), 10.1038/npjqi.2016.36] recently constructed a particular Z2×Z2×Z2 symmetry-protected topological state on the Union Jack lattice and established its quantum-computational universality. However, they suggested that the same construction on the triangular lattice might not lead to a universal resource. Instead of qubits, we generalize the construction to qudits and show that the resulting (d -1 ) qudit nontrivial Zd×Zd×Zd symmetry-protected topological states are universal on the triangular lattice, for d being a prime number greater than 2. The same construction also holds for other 3-colorable lattices, including the Union Jack lattice.

The explicit computation of integration algorithms and first integrals for ordinary differential equations with polynomials coefficients using trees

NASA Technical Reports Server (NTRS)

Crouch, P. E.; Grossman, Robert

1992-01-01

This note is concerned with the explicit symbolic computation of expressions involving differential operators and their actions on functions. The derivation of specialized numerical algorithms, the explicit symbolic computation of integrals of motion, and the explicit computation of normal forms for nonlinear systems all require such computations. More precisely, if R = k(x(sub 1),...,x(sub N)), where k = R or C, F denotes a differential operator with coefficients from R, and g member of R, we describe data structures and algorithms for efficiently computing g. The basic idea is to impose a multiplicative structure on the vector space with basis the set of finite rooted trees and whose nodes are labeled with the coefficients of the differential operators. Cancellations of two trees with r + 1 nodes translates into cancellation of O(N(exp r)) expressions involving the coefficient functions and their derivatives.

Volume 2: Explicit, multistage upwind schemes for Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Elmiligui, Alaa; Ash, Robert L.

1992-01-01

The objective of this study was to develop a high-resolution-explicit-multi-block numerical algorithm, suitable for efficient computation of the three-dimensional, time-dependent Euler and Navier-Stokes equations. The resulting algorithm has employed a finite volume approach, using monotonic upstream schemes for conservation laws (MUSCL)-type differencing to obtain state variables at cell interface. Variable interpolations were written in the k-scheme formulation. Inviscid fluxes were calculated via Roe's flux-difference splitting, and van Leer's flux-vector splitting techniques, which are considered state of the art. The viscous terms were discretized using a second-order, central-difference operator. Two classes of explicit time integration has been investigated for solving the compressible inviscid/viscous flow problems--two-state predictor-corrector schemes, and multistage time-stepping schemes. The coefficients of the multistage time-stepping schemes have been modified successfully to achieve better performance with upwind differencing. A technique was developed to optimize the coefficients for good high-frequency damping at relatively high CFL numbers. Local time-stepping, implicit residual smoothing, and multigrid procedure were added to the explicit time stepping scheme to accelerate convergence to steady-state. The developed algorithm was implemented successfully in a multi-block code, which provides complete topological and geometric flexibility. The only requirement is C degree continuity of the grid across the block interface. The algorithm has been validated on a diverse set of three-dimensional test cases of increasing complexity. The cases studied were: (1) supersonic corner flow; (2) supersonic plume flow; (3) laminar and turbulent flow over a flat plate; (4) transonic flow over an ONERA M6 wing; and (5) unsteady flow of a compressible jet impinging on a ground plane (with and without cross flow). The emphasis of the test cases was validation of code, and assessment of performance, as well as demonstration of flexibility.

Topology optimization under stochastic stiffness

NASA Astrophysics Data System (ADS)

Asadpoure, Alireza

Topology optimization is a systematic computational tool for optimizing the layout of materials within a domain for engineering design problems. It allows variation of structural boundaries and connectivities. This freedom in the design space often enables discovery of new, high performance designs. However, solutions obtained by performing the optimization in a deterministic setting may be impractical or suboptimal when considering real-world engineering conditions with inherent variabilities including (for example) variabilities in fabrication processes and operating conditions. The aim of this work is to provide a computational methodology for topology optimization in the presence of uncertainties associated with structural stiffness, such as uncertain material properties and/or structural geometry. Existing methods for topology optimization under deterministic conditions are first reviewed. Modifications are then proposed to improve the numerical performance of the so-called Heaviside Projection Method (HPM) in continuum domains. Next, two approaches, perturbation and Polynomial Chaos Expansion (PCE), are proposed to account for uncertainties in the optimization procedure. These approaches are intrusive, allowing tight and efficient coupling of the uncertainty quantification with the optimization sensitivity analysis. The work herein develops a robust topology optimization framework aimed at reducing the sensitivity of optimized solutions to uncertainties. The perturbation-based approach combines deterministic topology optimization with a perturbation method for the quantification of uncertainties. The use of perturbation transforms the problem of topology optimization under uncertainty to an augmented deterministic topology optimization problem. The PCE approach combines the spectral stochastic approach for the representation and propagation of uncertainties with an existing deterministic topology optimization technique. The resulting compact representations for the response quantities allow for efficient and accurate calculation of sensitivities of response statistics with respect to the design variables. The proposed methods are shown to be successful at generating robust optimal topologies. Examples from topology optimization in continuum and discrete domains (truss structures) under uncertainty are presented. It is also shown that proposed methods lead to significant computational savings when compared to Monte Carlo-based optimization which involve multiple formations and inversions of the global stiffness matrix and that results obtained from the proposed method are in excellent agreement with those obtained from a Monte Carlo-based optimization algorithm.

Quantum gates by periodic driving

PubMed Central

Shi, Z. C.; Wang, W.; Yi, X. X.

2016-01-01

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions—it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation. PMID:26911900

Quantum gates by periodic driving.

PubMed

Shi, Z C; Wang, W; Yi, X X

2016-02-25

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions-it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation.

A topological framework for interactive queries on 3D models in the Web.

PubMed

Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

A Topological Framework for Interactive Queries on 3D Models in the Web

PubMed Central

Figueiredo, Mauro; Rodrigues, José I.; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications. PMID:24977236

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mechanical topological insulator in zero dimensions

NASA Astrophysics Data System (ADS)

Lera, Natalia; Alvarez, J. V.

2018-04-01

We study linear vibrational modes in finite isostatic Maxwell lattices, mechanical systems where the number of degrees of freedom matches the number of constraints. Recent progress in topological mechanics exploits the nontrivial topology of BDI class Hamiltonians in one dimenson and arising topological floppy modes at the edges. A finite frame, or zero-dimensional system, also exhibits a nonzero topological index according to the classification table. We construct mechanical insulating models in zero dimensions that complete the BDI classification in the available real space dimensions. We compute and interpret its nontrivial invariant Z2.

Preliminary study of the use of the STAR-100 computer for transonic flow calculations

NASA Technical Reports Server (NTRS)

Keller, J. D.; Jameson, A.

1977-01-01

An explicit method for solving the transonic small-disturbance potential equation is presented. This algorithm, which is suitable for the new vector-processor computers such as the CDC STAR-100, is compared to successive line over-relaxation (SLOR) on a simple test problem. The convergence rate of the explicit scheme is slower than that of SLOR, however, the efficiency of the explicit scheme on the STAR-100 computer is sufficient to overcome the slower convergence rate and allow an overall speedup compared to SLOR on the CYBER 175 computer.

Towards building a robust computational framework to simulate multi-physics problems - a solution technique for three-phase (gas-liquid-solid) interactions

NASA Astrophysics Data System (ADS)

Zhang, Lucy

In this talk, we show a robust numerical framework to model and simulate gas-liquid-solid three-phase flows. The overall algorithm adopts a non-boundary-fitted approach that avoids frequent mesh-updating procedures by defining independent meshes and explicit interfacial points to represent each phase. In this framework, we couple the immersed finite element method (IFEM) and the connectivity-free front tracking (CFFT) method that model fluid-solid and gas-liquid interactions, respectively, for the three-phase models. The CFFT is used here to simulate gas-liquid multi-fluid flows that uses explicit interfacial points to represent the gas-liquid interface and for its easy handling of interface topology changes. Instead of defining different levels simultaneously as used in level sets, an indicator function naturally couples the two methods together to represent and track each of the three phases. Several 2-D and 3-D testing cases are performed to demonstrate the robustness and capability of the coupled numerical framework in dealing with complex three-phase problems, in particular free surfaces interacting with deformable solids. The solution technique offers accuracy and stability, which provides a means to simulate various engineering applications. The author would like to acknowledge the supports from NIH/DHHS R01-2R01DC005642-10A1 and the National Natural Science Foundation of China (NSFC) 11550110185.

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

PubMed

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

2016-01-01

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

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

Numerical simulation of phase transition problems with explicit interface tracking

DOE PAGES

Hu, Yijing; Shi, Qiangqiang; de Almeida, Valmor F.; ...

2015-12-19

Phase change is ubiquitous in nature and industrial processes. Started from the Stefan problem, it is a topic with a long history in applied mathematics and sciences and continues to generate outstanding mathematical problems. For instance, the explicit tracking of the Gibbs dividing surface between phases is still a grand challenge. Our work has been motivated by such challenge and here we report on progress made in solving the governing equations of continuum transport in the presence of a moving interface by the front tracking method. The most pressing issue is the accounting of topological changes suffered by the interfacemore » between phases wherein break up and/or merge takes place. The underlying physics of topological changes require the incorporation of space-time subscales not at reach at the moment. Therefore we use heuristic geometrical arguments to reconnect phases in space. This heuristic approach provides new insight in various applications and it is extensible to include subscale physics and chemistry in the future. We demonstrate the method on applications such as simulating freezing, melting, dissolution, and precipitation. The later examples also include the coupling of the phase transition solution with the Navier-Stokes equations for the effect of flow convection.« less

Wide baseline stereo matching based on double topological relationship consistency

NASA Astrophysics Data System (ADS)

Zou, Xiaohong; Liu, Bin; Song, Xiaoxue; Liu, Yang

2009-07-01

Stereo matching is one of the most important branches in computer vision. In this paper, an algorithm is proposed for wide-baseline stereo vision matching. Here, a novel scheme is presented called double topological relationship consistency (DCTR). The combination of double topological configuration includes the consistency of first topological relationship (CFTR) and the consistency of second topological relationship (CSTR). It not only sets up a more advanced model on matching, but discards mismatches by iteratively computing the fitness of the feature matches and overcomes many problems of traditional methods depending on the powerful invariance to changes in the scale, rotation or illumination across large view changes and even occlusions. Experimental examples are shown where the two cameras have been located in very different orientations. Also, epipolar geometry can be recovered using RANSAC by far the most widely method adopted possibly. By the method, we can obtain correspondences with high precision on wide baseline matching problems. Finally, the effectiveness and reliability of this method are demonstrated in wide-baseline experiments on the image pairs.

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.

Qudit quantum computation on matrix product states with global symmetry

NASA Astrophysics Data System (ADS)

Wang, Dongsheng; Stephen, David; Raussendorf, Robert

Resource states that contain nontrivial symmetry-protected topological order are identified for universal measurement-based quantum computation. Our resource states fall into two classes: one as the qudit generalizations of the qubit cluster state, and the other as the higher-symmetry generalizations of the spin-1 Affleck-Kennedy-Lieb-Tasaki (AKLT) state, namely, with unitary, orthogonal, or symplectic symmetry. The symmetry in cluster states protects information propagation (identity gate), while the higher symmetry in AKLT-type states enables nontrivial gate computation. This work demonstrates a close connection between measurement-based quantum computation and symmetry-protected topological order.

Qudit quantum computation on matrix product states with global symmetry

NASA Astrophysics Data System (ADS)

Wang, Dong-Sheng; Stephen, David T.; Raussendorf, Robert

2017-03-01

Resource states that contain nontrivial symmetry-protected topological order are identified for universal single-qudit measurement-based quantum computation. Our resource states fall into two classes: one as the qudit generalizations of the one-dimensional qubit cluster state, and the other as the higher-symmetry generalizations of the spin-1 Affleck-Kennedy-Lieb-Tasaki (AKLT) state, namely, with unitary, orthogonal, or symplectic symmetry. The symmetry in cluster states protects information propagation (identity gate), while the higher symmetry in AKLT-type states enables nontrivial gate computation. This work demonstrates a close connection between measurement-based quantum computation and symmetry-protected topological order.

Computer calculation of Witten's 3-manifold invariant

NASA Astrophysics Data System (ADS)

Freed, Daniel S.; Gompf, Robert E.

1991-10-01

Witten's 2+1 dimensional Chern-Simons theory is exactly solvable. We compute the partition function, a topological invariant of 3-manifolds, on generalized Seifert spaces. Thus we test the path integral using the theory of 3-manifolds. In particular, we compare the exact solution with the asymptotic formula predicted by perturbation theory. We conclude that this path integral works as advertised and gives an effective topological invariant.

The topological Anderson insulator phase in the Kane-Mele model

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

PubMed Central

Deng, Nanjie; Zhang, Bin W.; Levy, Ronald M.

2015-01-01

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions and protein-ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ~3 kcal/mol at only ~8 % of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the explicit/implicit thermodynamic cycle. PMID:26236174

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

PubMed

Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

2015-06-09

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

On a canonical quantization of 3D Anti de Sitter pure gravity

NASA Astrophysics Data System (ADS)

Kim, Jihun; Porrati, Massimo

2015-10-01

We perform a canonical quantization of pure gravity on AdS 3 using as a technical tool its equivalence at the classical level with a Chern-Simons theory with gauge group SL(2,{R})× SL(2,{R}) . We first quantize the theory canonically on an asymptotically AdS space -which is topologically the real line times a Riemann surface with one connected boundary. Using the "constrain first" approach we reduce canonical quantization to quantization of orbits of the Virasoro group and Kähler quantization of Teichmüller space. After explicitly computing the Kähler form for the torus with one boundary component and after extending that result to higher genus, we recover known results, such as that wave functions of SL(2,{R}) Chern-Simons theory are conformal blocks. We find new restrictions on the Hilbert space of pure gravity by imposing invariance under large diffeomorphisms and normalizability of the wave function. The Hilbert space of pure gravity is shown to be the target space of Conformal Field Theories with continuous spectrum and a lower bound on operator dimensions. A projection defined by topology changing amplitudes in Euclidean gravity is proposed. It defines an invariant subspace that allows for a dual interpretation in terms of a Liouville CFT. Problems and features of the CFT dual are assessed and a new definition of the Hilbert space, exempt from those problems, is proposed in the case of highly-curved AdS 3.

Chiral topological phases from artificial neural networks

NASA Astrophysics Data System (ADS)

Kaubruegger, Raphael; Pastori, Lorenzo; Budich, Jan Carl

2018-05-01

Motivated by recent progress in applying techniques from the field of artificial neural networks (ANNs) to quantum many-body physics, we investigate to what extent the flexibility of ANNs can be used to efficiently study systems that host chiral topological phases such as fractional quantum Hall (FQH) phases. With benchmark examples, we demonstrate that training ANNs of restricted Boltzmann machine type in the framework of variational Monte Carlo can numerically solve FQH problems to good approximation. Furthermore, we show by explicit construction how n -body correlations can be kept at an exact level with ANN wave functions exhibiting polynomial scaling with power n in system size. Using this construction, we analytically represent the paradigmatic Laughlin wave function as an ANN state.

An efficient, explicit finite-rate algorithm to compute flows in chemical nonequilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

An explicit finite-rate code was developed to compute hypersonic viscous chemically reacting flows about three-dimensional bodies. Equations describing the finite-rate chemical reactions were fully coupled to the gas dynamic equations using a new coupling technique. The new technique maintains stability in the explicit finite-rate formulation while permitting relatively large global time steps.

Latent Computational Complexity of Symmetry-Protected Topological Order with Fractional Symmetry.

PubMed

Miller, Jacob; Miyake, Akimasa

2018-04-27

An emerging insight is that ground states of symmetry-protected topological orders (SPTOs) possess latent computational complexity in terms of their many-body entanglement. By introducing a fractional symmetry of SPTO, which requires the invariance under 3-colorable symmetries of a lattice, we prove that every renormalization fixed-point state of 2D (Z_{2})^{m} SPTO with fractional symmetry can be utilized for universal quantum computation using only Pauli measurements, as long as it belongs to a nontrivial 2D SPTO phase. Our infinite family of fixed-point states may serve as a base model to demonstrate the idea of a "quantum computational phase" of matter, whose states share universal computational complexity ubiquitously.

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

Architecture and data processing alternatives for the TSE computer. Volume 2: Extraction of topological information from an image by the Tse computer

NASA Technical Reports Server (NTRS)

Jones, J. R.; Bodenheimer, R. E.

1976-01-01

A simple programmable Tse processor organization and arithmetic operations necessary for extraction of the desired topological information are described. Hardware additions to this organization are discussed along with trade-offs peculiar to the tse computing concept. An improved organization is presented along with the complementary software for the various arithmetic operations. The performance of the two organizations is compared in terms of speed, power, and cost. Software routines developed to extract the desired information from an image are included.

Probing topology by "heating": Quantized circular dichroism in ultracold atoms.

PubMed

Tran, Duc Thanh; Dauphin, Alexandre; Grushin, Adolfo G; Zoller, Peter; Goldman, Nathan

2017-08-01

We reveal an intriguing manifestation of topology, which appears in the depletion rate of topological states of matter in response to an external drive. This phenomenon is presented by analyzing the response of a generic two-dimensional (2D) Chern insulator subjected to a circular time-periodic perturbation. Because of the system's chiral nature, the depletion rate is shown to depend on the orientation of the circular shake; taking the difference between the rates obtained from two opposite orientations of the drive, and integrating over a proper drive-frequency range, provides a direct measure of the topological Chern number (ν) of the populated band: This "differential integrated rate" is directly related to the strength of the driving field through the quantized coefficient η 0 = ν/ ℏ 2 , where h = 2π ℏ is Planck's constant. Contrary to the integer quantum Hall effect, this quantized response is found to be nonlinear with respect to the strength of the driving field, and it explicitly involves interband transitions. We investigate the possibility of probing this phenomenon in ultracold gases and highlight the crucial role played by edge states in this effect. We extend our results to 3D lattices, establishing a link between depletion rates and the nonlinear photogalvanic effect predicted for Weyl semimetals. The quantized circular dichroism revealed in this work designates depletion rate measurements as a universal probe for topological order in quantum matter.

Black holes in quasi-topological gravity and conformal couplings

NASA Astrophysics Data System (ADS)

Chernicoff, Mariano; Fierro, Octavio; Giribet, Gaston; Oliva, Julio

2017-02-01

Lovelock theory of gravity provides a tractable model to investigate the effects of higher-curvature terms in the context of AdS/CFT. Yielding second order, ghost-free field equations, this theory represents a minimal setup in which higher-order gravitational couplings in asymptotically Anti-de Sitter (AdS) spaces, including black holes, can be solved analytically. This however has an obvious limitation as in dimensions lower than seven, the contribution from cubic or higher curvature terms is merely topological. Therefore, in order to go beyond quadratic order and study higher terms in AdS5 analytically, one is compelled to look for other toy models. One such model is the so-called quasi-topological gravity, which, despite being a higher-derivative theory, provides a tractable setup with R 3 and R 4 terms. In this paper, we investigate AdS5 black holes in quasi-topological gravity. We consider the theory conformally coupled to matter and in presence of Abelian gauge fields. We show that charged black holes in AdS5 which, in addition, exhibit a backreaction of the matter fields on the geometry can be found explicitly in this theory. These solutions generalize the black hole solution of quasi-topological gravity and exist in a region of the parameter spaces consistent with the constraints coming from causality and other consistency conditions. They have finite conserved charges and exhibit non-trivial thermodynamical properties.

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

Correlated spin currents generated by resonant-crossed Andreev reflections in topological superconductors

PubMed Central

He, James J.; Wu, Jiansheng; Choy, Ting-Pong; Liu, Xiong-Jun; Tanaka, Y.; Law, K. T.

2014-01-01

Topological superconductors, which support Majorana fermion excitations, have been the subject of intense studies due to their novel transport properties and their potential applications in fault-tolerant quantum computations. Here we propose a new type of topological superconductors that can be used as a novel source of correlated spin currents. We show that inducing superconductivity on a AIII class topological insulator wire, which respects a chiral symmetry and supports protected fermionic end states, will result in a topological superconductor. This topological superconductor supports two topological phases with one or two Majorana fermion end states, respectively. In the phase with two Majorana fermions, the superconductor can split Cooper pairs efficiently into electrons in two spatially separated leads due to Majorana-induced resonant-crossed Andreev reflections. The resulting currents in the leads are correlated and spin-polarized. Importantly, the proposed topological superconductors can be realized using quantum anomalous Hall insulators in proximity to superconductors. PMID:24492649

On the Certain Topological Indices of Titania Nanotube TiO2[m, n

NASA Astrophysics Data System (ADS)

Javaid, M.; Liu, Jia-Bao; Rehman, M. A.; Wang, Shaohui

2017-07-01

A numeric quantity that characterises the whole structure of a molecular graph is called the topological index that predicts the physical features, chemical reactivities, and boiling activities of the involved chemical compound in the molecular graph. In this article, we give new mathematical expressions for the multiple Zagreb indices, the generalised Zagreb index, the fourth version of atom-bond connectivity (ABC4) index, and the fifth version of geometric-arithmetic (GA5) index of TiO2[m, n]. In addition, we compute the latest developed topological index called by Sanskruti index. At the end, a comparison is also included to estimate the efficiency of the computed indices. Our results extended some known conclusions.

Robust quantum network architectures and topologies for entanglement distribution

NASA Astrophysics Data System (ADS)

Das, Siddhartha; Khatri, Sumeet; Dowling, Jonathan P.

2018-01-01

Entanglement distribution is a prerequisite for several important quantum information processing and computing tasks, such as quantum teleportation, quantum key distribution, and distributed quantum computing. In this work, we focus on two-dimensional quantum networks based on optical quantum technologies using dual-rail photonic qubits for the building of a fail-safe quantum internet. We lay out a quantum network architecture for entanglement distribution between distant parties using a Bravais lattice topology, with the technological constraint that quantum repeaters equipped with quantum memories are not easily accessible. We provide a robust protocol for simultaneous entanglement distribution between two distant groups of parties on this network. We also discuss a memory-based quantum network architecture that can be implemented on networks with an arbitrary topology. We examine networks with bow-tie lattice and Archimedean lattice topologies and use percolation theory to quantify the robustness of the networks. In particular, we provide figures of merit on the loss parameter of the optical medium that depend only on the topology of the network and quantify the robustness of the network against intermittent photon loss and intermittent failure of nodes. These figures of merit can be used to compare the robustness of different network topologies in order to determine the best topology in a given real-world scenario, which is critical in the realization of the quantum internet.

Computationally designed lattices with tuned properties for tissue engineering using 3D printing

PubMed Central

Gonella, Veronica C.; Engensperger, Max; Ferguson, Stephen J.; Shea, Kristina

2017-01-01

Tissue scaffolds provide structural support while facilitating tissue growth, but are challenging to design due to diverse property trade-offs. Here, a computational approach was developed for modeling scaffolds with lattice structures of eight different topologies and assessing properties relevant to bone tissue engineering applications. Evaluated properties include porosity, pore size, surface-volume ratio, elastic modulus, shear modulus, and permeability. Lattice topologies were generated by patterning beam-based unit cells, with design parameters for beam diameter and unit cell length. Finite element simulations were conducted for each topology and quantified how elastic modulus and shear modulus scale with porosity, and how permeability scales with porosity cubed over surface-volume ratio squared. Lattices were compared with controlled properties related to porosity and pore size. Relative comparisons suggest that lattice topology leads to specializations in achievable properties. For instance, Cube topologies tend to have high elastic and low shear moduli while Octet topologies have high shear moduli and surface-volume ratios but low permeability. The developed method was utilized to analyze property trade-offs as beam diameter was altered for a given topology, and used to prototype a 3D printed lattice embedded in an interbody cage for spinal fusion treatments. Findings provide a basis for modeling and understanding relative differences among beam-based lattices designed to facilitate bone tissue growth. PMID:28797066

Computationally designed lattices with tuned properties for tissue engineering using 3D printing.

PubMed

Egan, Paul F; Gonella, Veronica C; Engensperger, Max; Ferguson, Stephen J; Shea, Kristina

2017-01-01

Tissue scaffolds provide structural support while facilitating tissue growth, but are challenging to design due to diverse property trade-offs. Here, a computational approach was developed for modeling scaffolds with lattice structures of eight different topologies and assessing properties relevant to bone tissue engineering applications. Evaluated properties include porosity, pore size, surface-volume ratio, elastic modulus, shear modulus, and permeability. Lattice topologies were generated by patterning beam-based unit cells, with design parameters for beam diameter and unit cell length. Finite element simulations were conducted for each topology and quantified how elastic modulus and shear modulus scale with porosity, and how permeability scales with porosity cubed over surface-volume ratio squared. Lattices were compared with controlled properties related to porosity and pore size. Relative comparisons suggest that lattice topology leads to specializations in achievable properties. For instance, Cube topologies tend to have high elastic and low shear moduli while Octet topologies have high shear moduli and surface-volume ratios but low permeability. The developed method was utilized to analyze property trade-offs as beam diameter was altered for a given topology, and used to prototype a 3D printed lattice embedded in an interbody cage for spinal fusion treatments. Findings provide a basis for modeling and understanding relative differences among beam-based lattices designed to facilitate bone tissue growth.

Non-perturbative effects and wall-crossing from topological strings

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

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

NASA Astrophysics Data System (ADS)

Wiegmann, P. B.

1999-06-01

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

Topological mirror superconductivity.

PubMed

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

2013-08-02

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

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

PubMed

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

2016-11-14

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

Ring-array processor distribution topology for optical interconnects

NASA Technical Reports Server (NTRS)

Li, Yao; Ha, Berlin; Wang, Ting; Wang, Sunyu; Katz, A.; Lu, X. J.; Kanterakis, E.

1992-01-01

The existing linear and rectangular processor distribution topologies for optical interconnects, although promising in many respects, cannot solve problems such as clock skews, the lack of supporting elements for efficient optical implementation, etc. The use of a ring-array processor distribution topology, however, can overcome these problems. Here, a study of the ring-array topology is conducted with an aim of implementing various fast clock rate, high-performance, compact optical networks for digital electronic multiprocessor computers. Practical design issues are addressed. Some proof-of-principle experimental results are included.

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

USGS Publications Warehouse

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

1985-01-01

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

Topological quantum error correction in the Kitaev honeycomb model

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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.

On exact correlation functions of chiral ring operators in 2 d N=(2, 2) SCFTs via localization

NASA Astrophysics Data System (ADS)

Chen, Jin

2018-03-01

We study the extremal correlation functions of (twisted) chiral ring operators via superlocalization in N=(2, 2) superconformal field theories (SCFTs) with central charge c ≥ 3, especially for SCFTs with Calabi-Yau geometric phases. We extend the method in arXiv: 1602.05971 with mild modifications, so that it is applicable to disentangle operators mixing on S 2 in nilpotent (twisted) chiral rings of 2 d SCFTs. With the extended algorithm and technique of localization, we compute exactly the extremal correlators in 2 d N=(2, 2) (twisted) chiral rings as non-holomorphic functions of marginal parameters of the theories. Especially in the context of Calabi-Yau geometries, we give an explicit geometric interpretation to our algorithm as the Griffiths transversality with projection on the Hodge bundle over Calabi-Yau complex moduli. We also apply the method to compute extremal correlators in Kähler moduli, or say twisted chiral rings, of several interesting Calabi-Yau manifolds. In the case of complete intersections in toric varieties, we provide an alternative formalism for extremal correlators via localization onto Higgs branch. In addition, as a spinoff we find that, from the extremal correlators of the top element in twisted chiral rings, one can extract chiral correlators in A-twisted topological theories.

Discrete modes of social information processing predict individual behavior of fish in a group

PubMed Central

Harpaz, Roy; Tkačik, Gašper

2017-01-01

Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multimodal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species. PMID:28874581

Integrability and Linear Stability of Nonlinear Waves

NASA Astrophysics Data System (ADS)

Degasperis, Antonio; Lombardo, Sara; Sommacal, Matteo

2018-03-01

It is well known that the linear stability of solutions of 1+1 partial differential equations which are integrable can be very efficiently investigated by means of spectral methods. We present here a direct construction of the eigenmodes of the linearized equation which makes use only of the associated Lax pair with no reference to spectral data and boundary conditions. This local construction is given in the general N× N matrix scheme so as to be applicable to a large class of integrable equations, including the multicomponent nonlinear Schrödinger system and the multiwave resonant interaction system. The analytical and numerical computations involved in this general approach are detailed as an example for N=3 for the particular system of two coupled nonlinear Schrödinger equations in the defocusing, focusing and mixed regimes. The instabilities of the continuous wave solutions are fully discussed in the entire parameter space of their amplitudes and wave numbers. By defining and computing the spectrum in the complex plane of the spectral variable, the eigenfrequencies are explicitly expressed. According to their topological properties, the complete classification of these spectra in the parameter space is presented and graphically displayed. The continuous wave solutions are linearly unstable for a generic choice of the coupling constants.

Look and Feel: Haptic Interaction for Biomedicine

DTIC Science & Technology

1995-10-01

algorithm that is evaluated within the topology of the model. During each time step, forces are summed for each mobile atom based on external forces...volumetric properties; (b) conserving computation power by rendering media local to the interaction point; and (c) evaluating the simulation within...alteration of the model topology. Simulation of the DSM state is accomplished by a multi-step algorithm that is evaluated within the topology of the

Harmonic spinors on a family of Einstein manifolds

NASA Astrophysics Data System (ADS)

Franchetti, Guido

2018-06-01

The purpose of this paper is to study harmonic spinors defined on a 1-parameter family of Einstein manifolds which includes Taub–NUT, Eguchi–Hanson and with the Fubini–Study metric as particular cases. We discuss the existence of and explicitly solve for spinors harmonic with respect to the Dirac operator twisted by a geometrically preferred connection. The metrics examined are defined, for generic values of the parameter, on a non-compact manifold with the topology of and extend to as edge-cone metrics. As a consequence, the subtle boundary conditions of the Atiyah–Patodi–Singer index theorem need to be carefully considered in order to show agreement between the index of the twisted Dirac operator and the result obtained by counting the explicit solutions.

The integrable case of Adler-van Moerbeke. Discriminant set and bifurcation diagram

NASA Astrophysics Data System (ADS)

Ryabov, Pavel E.; Oshemkov, Andrej A.; Sokolov, Sergei V.

2016-09-01

The Adler-van Moerbeke integrable case of the Euler equations on the Lie algebra so(4) is investigated. For the L- A pair found by Reyman and Semenov-Tian-Shansky for this system, we explicitly present a spectral curve and construct the corresponding discriminant set. The singularities of the Adler-van Moerbeke integrable case and its bifurcation diagram are discussed. We explicitly describe singular points of rank 0, determine their types, and show that the momentum mapping takes them to self-intersection points of the real part of the discriminant set. In particular, the described structure of singularities of the Adler-van Moerbeke integrable case shows that it is topologically different from the other known integrable cases on so(4).

A framework for analyzing contagion in assortative banking networks

PubMed Central

Hurd, Thomas R.; Gleeson, James P.; Melnik, Sergey

2017-01-01

We introduce a probabilistic framework that represents stylized banking networks with the aim of predicting the size of contagion events. Most previous work on random financial networks assumes independent connections between banks, whereas our framework explicitly allows for (dis)assortative edge probabilities (i.e., a tendency for small banks to link to large banks). We analyze default cascades triggered by shocking the network and find that the cascade can be understood as an explicit iterated mapping on a set of edge probabilities that converges to a fixed point. We derive a cascade condition, analogous to the basic reproduction number R0 in epidemic modelling, that characterizes whether or not a single initially defaulted bank can trigger a cascade that extends to a finite fraction of the infinite network. This cascade condition is an easily computed measure of the systemic risk inherent in a given banking network topology. We use percolation theory for random networks to derive a formula for the frequency of global cascades. These analytical results are shown to provide limited quantitative agreement with Monte Carlo simulation studies of finite-sized networks. We show that edge-assortativity, the propensity of nodes to connect to similar nodes, can have a strong effect on the level of systemic risk as measured by the cascade condition. However, the effect of assortativity on systemic risk is subtle, and we propose a simple graph theoretic quantity, which we call the graph-assortativity coefficient, that can be used to assess systemic risk. PMID:28231324

A framework for analyzing contagion in assortative banking networks.

PubMed

Hurd, Thomas R; Gleeson, James P; Melnik, Sergey

2017-01-01

We introduce a probabilistic framework that represents stylized banking networks with the aim of predicting the size of contagion events. Most previous work on random financial networks assumes independent connections between banks, whereas our framework explicitly allows for (dis)assortative edge probabilities (i.e., a tendency for small banks to link to large banks). We analyze default cascades triggered by shocking the network and find that the cascade can be understood as an explicit iterated mapping on a set of edge probabilities that converges to a fixed point. We derive a cascade condition, analogous to the basic reproduction number R0 in epidemic modelling, that characterizes whether or not a single initially defaulted bank can trigger a cascade that extends to a finite fraction of the infinite network. This cascade condition is an easily computed measure of the systemic risk inherent in a given banking network topology. We use percolation theory for random networks to derive a formula for the frequency of global cascades. These analytical results are shown to provide limited quantitative agreement with Monte Carlo simulation studies of finite-sized networks. We show that edge-assortativity, the propensity of nodes to connect to similar nodes, can have a strong effect on the level of systemic risk as measured by the cascade condition. However, the effect of assortativity on systemic risk is subtle, and we propose a simple graph theoretic quantity, which we call the graph-assortativity coefficient, that can be used to assess systemic risk.

Shape Optimization by Bayesian-Validated Computer-Simulation Surrogates

NASA Technical Reports Server (NTRS)

Patera, Anthony T.

1997-01-01

A nonparametric-validated, surrogate approach to optimization has been applied to the computational optimization of eddy-promoter heat exchangers and to the experimental optimization of a multielement airfoil. In addition to the baseline surrogate framework, a surrogate-Pareto framework has been applied to the two-criteria, eddy-promoter design problem. The Pareto analysis improves the predictability of the surrogate results, preserves generality, and provides a means to rapidly determine design trade-offs. Significant contributions have been made in the geometric description used for the eddy-promoter inclusions as well as to the surrogate framework itself. A level-set based, geometric description has been developed to define the shape of the eddy-promoter inclusions. The level-set technique allows for topology changes (from single-body,eddy-promoter configurations to two-body configurations) without requiring any additional logic. The continuity of the output responses for input variations that cross the boundary between topologies has been demonstrated. Input-output continuity is required for the straightforward application of surrogate techniques in which simplified, interpolative models are fitted through a construction set of data. The surrogate framework developed previously has been extended in a number of ways. First, the formulation for a general, two-output, two-performance metric problem is presented. Surrogates are constructed and validated for the outputs. The performance metrics can be functions of both outputs, as well as explicitly of the inputs, and serve to characterize the design preferences. By segregating the outputs and the performance metrics, an additional level of flexibility is provided to the designer. The validated outputs can be used in future design studies and the error estimates provided by the output validation step still apply, and require no additional appeals to the expensive analysis. Second, a candidate-based a posteriori error analysis capability has been developed which provides probabilistic error estimates on the true performance for a design randomly selected near the surrogate-predicted optimal design.

One-Loop Test of Quantum Black Holes in anti–de Sitter Space

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

Liu, James T.; Pando Zayas, Leopoldo A.; Rathee, Vimal

Within 11-dimensional supergravity we compute the logarithmic correction to the entropy of magnetically charged asymptotically AdS4 black holes with arbitrary horizon topology. We find perfect agreement with the expected microscopic result arising from the dual field theory computation of the topologically twisted index. Our result relies crucially on a particular limit to the extremal black hole case and clarifies some aspects of quantum corrections in asymptotically AdS spacetimes.

One-Loop Test of Quantum Black Holes in anti–de Sitter Space

DOE PAGES

Liu, James T.; Pando Zayas, Leopoldo A.; Rathee, Vimal; ...

2018-06-01

Within 11-dimensional supergravity we compute the logarithmic correction to the entropy of magnetically charged asymptotically AdS4 black holes with arbitrary horizon topology. We find perfect agreement with the expected microscopic result arising from the dual field theory computation of the topologically twisted index. Our result relies crucially on a particular limit to the extremal black hole case and clarifies some aspects of quantum corrections in asymptotically AdS spacetimes.

One-Loop Test of Quantum Black Holes in anti-de Sitter Space

NASA Astrophysics Data System (ADS)

Liu, James T.; Pando Zayas, Leopoldo A.; Rathee, Vimal; Zhao, Wenli

2018-06-01

Within 11-dimensional supergravity we compute the logarithmic correction to the entropy of magnetically charged asymptotically AdS4 black holes with arbitrary horizon topology. We find perfect agreement with the expected microscopic result arising from the dual field theory computation of the topologically twisted index. Our result relies crucially on a particular limit to the extremal black hole case and clarifies some aspects of quantum corrections in asymptotically AdS spacetimes.

One-Loop Test of Quantum Black Holes in anti-de Sitter Space.

PubMed

Liu, James T; Pando Zayas, Leopoldo A; Rathee, Vimal; Zhao, Wenli

2018-06-01

Within 11-dimensional supergravity we compute the logarithmic correction to the entropy of magnetically charged asymptotically AdS_{4} black holes with arbitrary horizon topology. We find perfect agreement with the expected microscopic result arising from the dual field theory computation of the topologically twisted index. Our result relies crucially on a particular limit to the extremal black hole case and clarifies some aspects of quantum corrections in asymptotically AdS spacetimes.

Acoustic frequency filter based on anisotropic topological phononic crystals.

PubMed

Chen, Ze-Guo; Zhao, Jiajun; Mei, Jun; Wu, Ying

2017-11-08

We present a design of acoustic frequency filter based on a two-dimensional anisotropic phononic crystal. The anisotropic band structure exhibits either a directional or a combined (global + directional) bandgap at certain frequency regions, depending on the geometry. When the time-reversal symmetry is broken, it may introduce a topologically nontrivial bandgap. The induced nontrivial bandgap and the original directional bandgap result in various interesting wave propagation behaviors, such as frequency filter. We develop a tight-binding model to characterize the effective Hamiltonian of the system, from which the contribution of anisotropy is explicitly shown. Different from the isotropic cases, the Zeeman-type splitting is not linear and the anisotropic bandgap makes it possible to achieve anisotropic propagation characteristics along different directions and at different frequencies.

Quantized charge transport in chiral Majorana edge modes

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Conjugate gradient based projection - A new explicit methodology for frictional contact

NASA Technical Reports Server (NTRS)

Tamma, Kumar K.; Li, Maocheng; Sha, Desong

1993-01-01

With special attention towards the applicability to parallel computation or vectorization, a new and effective explicit approach for linear complementary formulations involving a conjugate gradient based projection methodology is proposed in this study for contact problems with Coulomb friction. The overall objectives are focussed towards providing an explicit methodology of computation for the complete contact problem with friction. In this regard, the primary idea for solving the linear complementary formulations stems from an established search direction which is projected to a feasible region determined by the non-negative constraint condition; this direction is then applied to the Fletcher-Reeves conjugate gradient method resulting in a powerful explicit methodology which possesses high accuracy, excellent convergence characteristics, fast computational speed and is relatively simple to implement for contact problems involving Coulomb friction.

Magnon Hall effect on the Lieb lattice.

PubMed

Cao, Xiaodong; Chen, Kai; He, Dahai

2015-04-29

Ferromagnetic insulators without inversion symmetry may show magnon Hall effect (MHE) in the presence of a temperature gradient due to the existence of Dzyaloshinskii-Moriya interaction (DMI). In this theoretical study, we investigate MHE on a lattice with inversion symmetry, namely the Lieb lattice, where the DMI is introduced by adding an external electric field. We show the nontrivial topology of this model by examining the existence of edge states and computing the topological phase diagram characterized by the Chern numbers of different bands. Together with the topological phase diagram, we can further determine the sign and magnitude of the transverse thermal conductivity. The impact of the flat band possessed by this model on the thermal conductivity is discussed by computing the Berry curvature analytically.

Structure of the entanglement entropy of (3+1)-dimensional gapped phases of matter

NASA Astrophysics Data System (ADS)

Zheng, Yunqin; He, Huan; Bradlyn, Barry; Cano, Jennifer; Neupert, Titus; Bernevig, B. Andrei

2018-05-01

We study the entanglement entropy of gapped phases of matter in three spatial dimensions. We focus in particular on size-independent contributions to the entropy across entanglement surfaces of arbitrary topologies. We show that for low energy fixed-point theories, the constant part of the entanglement entropy across any surface can be reduced to a linear combination of the entropies across a sphere and a torus. We first derive our results using strong sub-additivity inequalities along with assumptions about the entanglement entropy of fixed-point models, and identify the topological contribution by considering the renormalization group flow; in this way we give an explicit definition of topological entanglement entropy Stopo in (3+1)D, which sharpens previous results. We illustrate our results using several concrete examples and independent calculations, and show adding "twist" terms to the Lagrangian can change Stopo in (3+1)D. For the generalized Walker-Wang models, we find that the ground state degeneracy on a 3-torus is given by exp(-3 Stopo[T2] ) in terms of the topological entanglement entropy across a 2-torus. We conjecture that a similar relationship holds for Abelian theories in (d +1 ) dimensional spacetime, with the ground state degeneracy on the d -torus given by exp(-d Stopo[Td -1] ) .

Exotic dark spinor fields

NASA Astrophysics Data System (ADS)

Da Rocha, Roldão; Bernardini, Alex E.; da Silva, J. M. Hoff

2011-04-01

Exotic dark spinor fields are introduced and investigated in the context of inequivalent spin structures on arbitrary curved spacetimes, which induces an additional term on the associated Dirac operator, related to a Čech cohomology class. For the most kinds of spinor fields, any exotic term in the Dirac operator can be absorbed and encoded as a shift of the electromagnetic vector potential representing an element of the cohomology group {H^1}( {M,{{Z}_2}} ) . The possibility of concealing such an exotic term does not exist in case of dark (ELKO) spinor fields, as they cannot carry electromagnetic charge, so that the full topological analysis must be evaluated. Since exotic dark spinor fields also satisfy Klein-Gordon propagators, the dynamical constraints related to the exotic term in the Dirac equation can be explicitly calculated. It forthwith implies that the non-trivial topology associated to the spacetime can drastically engender — from the dynamics of dark spinor fields — constraints in the spacetime metric structure. Meanwhile, such constraints may be alleviated, at the cost of constraining the exotic spacetime topology. Besides being prime candidates to the dark matter problem, dark spinor fields are shown to be potential candidates to probe non-trivial topologies in spacetime, as well as probe the spacetime metric structure.

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

Topologically Guided, Automated Construction of Metal–Organic Frameworks and Their Evaluation for Energy-Related Applications

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

Colón, Yamil J.; Gómez-Gualdrón, Diego A.; Snurr, Randall Q.

Metal-organic frameworks (MOFs) are promising materials for a range of energy and environmental applications. Here we describe in detail a computational algorithm and code to generate MOFs based on edge-transitive topological nets for subsequent evaluation via molecular simulation. This algorithm has been previously used by us to construct and evaluate 13 512 MOFs of 41 different topologies for cryo-adsorbed hydrogen storage. Grand canonical Monte Carlo simulations are used here to evaluate the 13 512 structures for the storage of gaseous fuels such as hydrogen and methane and nondistillative separation of xenon/krypton mixtures at various operating conditions. MOF performance for bothmore » gaseous fuel storage and xenon/krypton separation is influenced by topology. Simulation data suggest that gaseous fuel storage performance is topology-dependent due to MOF properties such as void fraction and surface area combining differently in different topologies, whereas xenon/krypton separation performance is topology-dependent due to how topology constrains the pore size distribution.« less

Sensitivity of quantum walks to a boundary of two-dimensional lattices: approaches based on the CGMV method and topological phases

NASA Astrophysics Data System (ADS)

Endo, Takako; Konno, Norio; Obuse, Hideaki; Segawa, Etsuo

2017-11-01

In this paper, we treat quantum walks in a two-dimensional lattice with cutting edges along a straight boundary introduced by Asboth and Edge (2015 Phys. Rev. A 91 022324) in order to study one-dimensional edge states originating from topological phases of matter and to obtain collateral evidence of how a quantum walker reacts to the boundary. Firstly, we connect this model to the CMV matrix, which provides a 5-term recursion relation of the Laurent polynomial associated with spectral measure on the unit circle. Secondly, we explicitly derive the spectra of bulk and edge states of the quantum walk with the boundary using spectral analysis of the CMV matrix. Thirdly, while topological numbers of the model studied so far are well-defined only when gaps in the bulk spectrum exist, we find a new topological number defined only when there are no gaps in the bulk spectrum. We confirm that the existence of the spectrum for edge states derived from the CMV matrix is consistent with the prediction from a bulk-edge correspondence using topological numbers calculated in the cases where gaps in the bulk spectrum do or do not exist. Finally, we show how the edge states contribute to the asymptotic behavior of the quantum walk through limit theorems of the finding probability. Conversely, we also propose a differential equation using this limit distribution whose solution is the underlying edge state.

Probing topology by “heating”: Quantized circular dichroism in ultracold atoms

PubMed Central

Tran, Duc Thanh; Dauphin, Alexandre; Grushin, Adolfo G.; Zoller, Peter; Goldman, Nathan

2017-01-01

We reveal an intriguing manifestation of topology, which appears in the depletion rate of topological states of matter in response to an external drive. This phenomenon is presented by analyzing the response of a generic two-dimensional (2D) Chern insulator subjected to a circular time-periodic perturbation. Because of the system’s chiral nature, the depletion rate is shown to depend on the orientation of the circular shake; taking the difference between the rates obtained from two opposite orientations of the drive, and integrating over a proper drive-frequency range, provides a direct measure of the topological Chern number (ν) of the populated band: This “differential integrated rate” is directly related to the strength of the driving field through the quantized coefficient η0 = ν/ℏ2, where h = 2π ℏ is Planck’s constant. Contrary to the integer quantum Hall effect, this quantized response is found to be nonlinear with respect to the strength of the driving field, and it explicitly involves interband transitions. We investigate the possibility of probing this phenomenon in ultracold gases and highlight the crucial role played by edge states in this effect. We extend our results to 3D lattices, establishing a link between depletion rates and the nonlinear photogalvanic effect predicted for Weyl semimetals. The quantized circular dichroism revealed in this work designates depletion rate measurements as a universal probe for topological order in quantum matter. PMID:28835930

Universal measurement-based quantum computation in two-dimensional symmetry-protected topological phases

NASA Astrophysics Data System (ADS)

Wei, Tzu-Chieh; Huang, Ching-Yu

2017-09-01

Recent progress in the characterization of gapped quantum phases has also triggered the search for a universal resource for quantum computation in symmetric gapped phases. Prior works in one dimension suggest that it is a feature more common than previously thought, in that nontrivial one-dimensional symmetry-protected topological (SPT) phases provide quantum computational power characterized by the algebraic structure defining these phases. Progress in two and higher dimensions so far has been limited to special fixed points. Here we provide two families of two-dimensional Z2 symmetric wave functions such that there exists a finite region of the parameter in the SPT phases that supports universal quantum computation. The quantum computational power appears to lose its universality at the boundary between the SPT and the symmetry-breaking phases.

Two-dimensional topological crystalline insulator phase in Sb/Bi planar honeycomb with tunable Dirac gap

DOE PAGES

Hsu, Chia -Hsiu; Huang, Zhi -Quan; Crisostomo, Christian P.; ...

2016-01-14

We predict planar Sb/Bi honeycomb to harbor a two-dimensional (2D) topological crystalline insulator (TCI) phase based on first-principles computations. Although buckled Sb and Bi honeycombs support 2D topological insulator (TI) phases, their structure becomes planar under tensile strain. The planar Sb/Bi honeycomb structure restores the mirror symmetry, and is shown to exhibit non-zero mirror Chern numbers, indicating that the system can host topologically protected edge states. Our computations show that the electronic spectrum of a planar Sb/Bi nanoribbon with armchair or zigzag edges contains two Dirac cones within the band gap and an even number of edge bands crossing themore » Fermi level. Lattice constant of the planar Sb honeycomb is found to nearly match that of hexagonal-BN. As a result, the Sb nanoribbon on hexagonal-BN exhibits gapped edge states, which we show to be tunable by an out-of the-plane electric field, providing controllable gating of edge state important for device applications.« less

Scalable designs for quasiparticle-poisoning-protected topological quantum computation with Majorana zero modes

NASA Astrophysics Data System (ADS)

Karzig, Torsten; Knapp, Christina; Lutchyn, Roman M.; Bonderson, Parsa; Hastings, Matthew B.; Nayak, Chetan; Alicea, Jason; Flensberg, Karsten; Plugge, Stephan; Oreg, Yuval; Marcus, Charles M.; Freedman, Michael H.

2017-06-01

We present designs for scalable quantum computers composed of qubits encoded in aggregates of four or more Majorana zero modes, realized at the ends of topological superconducting wire segments that are assembled into superconducting islands with significant charging energy. Quantum information can be manipulated according to a measurement-only protocol, which is facilitated by tunable couplings between Majorana zero modes and nearby semiconductor quantum dots. Our proposed architecture designs have the following principal virtues: (1) the magnetic field can be aligned in the direction of all of the topological superconducting wires since they are all parallel; (2) topological T junctions are not used, obviating possible difficulties in their fabrication and utilization; (3) quasiparticle poisoning is abated by the charging energy; (4) Clifford operations are executed by a relatively standard measurement: detection of corrections to quantum dot energy, charge, or differential capacitance induced by quantum fluctuations; (5) it is compatible with strategies for producing good approximate magic states.

On topological RNA interaction structures.

PubMed

Qin, Jing; Reidys, Christian M

2013-07-01

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

Topological quantum computation of the Dold-Thom functor

NASA Astrophysics Data System (ADS)

Ospina, Juan

2014-05-01

A possible topological quantum computation of the Dold-Thom functor is presented. The method that will be used is the following: a) Certain 1+1-topological quantum field theories valued in symmetric bimonoidal categories are converted into stable homotopical data, using a machinery recently introduced by Elmendorf and Mandell; b) we exploit, in this framework, two recent results (independent of each other) on refinements of Khovanov homology: our refinement into a module over the connective k-theory spectrum and a stronger result by Lipshitz and Sarkar refining Khovanov homology into a stable homotopy type; c) starting from the Khovanov homotopy the Dold-Thom functor is constructed; d) the full construction is formulated as a topological quantum algorithm. It is conjectured that the Jones polynomial can be described as the analytical index of certain Dirac operator defined in the context of the Khovanov homotopy using the Dold-Thom functor. As a line for future research is interesting to study the corresponding supersymmetric model for which the Khovanov-Dirac operator plays the role of a supercharge.

Expert knowledge elicitation using computer simulation: the organization of frail elderly case management as an illustration.

PubMed

Chiêm, Jean-Christophe; Van Durme, Thérèse; Vandendorpe, Florence; Schmitz, Olivier; Speybroeck, Niko; Cès, Sophie; Macq, Jean

2014-08-01

Various elderly case management projects have been implemented in Belgium. This type of long-term health care intervention involves contextual factors and human interactions. These underlying complex mechanisms can be usefully informed with field experts' knowledge, which are hard to make explicit. However, computer simulation has been suggested as one possible method of overcoming the difficulty of articulating such elicited qualitative views. A simulation model of case management was designed using an agent-based methodology, based on the initial qualitative research material. Variables and rules of interaction were formulated into a simple conceptual framework. This model has been implemented and was used as a support for a structured discussion with experts in case management. The rigorous formulation provided by the agent-based methodology clarified the descriptions of the interventions and the problems encountered regarding: the diverse network topologies of health care actors in the project; the adaptation time required by the intervention; the communication between the health care actors; the institutional context; the organization of the care; and the role of the case manager and his or hers personal ability to interpret the informal demands of the frail older person. The simulation model should be seen primarily as a tool for thinking and learning. A number of insights were gained as part of a valuable cognitive process. Computer simulation supporting field experts' elicitation can lead to better-informed decisions in the organization of complex health care interventions. © 2013 John Wiley & Sons, Ltd.

A well-posed numerical method to track isolated conformal map singularities in Hele-Shaw flow

NASA Technical Reports Server (NTRS)

Baker, Gregory; Siegel, Michael; Tanveer, Saleh

1995-01-01

We present a new numerical method for calculating an evolving 2D Hele-Shaw interface when surface tension effects are neglected. In the case where the flow is directed from the less viscous fluid into the more viscous fluid, the motion of the interface is ill-posed; small deviations in the initial condition will produce significant changes in the ensuing motion. This situation is disastrous for numerical computation, as small round-off errors can quickly lead to large inaccuracies in the computed solution. Our method of computation is most easily formulated using a conformal map from the fluid domain into a unit disk. The method relies on analytically continuing the initial data and equations of motion into the region exterior to the disk, where the evolution problem becomes well-posed. The equations are then numerically solved in the extended domain. The presence of singularities in the conformal map outside of the disk introduces specific structures along the fluid interface. Our method can explicitly track the location of isolated pole and branch point singularities, allowing us to draw connections between the development of interfacial patterns and the motion of singularities as they approach the unit disk. In particular, we are able to relate physical features such as finger shape, side-branch formation, and competition between fingers to the nature and location of the singularities. The usefulness of this method in studying the formation of topological singularities (self-intersections of the interface) is also pointed out.

The impact of cost and network topology on urban mobility: a study of public bicycle usage in 2 U.S. cities.

PubMed

Jurdak, Raja

2013-01-01

Understanding the drivers of urban mobility is vital for epidemiology, urban planning, and communication networks. Human movements have so far been studied by observing people's positions in a given space and time, though most recent models only implicitly account for expected costs and returns for movements. This paper explores the explicit impact of cost and network topology on mobility dynamics, using data from 2 city-wide public bicycle share systems in the USA. User mobility is characterized through the distribution of trip durations, while network topology is characterized through the pairwise distances between stations and the popularity of stations and routes. Despite significant differences in station density and physical layout between the 2 cities, trip durations follow remarkably similar distributions that exhibit cost sensitive trends around pricing point boundaries, particularly with long-term users of the system. Based on the results, recommendations for dynamic pricing and incentive schemes are provided to positively influence mobility patterns and guide improved planning and management of public bicycle systems to increase uptake.

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

NASA Astrophysics Data System (ADS)

Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

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

Portable computing for taking part of the lab to the sample types of applications. From hand held personal digital assistants to smart phones for mobile spectrometry

NASA Astrophysics Data System (ADS)

Weagant, Scott; Karanassios, Vassili

2015-06-01

The use of portable hand held computing devices for the acquisition of spectrochemical data is briefly discussed using examples from the author's laboratory. Several network topologies are evaluated. At present, one topology that involves a portable computing device for data acquisition and spectrometer control and that has wireless access to the internet at one end and communicates with a smart phone at the other end appears to be better suited for "taking part of the lab to the sample" types of applications. Thus, spectrometric data can be accessed from anywhere in the world.

Computation of entropy and Lyapunov exponent by a shift transform.

PubMed

Matsuoka, Chihiro; Hiraide, Koichi

2015-10-01

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

Computation of entropy and Lyapunov exponent by a shift transform

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

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

2015-10-15

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

ChemoPy: freely available python package for computational biology and chemoinformatics.

PubMed

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.

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.

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

PubMed Central

Olson, Mark A.

2017-01-01

Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution. PMID:28197405

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

PubMed

Olson, Mark A

2017-01-01

Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution.

A new heterogeneous asynchronous explicit-implicit time integrator for nonsmooth dynamics

NASA Astrophysics Data System (ADS)

Fekak, Fatima-Ezzahra; Brun, Michael; Gravouil, Anthony; Depale, Bruno

2017-07-01

In computational structural dynamics, particularly in the presence of nonsmooth behavior, the choice of the time-step and the time integrator has a critical impact on the feasibility of the simulation. Furthermore, in some cases, as in the case of a bridge crane under seismic loading, multiple time-scales coexist in the same problem. In that case, the use of multi-time scale methods is suitable. Here, we propose a new explicit-implicit heterogeneous asynchronous time integrator (HATI) for nonsmooth transient dynamics with frictionless unilateral contacts and impacts. Furthermore, we present a new explicit time integrator for contact/impact problems where the contact constraints are enforced using a Lagrange multiplier method. In other words, the aim of this paper consists in using an explicit time integrator with a fine time scale in the contact area for reproducing high frequency phenomena, while an implicit time integrator is adopted in the other parts in order to reproduce much low frequency phenomena and to optimize the CPU time. In a first step, the explicit time integrator is tested on a one-dimensional example and compared to Moreau-Jean's event-capturing schemes. The explicit algorithm is found to be very accurate and the scheme has generally a higher order of convergence than Moreau-Jean's schemes and provides also an excellent energy behavior. Then, the two time scales explicit-implicit HATI is applied to the numerical example of a bridge crane under seismic loading. The results are validated in comparison to a fine scale full explicit computation. The energy dissipated in the implicit-explicit interface is well controlled and the computational time is lower than a full-explicit simulation.

Accounting for small scale heterogeneity in ecohydrologic watershed models

NASA Astrophysics Data System (ADS)

Bhaskar, A.; Fleming, B.; Hogan, D. M.

2016-12-01

Spatially distributed ecohydrologic models are inherently constrained by the spatial resolution of their smallest units, below which land and processes are assumed to be homogenous. At coarse scales, heterogeneity is often accounted for by computing store and fluxes of interest over a distribution of land cover types (or other sources of heterogeneity) within spatially explicit modeling units. However this approach ignores spatial organization and the lateral transfer of water and materials downslope. The challenge is to account both for the role of flow network topology and fine-scale heterogeneity. We present a new approach that defines two levels of spatial aggregation and that integrates spatially explicit network approach with a flexible representation of finer-scale aspatial heterogeneity. Critically, this solution does not simply increase the resolution of the smallest spatial unit, and so by comparison, results in improved computational efficiency. The approach is demonstrated by adapting Regional Hydro-Ecologic Simulation System (RHESSys), an ecohydrologic model widely used to simulate climate, land use, and land management impacts. We illustrate the utility of our approach by showing how the model can be used to better characterize forest thinning impacts on ecohydrology. Forest thinning is typically done at the scale of individual trees, and yet management responses of interest include impacts on watershed scale hydrology and on downslope riparian vegetation. Our approach allow us to characterize the variability in tree size/carbon reduction and water transfers between neighboring trees while still capturing hillslope to watershed scale effects, Our illustrative example demonstrates that accounting for these fine scale effects can substantially alter model estimates, in some cases shifting the impacts of thinning on downslope water availability from increases to decreases. We conclude by describing other use cases that may benefit from this approach including characterizing urban vegetation and storm water management features and their impact on watershed scale hydrology and biogeochemical cycling.

Accounting for small scale heterogeneity in ecohydrologic watershed models

NASA Astrophysics Data System (ADS)

Burke, W.; Tague, C.

2017-12-01

Spatially distributed ecohydrologic models are inherently constrained by the spatial resolution of their smallest units, below which land and processes are assumed to be homogenous. At coarse scales, heterogeneity is often accounted for by computing store and fluxes of interest over a distribution of land cover types (or other sources of heterogeneity) within spatially explicit modeling units. However this approach ignores spatial organization and the lateral transfer of water and materials downslope. The challenge is to account both for the role of flow network topology and fine-scale heterogeneity. We present a new approach that defines two levels of spatial aggregation and that integrates spatially explicit network approach with a flexible representation of finer-scale aspatial heterogeneity. Critically, this solution does not simply increase the resolution of the smallest spatial unit, and so by comparison, results in improved computational efficiency. The approach is demonstrated by adapting Regional Hydro-Ecologic Simulation System (RHESSys), an ecohydrologic model widely used to simulate climate, land use, and land management impacts. We illustrate the utility of our approach by showing how the model can be used to better characterize forest thinning impacts on ecohydrology. Forest thinning is typically done at the scale of individual trees, and yet management responses of interest include impacts on watershed scale hydrology and on downslope riparian vegetation. Our approach allow us to characterize the variability in tree size/carbon reduction and water transfers between neighboring trees while still capturing hillslope to watershed scale effects, Our illustrative example demonstrates that accounting for these fine scale effects can substantially alter model estimates, in some cases shifting the impacts of thinning on downslope water availability from increases to decreases. We conclude by describing other use cases that may benefit from this approach including characterizing urban vegetation and storm water management features and their impact on watershed scale hydrology and biogeochemical cycling.

Lattice Supersymmetry and Order-Disorder Coexistence in the Tricritical Ising Model

NASA Astrophysics Data System (ADS)

O'Brien, Edward; Fendley, Paul

2018-05-01

We introduce and analyze a quantum spin or Majorana chain with a tricritical Ising point separating a critical phase from a gapped phase with order-disorder coexistence. We show that supersymmetry is not only an emergent property of the scaling limit but also manifests itself on the lattice. Namely, we find explicit lattice expressions for the supersymmetry generators and currents. Writing the Hamiltonian in terms of these generators allows us to find the ground states exactly at a frustration-free coupling. These confirm the coexistence between two (topologically) ordered ground states and a disordered one in the gapped phase. Deforming the model by including explicit chiral symmetry breaking, we find the phases persist up to an unusual chiral phase transition where the supersymmetry becomes exact even on the lattice.

Grid Computing: Topology-Aware, Peer-to-Peer, Power-Aware, and Embedded Web Services

DTIC Science & Technology

2003-09-22

Dist Simulation • Time Management enables temporal causality to be enforced in Distributed Simulations • Typically enforced via a Lower Bound Time...algorithm • Distinguished Root Node Algorithm developed as a topology-aware time management service – Relies on a tree from end-hosts to a

Fractal nematic colloids

NASA Astrophysics Data System (ADS)

Hashemi, S. M.; Jagodič, U.; Mozaffari, M. R.; Ejtehadi, M. R.; Muševič, I.; Ravnik, M.

2017-01-01

Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter.

On the background independence of two-dimensional topological gravity

NASA Astrophysics Data System (ADS)

Imbimbo, Camillo

1995-04-01

We formulate two-dimensional topological gravity in a background covariant Lagrangian framework. We derive the Ward identities which characterize the dependence of physical correlators on the background world-sheet metric defining the gauge-slice. We point out the existence of an "anomaly" in Ward identitites involving correlators of observables with higher ghost number. This "anomaly" represents an obstruction for physical correlators to be globally defined forms on moduli space which could be integrated in a background independent way. Starting from the anomalous Ward identities, we derive "descent" equations whose solutions are cocycles of the Lie algebra of the diffeomorphism group with values in the space of local forms on the moduli space. We solve the descent equations and provide explicit formulas for the cocycles, which allow for the definition of background independent integrals of physical correlators on the moduli space.

Adjoint Techniques for Topology Optimization of Structures Under Damage Conditions

NASA Technical Reports Server (NTRS)

Akgun, Mehmet A.; Haftka, Raphael T.

2000-01-01

The objective of this cooperative agreement was to seek computationally efficient ways to optimize aerospace structures subject to damage tolerance criteria. Optimization was to involve sizing as well as topology optimization. The work was done in collaboration with Steve Scotti, Chauncey Wu and Joanne Walsh at the NASA Langley Research Center. Computation of constraint sensitivity is normally the most time-consuming step of an optimization procedure. The cooperative work first focused on this issue and implemented the adjoint method of sensitivity computation (Haftka and Gurdal, 1992) in an optimization code (runstream) written in Engineering Analysis Language (EAL). The method was implemented both for bar and plate elements including buckling sensitivity for the latter. Lumping of constraints was investigated as a means to reduce the computational cost. Adjoint sensitivity computation was developed and implemented for lumped stress and buckling constraints. Cost of the direct method and the adjoint method was compared for various structures with and without lumping. The results were reported in two papers (Akgun et al., 1998a and 1999). It is desirable to optimize topology of an aerospace structure subject to a large number of damage scenarios so that a damage tolerant structure is obtained. Including damage scenarios in the design procedure is critical in order to avoid large mass penalties at later stages (Haftka et al., 1983). A common method for topology optimization is that of compliance minimization (Bendsoe, 1995) which has not been used for damage tolerant design. In the present work, topology optimization is treated as a conventional problem aiming to minimize the weight subject to stress constraints. Multiple damage configurations (scenarios) are considered. Each configuration has its own structural stiffness matrix and, normally, requires factoring of the matrix and solution of the system of equations. Damage that is expected to be tolerated is local and represents a small change in the stiffness matrix compared to the baseline (undamaged) structure. The exact solution to a slightly modified set of equations can be obtained from the baseline solution economically without actually solving the modified system.. Shennan-Morrison-Woodbury (SMW) formulas are matrix update formulas that allow this (Akgun et al., 1998b). SMW formulas were therefore used here to compute adjoint displacements for sensitivity computation and structural displacements in damaged configurations.

Chiral magnetic conductivity and surface states of Weyl semimetals in topological insulator ultra-thin film multilayer.

PubMed

Owerre, S A

2016-06-15

We investigate an ultra-thin film of topological insulator (TI) multilayer as a model for a three-dimensional (3D) Weyl semimetal. We introduce tunneling parameters t S, [Formula: see text], and t D, where the former two parameters couple layers of the same thin film at small and large momenta, and the latter parameter couples neighbouring thin film layers along the z-direction. The Chern number is computed in each topological phase of the system and we find that for [Formula: see text], the tunneling parameter [Formula: see text] changes from positive to negative as the system transits from Weyl semi-metallic phase to insulating phases. We further study the chiral magnetic effect (CME) of the system in the presence of a time dependent magnetic field. We compute the low-temperature dependence of the chiral magnetic conductivity and show that it captures three distinct phases of the system separated by plateaus. Furthermore, we propose and study a 3D lattice model of Porphyrin thin film, an organic material known to support topological Frenkel exciton edge states. We show that this model exhibits a 3D Weyl semi-metallic phase and also supports a 2D Weyl semi-metallic phase. We further show that this model recovers that of 3D Weyl semimetal in topological insulator thin film multilayer. Thus, paving the way for simulating a 3D Weyl semimetal in topological insulator thin film multilayer. We obtain the surface states (Fermi arcs) in the 3D model and the chiral edge states in the 2D model and analyze their topological properties.

Fault-tolerance thresholds for the surface code with fabrication errors

NASA Astrophysics Data System (ADS)

Auger, James M.; Anwar, Hussain; Gimeno-Segovia, Mercedes; Stace, Thomas M.; Browne, Dan E.

2017-10-01

The construction of topological error correction codes requires the ability to fabricate a lattice of physical qubits embedded on a manifold with a nontrivial topology such that the quantum information is encoded in the global degrees of freedom (i.e., the topology) of the manifold. However, the manufacturing of large-scale topological devices will undoubtedly suffer from fabrication errors—permanent faulty components such as missing physical qubits or failed entangling gates—introducing permanent defects into the topology of the lattice and hence significantly reducing the distance of the code and the quality of the encoded logical qubits. In this work we investigate how fabrication errors affect the performance of topological codes, using the surface code as the test bed. A known approach to mitigate defective lattices involves the use of primitive swap gates in a long sequence of syndrome extraction circuits. Instead, we show that in the presence of fabrication errors the syndrome can be determined using the supercheck operator approach and the outcome of the defective gauge stabilizer generators without any additional computational overhead or use of swap gates. We report numerical fault-tolerance thresholds in the presence of both qubit fabrication and gate fabrication errors using a circuit-based noise model and the minimum-weight perfect-matching decoder. Our numerical analysis is most applicable to two-dimensional chip-based technologies, but the techniques presented here can be readily extended to other topological architectures. We find that in the presence of 8 % qubit fabrication errors, the surface code can still tolerate a computational error rate of up to 0.1 % .

Superconducting thin films of (100) and (111) oriented indium doped topological crystalline insulator SnTe

DOE PAGES

Si, W.; Zhang, C.; Wu, L.; ...

2015-09-01

Recent discovery of the topological crystalline insulator SnTe has triggered a search for topological superconductors, which have potential application to topological quantum computing. The present work reports on the superconducting properties of indium doped SnTe thin films. The (100) and (111) oriented thin films were epitaxially grown by pulsed-laser deposition on (100) and (111) BaF2 crystalline substrates respectively. The onset superconducting transition temperatures are about 3.8 K for (100) and 3.6 K for (111) orientations, slightly lower than that of the bulk. Magneto-resistive measurements indicate that these thin films may have upper critical fields higher than that of the bulk.more » With large surface-to-bulk ratio, superconducting indium doped SnTe thin films provide a rich platform for the study of topological superconductivity and potential device applications based on topological superconductors.« less

Superconducting thin films of (100) and (111) oriented indium doped topological crystalline insulator SnTe

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

Si, Weidong, E-mail: wds@bnl.gov, E-mail: qiangli@bnl.gov; Zhang, Cheng; Wu, Lijun

2015-08-31

Recent discovery of the topological crystalline insulator SnTe has triggered a search for topological superconductors, which have potential application to topological quantum computing. The present work reports on the superconducting properties of indium doped SnTe thin films. The (100) and (111) oriented thin films were epitaxially grown by pulsed-laser deposition on (100) and (111) BaF{sub 2} crystalline substrates, respectively. The onset superconducting transition temperatures are about 3.8 K for (100) and 3.6 K for (111) orientations, slightly lower than that of the bulk. Magneto-resistive measurements indicate that these thin films may have upper critical fields higher than that of the bulk. Withmore » large surface-to-bulk ratio, superconducting indium doped SnTe thin films provide a rich platform for the study of topological superconductivity and potential device applications based on topological superconductors.« less

Josephson Radiation from Gapless Andreev Bound States in HgTe-Based Topological Junctions

NASA Astrophysics Data System (ADS)

Deacon, R. S.; Wiedenmann, J.; Bocquillon, E.; Domínguez, F.; Klapwijk, T. M.; Leubner, P.; Brüne, C.; Hankiewicz, E. M.; Tarucha, S.; Ishibashi, K.; Buhmann, H.; Molenkamp, L. W.

2017-04-01

Frequency analysis of the rf emission of oscillating Josephson supercurrent is a powerful passive way of probing properties of topological Josephson junctions. In particular, measurements of the Josephson emission enable the detection of topological gapless Andreev bound states that give rise to emission at half the Josephson frequency fJ rather than conventional emission at fJ. Here, we report direct measurement of rf emission spectra on Josephson junctions made of HgTe-based gate-tunable topological weak links. The emission spectra exhibit a clear signal at half the Josephson frequency fJ/2 . The linewidths of emission lines indicate a coherence time of 0.3-4 ns for the fJ/2 line, much shorter than for the fJ line (3-4 ns). These observations strongly point towards the presence of topological gapless Andreev bound states and pave the way for a future HgTe-based platform for topological quantum computation.

Quantum glassiness in strongly correlated clean systems: an example of topological overprotection.

PubMed

Chamon, Claudio

2005-02-04

This Letter presents solvable examples of quantum many-body Hamiltonians of systems that are unable to reach their ground states as the environment temperature is lowered to absolute zero. These examples, three-dimensional generalizations of quantum Hamiltonians proposed for topological quantum computing, (1) have no quenched disorder, (2) have solely local interactions, (3) have an exactly solvable spectrum, (4) have topologically ordered ground states, and (5) have slow dynamical relaxation rates akin to those of strong structural glasses.

Quantum Glassiness in Strongly Correlated Clean Systems: An Example of Topological Overprotection

NASA Astrophysics Data System (ADS)

Chamon, Claudio

2005-01-01

This Letter presents solvable examples of quantum many-body Hamiltonians of systems that are unable to reach their ground states as the environment temperature is lowered to absolute zero. These examples, three-dimensional generalizations of quantum Hamiltonians proposed for topological quantum computing, (1)have no quenched disorder, (2)have solely local interactions, (3)have an exactly solvable spectrum, (4)have topologically ordered ground states, and (5)have slow dynamical relaxation rates akin to those of strong structural glasses.

Topological vertex formalism with O5-plane

NASA Astrophysics Data System (ADS)

Kim, Sung-Soo; Yagi, Futoshi

2018-01-01

We propose a new topological vertex formalism for a type IIB (p ,q ) 5-brane web with an O5-plane. We apply our proposal to five-dimensional N =1 Sp(1) gauge theory with Nf=0 , 1, 8 flavors to compute the topological string partition functions and check the agreement with the known results. Especially for the Nf=8 case, which corresponds to E-string theory on a circle, we obtain a new, yet simple, expression of the partition function with a two Young diagram sum.

A new computational strategy for identifying essential proteins based on network topological properties and biological information.

PubMed

Qin, Chao; Sun, Yongqi; Dong, Yadong

2017-01-01

Essential proteins are the proteins that are indispensable to the survival and development of an organism. Deleting a single essential protein will cause lethality or infertility. Identifying and analysing essential proteins are key to understanding the molecular mechanisms of living cells. There are two types of methods for predicting essential proteins: experimental methods, which require considerable time and resources, and computational methods, which overcome the shortcomings of experimental methods. However, the prediction accuracy of computational methods for essential proteins requires further improvement. In this paper, we propose a new computational strategy named CoTB for identifying essential proteins based on a combination of topological properties, subcellular localization information and orthologous protein information. First, we introduce several topological properties of the protein-protein interaction (PPI) network. Second, we propose new methods for measuring orthologous information and subcellular localization and a new computational strategy that uses a random forest prediction model to obtain a probability score for the proteins being essential. Finally, we conduct experiments on four different Saccharomyces cerevisiae datasets. The experimental results demonstrate that our strategy for identifying essential proteins outperforms traditional computational methods and the most recently developed method, SON. In particular, our strategy improves the prediction accuracy to 89, 78, 79, and 85 percent on the YDIP, YMIPS, YMBD and YHQ datasets at the top 100 level, respectively.

Explicit Content Caching at Mobile Edge Networks with Cross-Layer Sensing

PubMed Central

Chen, Lingyu; Su, Youxing; Luo, Wenbin; Hong, Xuemin; Shi, Jianghong

2018-01-01

The deployment density and computational power of small base stations (BSs) are expected to increase significantly in the next generation mobile communication networks. These BSs form the mobile edge network, which is a pervasive and distributed infrastructure that can empower a variety of edge/fog computing applications. This paper proposes a novel edge-computing application called explicit caching, which stores selective contents at BSs and exposes such contents to local users for interactive browsing and download. We formulate the explicit caching problem as a joint content recommendation, caching, and delivery problem, which aims to maximize the expected user quality-of-experience (QoE) with varying degrees of cross-layer sensing capability. Optimal and effective heuristic algorithms are presented to solve the problem. The theoretical performance bounds of the explicit caching system are derived in simplified scenarios. The impacts of cache storage space, BS backhaul capacity, cross-layer information, and user mobility on the system performance are simulated and discussed in realistic scenarios. Results suggest that, compared with conventional implicit caching schemes, explicit caching can better exploit the mobile edge network infrastructure for personalized content dissemination. PMID:29565313

Explicit Content Caching at Mobile Edge Networks with Cross-Layer Sensing.

PubMed

Chen, Lingyu; Su, Youxing; Luo, Wenbin; Hong, Xuemin; Shi, Jianghong

2018-03-22

The deployment density and computational power of small base stations (BSs) are expected to increase significantly in the next generation mobile communication networks. These BSs form the mobile edge network, which is a pervasive and distributed infrastructure that can empower a variety of edge/fog computing applications. This paper proposes a novel edge-computing application called explicit caching, which stores selective contents at BSs and exposes such contents to local users for interactive browsing and download. We formulate the explicit caching problem as a joint content recommendation, caching, and delivery problem, which aims to maximize the expected user quality-of-experience (QoE) with varying degrees of cross-layer sensing capability. Optimal and effective heuristic algorithms are presented to solve the problem. The theoretical performance bounds of the explicit caching system are derived in simplified scenarios. The impacts of cache storage space, BS backhaul capacity, cross-layer information, and user mobility on the system performance are simulated and discussed in realistic scenarios. Results suggest that, compared with conventional implicit caching schemes, explicit caching can better exploit the mobile edge network infrastructure for personalized content dissemination.

Dual-scale topology optoelectronic processor.

PubMed

Marsden, G C; Krishnamoorthy, A V; Esener, S C; Lee, S H

1991-12-15

The dual-scale topology optoelectronic processor (D-STOP) is a parallel optoelectronic architecture for matrix algebraic processing. The architecture can be used for matrix-vector multiplication and two types of vector outer product. The computations are performed electronically, which allows multiplication and summation concepts in linear algebra to be generalized to various nonlinear or symbolic operations. This generalization permits the application of D-STOP to many computational problems. The architecture uses a minimum number of optical transmitters, which thereby reduces fabrication requirements while maintaining area-efficient electronics. The necessary optical interconnections are space invariant, minimizing space-bandwidth requirements.

Observation of topological superconductivity on the surface of an iron-based superconductor

NASA Astrophysics Data System (ADS)

Zhang, Peng; Yaji, Koichiro; Hashimoto, Takahiro; Ota, Yuichi; Kondo, Takeshi; Okazaki, Kozo; Wang, Zhijun; Wen, Jinsheng; Gu, G. D.; Ding, Hong; Shin, Shik

2018-04-01

Topological superconductors are predicted to host exotic Majorana states that obey non-Abelian statistics and can be used to implement a topological quantum computer. Most of the proposed topological superconductors are realized in difficult-to-fabricate heterostructures at very low temperatures. By using high-resolution spin-resolved and angle-resolved photoelectron spectroscopy, we find that the iron-based superconductor FeTe1–xSex (x = 0.45; superconducting transition temperature Tc = 14.5 kelvin) hosts Dirac-cone–type spin-helical surface states at the Fermi level; the surface states exhibit an s-wave superconducting gap below Tc. Our study shows that the surface states of FeTe0.55Se0.45 are topologically superconducting, providing a simple and possibly high-temperature platform for realizing Majorana states.

Reading off the nongeometric scalar potentials via the topological data of the compactifying Calabi-Yau manifolds

NASA Astrophysics Data System (ADS)

Shukla, Pramod

2016-10-01

In the context of studying the 4D-effective potentials of type IIB nongeometric flux compactifications, this article has a twofold goal. First, we present a modular invariant symplectic rearrangement of the tree level nongeometric scalar potential arising from a flux superpotential which includes the S-dual pairs of nongeometric fluxes (Q , P ), the standard NS-NS and RR three-form fluxes (F3 , H3 ), and the geometric flux (ω ). This "symplectic formulation" is valid for arbitrary numbers of Kähler moduli, and the complex structure moduli which are implicitly encoded in a set of symplectic matrices. In the second part, we further explicitly rewrite all the symplectic ingredients in terms of saxionic and axionic components of the complex structure moduli. The same leads to a compact form of the generic scalar potential being explicitly written out in terms of all the real moduli/axions. Moreover, the final form of the scalar potential needs only the knowledge of some topological data (such as Hodge numbers and the triple-intersection numbers) of the compactifying threefolds and their respective mirrors. Finally, we demonstrate how the same is equivalent to say that, for a given concrete example, various pieces of the scalar potential can be directly read off from our generic proposal, without the need of starting from the Kähler and superpotentials.

Exact solutions of massive gravity in three dimensions

NASA Astrophysics Data System (ADS)

Chakhad, Mohamed

In recent years, there has been an upsurge in interest in three-dimensional theories of gravity. In particular, two theories of massive gravity in three dimensions hold strong promise in the search for fully consistent theories of quantum gravity, an understanding of which will shed light on the problems of quantum gravity in four dimensions. One of these theories is the "old" third-order theory of topologically massive gravity (TMG) and the other one is a "new" fourth-order theory of massive gravity (NMG). Despite this increase in research activity, the problem of finding and classifying solutions of TMG and NMG remains a wide open area of research. In this thesis, we provide explicit new solutions of massive gravity in three dimensions and suggest future directions of research. These solutions belong to the Kundt class of spacetimes. A systematic analysis of the Kundt solutions with constant scalar polynomial curvature invariants provides a glimpse of the structure of the spaces of solutions of the two theories of massive gravity. We also find explicit solutions of topologically massive gravity whose scalar polynomial curvature invariants are not all constant, and these are the first such solutions. A number of properties of Kundt solutions of TMG and NMG, such as an identification of solutions which lie at the intersection of the full nonlinear and linearized theories, are also derived.

Resource quality of a symmetry-protected topologically ordered phase for quantum computation.

PubMed

Miller, Jacob; Miyake, Akimasa

2015-03-27

We investigate entanglement naturally present in the 1D topologically ordered phase protected with the on-site symmetry group of an octahedron as a potential resource for teleportation-based quantum computation. We show that, as long as certain characteristic lengths are finite, all its ground states have the capability to implement any unit-fidelity one-qubit gate operation asymptotically as a key computational building block. This feature is intrinsic to the entire phase, in that perfect gate fidelity coincides with perfect string order parameters under a state-insensitive renormalization procedure. Our approach may pave the way toward a novel program to classify quantum many-body systems based on their operational use for quantum information processing.

Resource Quality of a Symmetry-Protected Topologically Ordered Phase for Quantum Computation

NASA Astrophysics Data System (ADS)

Miller, Jacob; Miyake, Akimasa

2015-03-01

We investigate entanglement naturally present in the 1D topologically ordered phase protected with the on-site symmetry group of an octahedron as a potential resource for teleportation-based quantum computation. We show that, as long as certain characteristic lengths are finite, all its ground states have the capability to implement any unit-fidelity one-qubit gate operation asymptotically as a key computational building block. This feature is intrinsic to the entire phase, in that perfect gate fidelity coincides with perfect string order parameters under a state-insensitive renormalization procedure. Our approach may pave the way toward a novel program to classify quantum many-body systems based on their operational use for quantum information processing.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

Explicitly represented polygon wall boundary model for the explicit MPS method

NASA Astrophysics Data System (ADS)

Mitsume, Naoto; Yoshimura, Shinobu; Murotani, Kohei; Yamada, Tomonori

2015-05-01

This study presents an accurate and robust boundary model, the explicitly represented polygon (ERP) wall boundary model, to treat arbitrarily shaped wall boundaries in the explicit moving particle simulation (E-MPS) method, which is a mesh-free particle method for strong form partial differential equations. The ERP model expresses wall boundaries as polygons, which are explicitly represented without using the distance function. These are derived so that for viscous fluids, and with less computational cost, they satisfy the Neumann boundary condition for the pressure and the slip/no-slip condition on the wall surface. The proposed model is verified and validated by comparing computed results with the theoretical solution, results obtained by other models, and experimental results. Two simulations with complex boundary movements are conducted to demonstrate the applicability of the E-MPS method to the ERP model.

Using Embedded Computer-Assisted Explicit Instruction to Teach Science to Students with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Smith, Bethany R.; Spooner, Fred; Wood, Charles L.

2013-01-01

For students with Autism Spectrum Disorders and intellectual disability, the need for scientific literacy is further complicated by the need for individualized instruction necessary to teach new skills, especially when those skills are academic. This study investigated the effects of embedded, computer-assisted explicit instruction to teach…

Fidelity of Majorana-based quantum operations

NASA Astrophysics Data System (ADS)

Tanhayi Ahari, Mostafa; Ortiz, Gerardo; Seradjeh, Babak

2015-03-01

It is well known that one-dimensional p-wave superconductor, the so-called Kitaev model, has topologically distinct phases that are distinguished by the presence of Majorana fermions. Owing to their topological protection, these Majorana fermions have emerged as candidates for fault-tolerant quantum computation. They furnish the operation of such a computation via processes that produce, braid, and annihilate them in pairs. In this work we study some of these processes from the dynamical perspective. In particular, we determine the fidelity of the Majorana fermions when they are produced or annihilated by tuning the system through the corresponding topological phase transition. For a simple linear protocol, we derive analytical expressions for fidelity and test various perturbative schemes. For more general protocols, we present exact numerics. Our results are relevant for the operation of Majorana-based quantum gates and quantum memories.

Majorana fermion surface code for universal quantum computation

DOE PAGES

Vijay, Sagar; Hsieh, Timothy H.; Fu, Liang

2015-12-10

In this study, we introduce an exactly solvable model of interacting Majorana fermions realizing Z 2 topological order with a Z 2 fermion parity grading and lattice symmetries permuting the three fundamental anyon types. We propose a concrete physical realization by utilizing quantum phase slips in an array of Josephson-coupled mesoscopic topological superconductors, which can be implemented in a wide range of solid-state systems, including topological insulators, nanowires, or two-dimensional electron gases, proximitized by s-wave superconductors. Our model finds a natural application as a Majorana fermion surface code for universal quantum computation, with a single-step stabilizer measurement requiring no physicalmore » ancilla qubits, increased error tolerance, and simpler logical gates than a surface code with bosonic physical qubits. We thoroughly discuss protocols for stabilizer measurements, encoding and manipulating logical qubits, and gate implementations.« less

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

Charge-spin Transport in Surface-disordered Three-dimensional Topological Insulators

NASA Astrophysics Data System (ADS)

Peng, Xingyue

As one of the most promising candidates for the building block of the novel spintronic circuit, the topological insulator (TI) has attracted world-wide interest of study. Robust topological order protected by time-reversal symmetry (TRS) makes charge transport and spin generation in TIs significantly different from traditional three-dimensional (3D) or two-dimensional (2D) electronic systems. However, to date, charge transport and spin generation in 3D TIs are still primarily modeled as single-surface phenomena, happening independently on top and bottom surfaces. In this dissertation, I will demonstrate via both experimental findings and theoretical modeling that this "single surface'' theory neither correctly describes a realistic 3D TI-based device nor reveals the amazingly distinct physical picture of spin transport dynamics in 3D TIs. Instead, I present a new viewpoint of the spin transport dynamics where the role of the insulating yet topologically non-trivial bulk of a 3D TI becomes explicit. Within this new theory, many mysterious transport and magneto-transport anomalies can be naturally explained. The 3D TI system turns out to be more similar to its low dimensional sibling--2D TI rather than some other systems sharing the Dirac dispersion, such as graphene. This work not only provides valuable fundamental physical insights on charge-spin transport in 3D TIs, but also offers important guidance to the design of 3D TI-based spintronic devices.

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.

Topological defects in the Georgi-Machacek model

NASA Astrophysics Data System (ADS)

Chatterjee, Chandrasekar; Kurachi, Masafumi; Nitta, Muneto

2018-06-01

We study topological defects in the Georgi-Machacek model in a hierarchical symmetry breaking in which extra triplets acquire vacuum expectation values before the doublet. We find a possibility of topologically stable non-Abelian domain walls and non-Abelian flux tubes (vortices or cosmic strings) in this model. In the limit of the vanishing U (1 )Y gauge coupling in which the custodial symmetry becomes exact, the presence of a vortex spontaneously breaks the custodial symmetry, giving rise to S2 Nambu-Goldstone (NG) modes localized around the vortex corresponding to non-Abelian fluxes. Vortices are continuously degenerated by these degrees of freedom, thereby called non-Abelian. By taking into account the U (1 )Y gauge coupling, the custodial symmetry is explicitly broken, the NG modes are lifted to become pseudo-NG modes, and all non-Abelian vortices fall into a topologically stable Z string. This is in contrast to the standard model in which Z strings are nontopological and are unstable in the realistic parameter region. Non-Abelian domain walls also break the custodial symmetry and are accompanied by localized S2 NG modes. Finally, we discuss the existence of domain wall solutions bounded by flux tubes, where their S2 NG modes match. The domain walls may quantum mechanically decay by creating a hole bounded by a flux tube loop, and would be cosmologically safe. Gravitational waves produced from unstable domain walls could be detected by future experiments.

Network Design: Best Practices for Alberta School Jurisdictions.

ERIC Educational Resources Information Center

Schienbein, Ralph

This report examines subsections of the computer network topology that relate to end-to-end performance and capacity planning in schools. Active star topology, Category 5 wiring, Ethernet, and intelligent devices are assumed. The report describes a model that can be used to project WAN (wide area network) connection speeds based on user traffic,…

Degree counting and Shadow system for Toda system of rank two: One bubbling

NASA Astrophysics Data System (ADS)

Lee, Youngae; Lin, Chang-Shou; Wei, Juncheng; Yang, Wen

2018-04-01

We initiate the program for computing the Leray-Schauder topological degree for Toda systems of rank two. This program still contains a lot of challenging problems for analysts. As the first step, we prove that if a sequence of solutions (u1k ,u2k) blows up, then one of hje ujk/∫Mhje ujk dvg, j = 1 , 2 tends to a sum of Dirac measures. This is so-called the phenomena of weak concentration. Our purposes in this article are (i) to introduce the shadow system due to the bubbling phenomena when one of parameters ρi crosses 4π and ρj ∉ 4 πN where 1 ≤ i ≠ j ≤ 2; (ii) to show how to calculate the topological degree of Toda systems by computing the topological degree of the general shadow systems; (iii) to calculate the topological degree of the shadow system for one point blow up. We believe that the degree counting formula for the shadow system would be useful in other problems.

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

PubMed

Durán, Claudio; Daminelli, Simone; Thomas, Josephine M; Haupt, V Joachim; Schroeder, Michael; Cannistraci, Carlo Vittorio

2017-04-26

The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared-using standard and innovative validation frameworks-with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks. Surprisingly, our results show that the bipartite topology alone, if adequately exploited by means of the recently proposed local-community-paradigm (LCP) theory-initially detected in brain-network topological self-organization and afterwards generalized to any complex network-is able to suggest highly reliable predictions, with comparable performance with the state-of-the-art-supervised methods that exploit additional (non-topological, for instance biochemical) DTI knowledge. Furthermore, a detailed analysis of the novel predictions revealed that each class of methods prioritizes distinct true interactions; hence, combining methodologies based on diverse principles represents a promising strategy to improve drug-target discovery. To conclude, this study promotes the power of bio-inspired computing, demonstrating that simple unsupervised rules inspired by principles of topological self-organization and adaptiveness arising during learning in living intelligent systems (like the brain) can efficiently equal perform complicated algorithms based on advanced, supervised and knowledge-based engineering. © The Author 2017. Published by Oxford University Press.

A surface code quantum computer in silicon

PubMed Central

Hill, Charles D.; Peretz, Eldad; Hile, Samuel J.; House, Matthew G.; Fuechsle, Martin; Rogge, Sven; Simmons, Michelle Y.; Hollenberg, Lloyd C. L.

2015-01-01

The exceptionally long quantum coherence times of phosphorus donor nuclear spin qubits in silicon, coupled with the proven scalability of silicon-based nano-electronics, make them attractive candidates for large-scale quantum computing. However, the high threshold of topological quantum error correction can only be captured in a two-dimensional array of qubits operating synchronously and in parallel—posing formidable fabrication and control challenges. We present an architecture that addresses these problems through a novel shared-control paradigm that is particularly suited to the natural uniformity of the phosphorus donor nuclear spin qubit states and electronic confinement. The architecture comprises a two-dimensional lattice of donor qubits sandwiched between two vertically separated control layers forming a mutually perpendicular crisscross gate array. Shared-control lines facilitate loading/unloading of single electrons to specific donors, thereby activating multiple qubits in parallel across the array on which the required operations for surface code quantum error correction are carried out by global spin control. The complexities of independent qubit control, wave function engineering, and ad hoc quantum interconnects are explicitly avoided. With many of the basic elements of fabrication and control based on demonstrated techniques and with simulated quantum operation below the surface code error threshold, the architecture represents a new pathway for large-scale quantum information processing in silicon and potentially in other qubit systems where uniformity can be exploited. PMID:26601310

A surface code quantum computer in silicon.

PubMed

Hill, Charles D; Peretz, Eldad; Hile, Samuel J; House, Matthew G; Fuechsle, Martin; Rogge, Sven; Simmons, Michelle Y; Hollenberg, Lloyd C L

2015-10-01

The exceptionally long quantum coherence times of phosphorus donor nuclear spin qubits in silicon, coupled with the proven scalability of silicon-based nano-electronics, make them attractive candidates for large-scale quantum computing. However, the high threshold of topological quantum error correction can only be captured in a two-dimensional array of qubits operating synchronously and in parallel-posing formidable fabrication and control challenges. We present an architecture that addresses these problems through a novel shared-control paradigm that is particularly suited to the natural uniformity of the phosphorus donor nuclear spin qubit states and electronic confinement. The architecture comprises a two-dimensional lattice of donor qubits sandwiched between two vertically separated control layers forming a mutually perpendicular crisscross gate array. Shared-control lines facilitate loading/unloading of single electrons to specific donors, thereby activating multiple qubits in parallel across the array on which the required operations for surface code quantum error correction are carried out by global spin control. The complexities of independent qubit control, wave function engineering, and ad hoc quantum interconnects are explicitly avoided. With many of the basic elements of fabrication and control based on demonstrated techniques and with simulated quantum operation below the surface code error threshold, the architecture represents a new pathway for large-scale quantum information processing in silicon and potentially in other qubit systems where uniformity can be exploited.

Proportional Topology Optimization: A New Non-Sensitivity Method for Solving Stress Constrained and Minimum Compliance Problems and Its Implementation in MATLAB

PubMed Central

Biyikli, Emre; To, Albert C.

2015-01-01

A new topology optimization method called the Proportional Topology Optimization (PTO) is presented. As a non-sensitivity method, PTO is simple to understand, easy to implement, and is also efficient and accurate at the same time. It is implemented into two MATLAB programs to solve the stress constrained and minimum compliance problems. Descriptions of the algorithm and computer programs are provided in detail. The method is applied to solve three numerical examples for both types of problems. The method shows comparable efficiency and accuracy with an existing optimality criteria method which computes sensitivities. Also, the PTO stress constrained algorithm and minimum compliance algorithm are compared by feeding output from one algorithm to the other in an alternative manner, where the former yields lower maximum stress and volume fraction but higher compliance compared to the latter. Advantages and disadvantages of the proposed method and future works are discussed. The computer programs are self-contained and publicly shared in the website www.ptomethod.org. PMID:26678849

The development of an explicit thermochemical nonequilibrium algorithm and its application to compute three dimensional AFE flowfields

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

This study presents a three-dimensional explicit, finite-difference, shock-capturing numerical algorithm applied to viscous hypersonic flows in thermochemical nonequilibrium. The algorithm employs a two-temperature physical model. Equations governing the finite-rate chemical reactions are fully-coupled to the gas dynamic equations using a novel coupling technique. The new coupling method maintains stability in the explicit, finite-rate formulation while allowing relatively large global time steps. The code uses flux-vector accuracy. Comparisons with experimental data and other numerical computations verify the accuracy of the present method. The code is used to compute the three-dimensional flowfield over the Aeroassist Flight Experiment (AFE) vehicle at one of its trajectory points.

Fivebranes and 3-manifold homology

NASA Astrophysics Data System (ADS)

Gukov, Sergei; Putrov, Pavel; Vafa, Cumrun

2017-07-01

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

Knotted optical vortices in exact solutions to Maxwell's equations

NASA Astrophysics Data System (ADS)

de Klerk, Albertus J. J. M.; van der Veen, Roland I.; Dalhuisen, Jan Willem; Bouwmeester, Dirk

2017-05-01

We construct a family of exact solutions to Maxwell's equations in which the points of zero intensity form knotted lines topologically equivalent to a given but arbitrary algebraic link. These lines of zero intensity, more commonly referred to as optical vortices, and their topology are preserved as time evolves and the fields have finite energy. To derive explicit expressions for these new electromagnetic fields that satisfy the nullness property, we make use of the Bateman variables for the Hopf field as well as complex polynomials in two variables whose zero sets give rise to algebraic links. The class of algebraic links includes not only all torus knots and links thereof, but also more intricate cable knots. While the unknot has been considered before, the solutions presented here show that more general knotted structures can also arise as optical vortices in exact solutions to Maxwell's equations.

Topology Counts: Force Distributions in Circular Spring Networks.

PubMed

Heidemann, Knut M; Sageman-Furnas, Andrew O; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F; Wardetzky, Max

2018-02-09

Filamentous polymer networks govern the mechanical properties of many biological materials. Force distributions within these networks are typically highly inhomogeneous, and, although the importance of force distributions for structural properties is well recognized, they are far from being understood quantitatively. Using a combination of probabilistic and graph-theoretical techniques, we derive force distributions in a model system consisting of ensembles of random linear spring networks on a circle. We show that characteristic quantities, such as the mean and variance of the force supported by individual springs, can be derived explicitly in terms of only two parameters: (i) average connectivity and (ii) number of nodes. Our analysis shows that a classical mean-field approach fails to capture these characteristic quantities correctly. In contrast, we demonstrate that network topology is a crucial determinant of force distributions in an elastic spring network. Our results for 1D linear spring networks readily generalize to arbitrary dimensions.

Renormalization of entanglement entropy from topological terms

NASA Astrophysics Data System (ADS)

Anastasiou, Giorgos; Araya, Ignacio J.; Olea, Rodrigo

2018-05-01

We propose a renormalization scheme for entanglement entropy of three-dimensional CFTs with a four-dimensional asymptotically AdS gravity dual in the context of the gauge/gravity correspondence. The procedure consists in adding the Chern form as a boundary term to the area functional of the Ryu-Takayanagi minimal surface. We provide an explicit prescription for the renormalized entanglement entropy, which is derived via the replica trick. This is achieved by considering a Euclidean gravitational action renormalized by the addition of the Chern form at the spacetime boundary, evaluated in the conically-singular replica manifold. We show that the addition of this boundary term cancels the divergent part of the entanglement entropy, recovering the results obtained by Taylor and Woodhead. We comment on how this prescription for renormalizing the entanglement entropy is in line with the general program of topological renormalization in asymptotically AdS gravity.

Recursive thoughts on the simulation of the flexible multibody dynamics of slender offshore structures

NASA Astrophysics Data System (ADS)

Schilder, J.; Ellenbroek, M.; de Boer, A.

2017-12-01

In this work, the floating frame of reference formulation is used to create a flexible multibody model of slender offshore structures such as pipelines and risers. It is shown that due to the chain-like topology of the considered structures, the equation of motion can be expressed in terms of absolute interface coordinates. In the presented form, kinematic constraint equations are satisfied explicitly and the Lagrange multipliers are eliminated from the equations. Hence, the structures can be conveniently coupled to finite element or multibody models of for example seabed and vessel. The chain-like topology enables the efficient use of recursive solution procedures for both transient dynamic analysis and equilibrium analysis. For this, the transfer matrix method is used. In order to improve the convergence of the equilibrium analysis, the analytical solution of an ideal catenary is used as an initial configuration, reducing the number of required iterations.

Fractal nematic colloids

PubMed Central

Hashemi, S. M.; Jagodič, U.; Mozaffari, M. R.; Ejtehadi, M. R.; Muševič, I.; Ravnik, M.

2017-01-01

Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter. PMID:28117325

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

Topologically massive gravity and Ricci-Cotton flow

NASA Astrophysics Data System (ADS)

Lashkari, Nima; Maloney, Alexander

2011-05-01

We consider topologically massive gravity (TMG), which is three-dimensional general relativity with a cosmological constant and a gravitational Chern-Simons term. When the cosmological constant is negative the theory has two potential vacuum solutions: anti-de Sitter space and warped anti-de Sitter space. The theory also contains a massive graviton state which renders these solutions unstable for certain values of the parameters and boundary conditions. We study the decay of these solutions due to the condensation of the massive graviton mode using Ricci-Cotton flow, which is the appropriate generalization of Ricci flow to TMG. When the Chern-Simons coupling is small the AdS solution flows to warped AdS by the condensation of the massive graviton mode. When the coupling is large the situation is reversed, and warped AdS flows to AdS. Minisuperspace models are constructed where these flows are studied explicitly.

New dimensions for wound strings: The modular transformation of geometry to topology

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

McGreevy, John; Silverstein, Eva; Starr, David

2007-02-15

We show, using a theorem of Milnor and Margulis, that string theory on compact negatively curved spaces grows new effective dimensions as the space shrinks, generalizing and contextualizing the results in E. Silverstein, Phys. Rev. D 73, 086004 (2006).. Milnor's theorem relates negative sectional curvature on a compact Riemannian manifold to exponential growth of its fundamental group, which translates in string theory to a higher effective central charge arising from winding strings. This exponential density of winding modes is related by modular invariance to the infrared small perturbation spectrum. Using self-consistent approximations valid at large radius, we analyze this correspondencemore » explicitly in a broad set of time-dependent solutions, finding precise agreement between the effective central charge and the corresponding infrared small perturbation spectrum. This indicates a basic relation between geometry, topology, and dimensionality in string theory.« less

Toric Calabi-Yau threefolds as quantum integrable systems. R-matrix and RTT relations

NASA Astrophysics Data System (ADS)

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

2016-10-01

R-matrix is explicitly constructed for simplest representations of the Ding-Iohara-Miki algebra. Calculation is straightforward and significantly simpler than the one through the universal R-matrix used for a similar calculation in the Yangian case by A. Smirnov but less general. We investigate the interplay between the R-matrix structure and the structure of DIM algebra intertwiners, i.e. of refined topological vertices and show that the R-matrix is diagonalized by the action of the spectral duality belonging to the SL(2, ℤ) group of DIM algebra automorphisms. We also construct the T-operators satisfying the RTT relations with the R-matrix from refined amplitudes on resolved conifold. We thus show that topological string theories on the toric Calabi-Yau threefolds can be naturally interpreted as lattice integrable models. Integrals of motion for these systems are related to q-deformation of the reflection matrices of the Liouville/Toda theories.

Optimal Diabatic Dynamics of Majoarana-based Topological Qubits

NASA Astrophysics Data System (ADS)

Seradjeh, Babak; Rahmani, Armin; Franz, Marcel

In topological quantum computing, unitary operations on qubits are performed by adiabatic braiding of non-Abelian quasiparticles such as Majorana zero modes and are protected from local environmental perturbations. This scheme requires slow operations. By using the Pontryagin's maximum principle, here we show the same quantum gates can be implemented in much shorter times through optimal diabatic pulses. While our fast diabatic gates no not enjoy topological protection, they provide significant practical advantages due to their optimal speed and remarkable robustness to calibration errors and noise. NSERC, CIfAR, NSF DMR- 1350663, BSF 2014345.

Strict Correlation of HOMO Topology and Magnetic Aromaticity Indices in d-Block Metalloaromatics.

PubMed

Mauksch, Michael; Tsogoeva, Svetlana B

2018-05-16

Magnetic aromaticity and antiaromaticity of closed shell metalloaromatics with 4d transition metals (Nb, Tc, Rh) is strictly correlated with orbital topology (Möbius or Hückel) of their π-HOMO, investigated computationally with DFT methods. A surprisingly simple rule emerged: the metallacycle is aromatic (antiaromatic) when the number of π MO's is even and the π-HOMO is of Möbius (Hückel) topology - and vice versa when the number of π MO's is odd. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A customized MILP approach to the synthesis of heat recovery networks reaching specified topology targets

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

Galli, M.R.; Cerda, J.

1998-06-01

A mathematical representation of a heat-exchanger network structure that explicitly accounts for the relative location of heat-transfer units, splitters, and mixers is presented. It is the basis of a mixed-integer linear programming sequential approach to the synthesis of heat-exchanger networks that allows the designer to specify beforehand some desired topology features as further design targets. Such structural information stands for additional problem data to be considered in the problem formulation, thus enhancing the involvement of the design engineer in the synthesis task. The topology constraints are expressed in terms of (1) the equipment items (heat exchangers, splitters, and mixers) thatmore » could be incorporated into the network, (2) the feasible neighbors for every potential unit, and (3) the heat matches, if any, with which a heat exchanger can be accomplished in parallel over any process stream. Moreover, the number and types of splitters being arranged over either a particular stream or the whole network can also be restrained. The new approach has been successfully applied to the solution of five example problems at each of which a wide variety of structural design restrictions were specified.« less

Topological superconductivity in the extended Kitaev-Heisenberg model

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Enhancing robustness and immunization in geographical networks

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

Huang Liang; Department of Physics, Lanzhou University, Lanzhou 730000; Yang Kongqing

2007-03-15

We find that different geographical structures of networks lead to varied percolation thresholds, although these networks may have similar abstract topological structures. Thus, strategies for enhancing robustness and immunization of a geographical network are proposed. Using the generating function formalism, we obtain an explicit form of the percolation threshold q{sub c} for networks containing arbitrary order cycles. For three-cycles, the dependence of q{sub c} on the clustering coefficients is ascertained. The analysis substantiates the validity of the strategies with analytical evidence.

Trojan War displayed as a full annihilation-diffusion-reaction model

NASA Astrophysics Data System (ADS)

Flores, J. C.

2017-02-01

The diffusive pair annihilation model with embedded topological domains and archaeological data is applied in an analysis of the hypothetical Trojan-Greek war during the late Bronze Age. Estimations of parameter are explicitly made for critical dynamics of the model. In particular, the 8-metre walls of Troy could be viewed as the effective shield that provided the technological difference between the two armies. Suggestively, the numbers in The Iliad are quite sound, being in accord with Lanchester's laws of warfare.

Kundt solutions of minimal massive 3D gravity

NASA Astrophysics Data System (ADS)

Deger, Nihat Sadik; Sarıoǧlu, Ã.-zgür

2015-11-01

We construct Kundt solutions of minimal massive gravity theory and show that, similar to topologically massive gravity (TMG), most of them are constant scalar invariant (CSI) spacetimes that correspond to deformations of round and warped (A)dS. We also find an explicit non-CSI Kundt solution at the merger point. Finally, we give their algebraic classification with respect to the traceless Ricci tensor (Segre classification) and show that their Segre types match with the types of their counterparts in TMG.

The formal de Rham complex

NASA Astrophysics Data System (ADS)

Zharinov, V. V.

2013-02-01

We propose a formal construction generalizing the classic de Rham complex to a wide class of models in mathematical physics and analysis. The presentation is divided into a sequence of definitions and elementary, easily verified statements; proofs are therefore given only in the key case. Linear operations are everywhere performed over a fixed number field {F} = {R},{C}. All linear spaces, algebras, and modules, although not stipulated explicitly, are by definition or by construction endowed with natural locally convex topologies, and their morphisms are continuous.

Nonadiabatic Berry phase in nanocrystalline magnets

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

Skomski, R.; Sellmyer, D. J.

2016-12-20

In this study, it is investigated how a Berry phase is created in polycrystalline nanomagnets and how the phase translates into an emergent magnetic field and into a topological Hall-effect contribution. The analysis starts directly from the spin of the conduction electrons and does not involve any adiabatic Hamiltonian. Completely random spin alignment in the nanocrystallites does not lead to a nonzero emergent field, but a modulation of the local magnetization does. As an explicit example, we consider a wire with a modulated cone angle.

Broadcasting Topology and Routing Information in Computer Networks

DTIC Science & Technology

1985-05-01

DOWN\\ linki inki FIgwre 1.2.1: Topology Problem Example messages from node 2 before receiving the first DOWN message from node 3. Now assume that before...node to each of the link’s end nodes. 54 link.1 cc 4 1 -. distances to linki Figue 3.4.2: SPTA Port Distance Table Example An example of these

A note on the extended dispersionless Toda hierarchy

NASA Astrophysics Data System (ADS)

Lee, Niann-Chern; Tu, Ming-Hsien

2013-04-01

We derive dispersionless Hirota equations for the extended dispersionless Toda hierarchy. We show that the dispersionless Hirota equations are just a direct consequence of the genus-zero topological recurrence relation for the topological ℂP1 model. Using the dispersionless Hirota equations, we compute the twopoint functions and express the result in terms of Catalan numbers

Real-space mapping of topological invariants using artificial neural networks

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Two-dimensional topological photonic systems

NASA Astrophysics Data System (ADS)

Sun, Xiao-Chen; He, Cheng; Liu, Xiao-Ping; Lu, Ming-Hui; Zhu, Shi-Ning; Chen, Yan-Feng

2017-09-01

The topological phase of matter, originally proposed and first demonstrated in fermionic electronic systems, has drawn considerable research attention in the past decades due to its robust transport of edge states and its potential with respect to future quantum information, communication, and computation. Recently, searching for such a unique material phase in bosonic systems has become a hot research topic worldwide. So far, many bosonic topological models and methods for realizing them have been discovered in photonic systems, acoustic systems, mechanical systems, etc. These discoveries have certainly yielded vast opportunities in designing material phases and related properties in the topological domain. In this review, we first focus on some of the representative photonic topological models and employ the underlying Dirac model to analyze the edge states and geometric phase. On the basis of these models, three common types of two-dimensional topological photonic systems are discussed: 1) photonic quantum Hall effect with broken time-reversal symmetry; 2) photonic topological insulator and the associated pseudo-time-reversal symmetry-protected mechanism; 3) time/space periodically modulated photonic Floquet topological insulator. Finally, we provide a summary and extension of this emerging field, including a brief introduction to the Weyl point in three-dimensional systems.

Persistent topological features of dynamical systems

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

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

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

Hybrid Topological Lie-Hamiltonian Learning in Evolving Energy Landscapes

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

In this Chapter, a novel bidirectional algorithm for hybrid (discrete + continuous-time) Lie-Hamiltonian evolution in adaptive energy landscape-manifold is designed and its topological representation is proposed. The algorithm is developed within a geometrically and topologically extended framework of Hopfield's neural nets and Haken's synergetics (it is currently designed in Mathematica, although with small changes it could be implemented in Symbolic C++ or any other computer algebra system). The adaptive energy manifold is determined by the Hamiltonian multivariate cost function H, based on the user-defined vehicle-fleet configuration matrix W, which represents the pseudo-Riemannian metric tensor of the energy manifold. Search for the global minimum of H is performed using random signal differential Hebbian adaptation. This stochastic gradient evolution is driven (or, pulled-down) by `gravitational forces' defined by the 2nd Lie derivatives of H. Topological changes of the fleet matrix W are observed during the evolution and its topological invariant is established. The evolution stops when the W-topology breaks down into several connectivity-components, followed by topology-breaking instability sequence (i.e., a series of phase transitions).

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

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

2015-07-01

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

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.

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

A well-posed numerical method to track isolated conformal map singularities in Hele-Shaw flow

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

Baker, G.; Siegel, M.; Tanveer, S.

1995-09-01

We present a new numerical method for calculating an evolving 2D Hele-Shaw interface when surface tension effects are neglected. In the case where the flow is directed from the less viscous fluid into the more viscous fluid, the motion of the interface is ill-posed; small deviations in the initial condition will produce significant changes in the ensuing motion. The situation is disastrous for numerical computation, as small roundoff errors can quickly lead to large inaccuracies in the computed solution. Our method of computation is most easily formulated using a conformal map from the fluid domain into a unit disk. Themore » method relies on analytically continuing the initial data and equations of motion into the region exterior to the disk, where the evolution problem becomes well-posed. The equations are then numerically solved in the extended domain. The presence of singularities in the conformal map outside of the disk introduces specific structures along the fluid interface. Our method can explicitly track the location of isolated pole and branch point singularities, allowing us to draw connections between the development of interfacial patterns and the motion of singularities as they approach the unit disk. In particular, we are able to relate physical features such as finger shape, side-branch formation, and competition between fingers to the nature and location of the singularities. The usefulness of this method in studying the formation of topological singularities (self-intersections of the interface) is also pointed out. 47 refs., 10 figs., 1 tab.« less

Testing the monogamy relations via rank-2 mixtures

NASA Astrophysics Data System (ADS)

Jung, Eylee; Park, DaeKil

2016-10-01

We introduce two tangle-based four-party entanglement measures t1 and t2, and two negativity-based measures n1 and n2, which are derived from the monogamy relations. These measures are computed for three four-qubit maximally entangled and W states explicitly. We also compute these measures for the rank-2 mixture ρ4=p | GHZ4>< GHZ4|+(1 -p ) | W4>< W4| by finding the corresponding optimal decompositions. It turns out that t1(ρ4) is trivial and the corresponding optimal decomposition is equal to the spectral decomposition. Probably, this triviality is a sign of the fact that the corresponding monogamy inequality is not sufficiently tight. We fail to compute t2(ρ4) due to the difficulty in the calculation of the residual entanglement. The negativity-based measures n1(ρ4) and n2(ρ4) are explicitly computed and the corresponding optimal decompositions are also derived explicitly.

Beyond CMOS computing with spin and polarization

NASA Astrophysics Data System (ADS)

Manipatruni, Sasikanth; Nikonov, Dmitri E.; Young, Ian A.

2018-04-01

Spintronic and multiferroic systems are leading candidates for achieving attojoule-class logic gates for computing, thereby enabling the continuation of Moore's law for transistor scaling. However, shifting the materials focus of computing towards oxides and topological materials requires a holistic approach addressing energy, stochasticity and complexity.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

Routine human-competitive machine intelligence by means of genetic programming

NASA Astrophysics Data System (ADS)

Koza, John R.; Streeter, Matthew J.; Keane, Martin

2004-01-01

Genetic programming is a systematic method for getting computers to automatically solve a problem. Genetic programming starts from a high-level statement of what needs to be done and automatically creates a computer program to solve the problem. The paper demonstrates that genetic programming (1) now routinely delivers high-return human-competitive machine intelligence; (2) is an automated invention machine; (3) can automatically create a general solution to a problem in the form of a parameterized topology; and (4) has delivered a progression of qualitatively more substantial results in synchrony with five approximately order-of-magnitude increases in the expenditure of computer time. Recent results involving the automatic synthesis of the topology and sizing of analog electrical circuits and controllers demonstrate these points.

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.

Topological Superconductivity on the Surface of Fe-Based Superconductors.

PubMed

Xu, Gang; Lian, Biao; Tang, Peizhe; Qi, Xiao-Liang; Zhang, Shou-Cheng

2016-07-22

As one of the simplest systems for realizing Majorana fermions, the topological superconductor plays an important role in both condensed matter physics and quantum computations. Based on ab initio calculations and the analysis of an effective 8-band model with superconducting pairing, we demonstrate that the three-dimensional extended s-wave Fe-based superconductors such as Fe_{1+y}Se_{0.5}Te_{0.5} have a metallic topologically nontrivial band structure, and exhibit a normal-topological-normal superconductivity phase transition on the (001) surface by tuning the bulk carrier doping level. In the topological superconductivity (TSC) phase, a Majorana zero mode is trapped at the end of a magnetic vortex line. We further show that the surface TSC phase only exists up to a certain bulk pairing gap, and there is a normal-topological phase transition driven by the temperature, which has not been discussed before. These results pave an effective way to realize the TSC and Majorana fermions in a large class of superconductors.

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.

PubMed

Sedwards, Sean; Mazza, Tommaso

2007-10-15

Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. While it is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, few, if any, explicitly model the topology of the membranes themselves. Discrete stochastic simulation potentially offers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described at the lowest level, i.e. by mass action. Simulation is a form of computer-aided analysis, relying on human interpretation to derive meaning. To improve efficiency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on formal language theory and has been shown to have decidable properties (Cavaliere and Sedwards, 2006), allowing formal analysis in addition to simulation. The simulator provides variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations. In addition to its compact native syntax, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB m-files. Cyto-Sim is available free, either as an applet or a stand-alone Java program via the web page (http://www.cosbi.eu/Rpty_Soft_CytoSim.php). Other versions can be made available upon request.

Explicitly computing geodetic coordinates from Cartesian coordinates

NASA Astrophysics Data System (ADS)

Zeng, Huaien

2013-04-01

This paper presents a new form of quartic equation based on Lagrange's extremum law and a Groebner basis under the constraint that the geodetic height is the shortest distance between a given point and the reference ellipsoid. A very explicit and concise formulae of the quartic equation by Ferrari's line is found, which avoids the need of a good starting guess for iterative methods. A new explicit algorithm is then proposed to compute geodetic coordinates from Cartesian coordinates. The convergence region of the algorithm is investigated and the corresponding correct solution is given. Lastly, the algorithm is validated with numerical experiments.

Explicit robust schemes for implementation of a class of principal value-based constitutive models: Symbolic and numeric implementation

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.; Tan, H. Q.; Zhang, Y.

1993-01-01

The issue of developing effective and robust schemes to implement a class of the Ogden-type hyperelastic constitutive models is addressed. To this end, special purpose functions (running under MACSYMA) are developed for the symbolic derivation, evaluation, and automatic FORTRAN code generation of explicit expressions for the corresponding stress function and material tangent stiffness tensors. These explicit forms are valid over the entire deformation range, since the singularities resulting from repeated principal-stretch values have been theoretically removed. The required computational algorithms are outlined, and the resulting FORTRAN computer code is presented.

Making classical and quantum canonical general relativity computable through a power series expansion in the inverse cosmological constant.

PubMed

Gambini, R; Pullin, J

2000-12-18

We consider general relativity with a cosmological constant as a perturbative expansion around a completely solvable diffeomorphism invariant field theory. This theory is the lambda --> infinity limit of general relativity. This allows an explicit perturbative computational setup in which the quantum states of the theory and the classical observables can be explicitly computed. An unexpected relationship arises at a quantum level between the discrete spectrum of the volume operator and the allowed values of the cosmological constant.

Effects of Explicit and Implicit Prompts on Students' Inquiry Practices in Computer-Supported Learning Environments in High School Earth Science

ERIC Educational Resources Information Center

Fang, Su-Chi; Hsu, Ying-Shao; Hsu, Wei Hsiu

2016-01-01

The study explored how to best use scaffolds for supporting students' inquiry practices in computer-supported learning environments. We designed a series of inquiry units assisted with three versions of written inquiry prompts (generic and context-specific); that is, three scaffold-fading conditions: implicit, explicit, and fading. We then…

Using maximum topology matching to explore differences in species distribution models

USGS Publications Warehouse

Poco, Jorge; Doraiswamy, Harish; Talbert, Marian; Morisette, Jeffrey; Silva, Claudio

2015-01-01

Species distribution models (SDM) are used to help understand what drives the distribution of various plant and animal species. These models are typically high dimensional scalar functions, where the dimensions of the domain correspond to predictor variables of the model algorithm. Understanding and exploring the differences between models help ecologists understand areas where their data or understanding of the system is incomplete and will help guide further investigation in these regions. These differences can also indicate an important source of model to model uncertainty. However, it is cumbersome and often impractical to perform this analysis using existing tools, which allows for manual exploration of the models usually as 1-dimensional curves. In this paper, we propose a topology-based framework to help ecologists explore the differences in various SDMs directly in the high dimensional domain. In order to accomplish this, we introduce the concept of maximum topology matching that computes a locality-aware correspondence between similar extrema of two scalar functions. The matching is then used to compute the similarity between two functions. We also design a visualization interface that allows ecologists to explore SDMs using their topological features and to study the differences between pairs of models found using maximum topological matching. We demonstrate the utility of the proposed framework through several use cases using different data sets and report the feedback obtained from ecologists.

Optimization of Aerospace Structure Subject to Damage Tolerance Criteria

NASA Technical Reports Server (NTRS)

Akgun, Mehmet A.

1999-01-01

The objective of this cooperative agreement was to seek computationally efficient ways to optimize aerospace structures subject to damage tolerance criteria. Optimization was to involve sizing as well as topology optimization. The work was done in collaboration with Steve Scotti, Chauncey Wu and Joanne Walsh at the NASA Langley Research Center. Computation of constraint sensitivity is normally the most time-consuming step of an optimization procedure. The cooperative work first focused on this issue and implemented the adjoint method of sensitivity computation in an optimization code (runstream) written in Engineering Analysis Language (EAL). The method was implemented both for bar and plate elements including buckling sensitivity for the latter. Lumping of constraints was investigated as a means to reduce the computational cost. Adjoint sensitivity computation was developed and implemented for lumped stress and buckling constraints. Cost of the direct method and the adjoint method was compared for various structures with and without lumping. The results were reported in two papers. It is desirable to optimize topology of an aerospace structure subject to a large number of damage scenarios so that a damage tolerant structure is obtained. Including damage scenarios in the design procedure is critical in order to avoid large mass penalties at later stages. A common method for topology optimization is that of compliance minimization which has not been used for damage tolerant design. In the present work, topology optimization is treated as a conventional problem aiming to minimize the weight subject to stress constraints. Multiple damage configurations (scenarios) are considered. Each configuration has its own structural stiffness matrix and, normally, requires factoring of the matrix and solution of the system of equations. Damage that is expected to be tolerated is local and represents a small change in the stiffness matrix compared to the baseline (undamaged) structure. The exact solution to a slightly modified set of equations can be obtained from the baseline solution economically without actually solving the modified system. Sherrnan-Morrison-Woodbury (SMW) formulas are matrix update formulas that allow this. SMW formulas were therefore used here to compute adjoint displacements for sensitivity computation and structural displacements in damaged configurations.

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

Statistical Analysis of Protein Ensembles

NASA Astrophysics Data System (ADS)

Máté, Gabriell; Heermann, Dieter

2014-04-01

As 3D protein-configuration data is piling up, there is an ever-increasing need for well-defined, mathematically rigorous analysis approaches, especially that the vast majority of the currently available methods rely heavily on heuristics. We propose an analysis framework which stems from topology, the field of mathematics which studies properties preserved under continuous deformations. First, we calculate a barcode representation of the molecules employing computational topology algorithms. Bars in this barcode represent different topological features. Molecules are compared through their barcodes by statistically determining the difference in the set of their topological features. As a proof-of-principle application, we analyze a dataset compiled of ensembles of different proteins, obtained from the Ensemble Protein Database. We demonstrate that our approach correctly detects the different protein groupings.

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.

Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems.

PubMed

Setiawan, F; Sengupta, K; Spielman, I B; Sau, Jay D

2015-11-06

We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems

NASA Astrophysics Data System (ADS)

Setiawan, F.; Sengupta, K.; Spielman, I. B.; Sau, Jay D.

2015-11-01

We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

Invariance of Topological Indices Under Hilbert Space Truncation

DOE PAGES

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

2018-01-05

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

Observation of topological superconductivity on the surface of an iron-based superconductor.

PubMed

Zhang, Peng; Yaji, Koichiro; Hashimoto, Takahiro; Ota, Yuichi; Kondo, Takeshi; Okazaki, Kozo; Wang, Zhijun; Wen, Jinsheng; Gu, G D; Ding, Hong; Shin, Shik

2018-04-13

Topological superconductors are predicted to host exotic Majorana states that obey non-Abelian statistics and can be used to implement a topological quantum computer. Most of the proposed topological superconductors are realized in difficult-to-fabricate heterostructures at very low temperatures. By using high-resolution spin-resolved and angle-resolved photoelectron spectroscopy, we find that the iron-based superconductor FeTe 1- x Se x ( x = 0.45; superconducting transition temperature T c = 14.5 kelvin) hosts Dirac-cone-type spin-helical surface states at the Fermi level; the surface states exhibit an s-wave superconducting gap below T c Our study shows that the surface states of FeTe 0.55 Se 0.45 are topologically superconducting, providing a simple and possibly high-temperature platform for realizing Majorana states. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Photonic zero mode in a non-Hermitian photonic lattice.

PubMed

Pan, Mingsen; Zhao, Han; Miao, Pei; Longhi, Stefano; Feng, Liang

2018-04-03

Zero-energy particles (such as Majorana fermions) are newly predicted quasiparticles and are expected to play an important role in fault-tolerant quantum computation. In conventional Hermitian quantum systems, however, such zero states are vulnerable and even become vanishing if couplings with surroundings are of the same topological nature. Here we demonstrate a robust photonic zero mode sustained by a spatial non-Hermitian phase transition in a parity-time (PT) symmetric lattice, despite the same topological order across the entire system. The non-Hermitian-enhanced topological protection ensures the reemergence of the zero mode at the phase transition interface when the two semi-lattices under different PT phases are decoupled effectively in their real spectra. Residing at the midgap level of the PT symmetric spectrum, the zero mode is topologically protected against topological disorder. We experimentally validated the robustness of the zero-energy mode by ultrafast heterodyne measurements of light transport dynamics in a silicon waveguide lattice.

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

PubMed

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

2017-02-13

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

Edge-mode superconductivity in a two-dimensional topological insulator.

PubMed

Pribiag, Vlad S; Beukman, Arjan J A; Qu, Fanming; Cassidy, Maja C; Charpentier, Christophe; Wegscheider, Werner; Kouwenhoven, Leo P

2015-07-01

Topological superconductivity is an exotic state of matter that supports Majorana zero-modes, which have been predicted to occur in the surface states of three-dimensional systems, in the edge states of two-dimensional systems, and in one-dimensional wires. Localized Majorana zero-modes obey non-Abelian exchange statistics, making them interesting building blocks for topological quantum computing. Here, we report superconductivity induced in the edge modes of semiconducting InAs/GaSb quantum wells, a two-dimensional topological insulator. Using superconducting quantum interference we demonstrate gate-tuning between edge-dominated and bulk-dominated regimes of superconducting transport. The edge-dominated regime arises only under conditions of high-bulk resistivity, which we associate with the two-dimensional topological phase. These experiments establish InAs/GaSb as a promising platform for the confinement of Majoranas into localized states, enabling future investigations of non-Abelian statistics.

Invariance of Topological Indices Under Hilbert Space Truncation

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

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

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

Evidence for fish dispersal from spatial analysis of stream network topology

USGS Publications Warehouse

Hitt, N.P.; Angermeier, P.L.

2008-01-01

Developing spatially explicit conservation strategies for stream fishes requires an understanding of the spatial structure of dispersal within stream networks. We explored spatial patterns of stream fish dispersal by evaluating how the size and proximity of connected streams (i.e., stream network topology) explained variation in fish assemblage structure and how this relationship varied with local stream size. We used data from the US Environmental Protection Agency's Environmental Monitoring and Assessment Program in wadeable streams of the Mid-Atlantic Highlands region (n = 308 sites). We quantified stream network topology with a continuous analysis based on the rate of downstream flow accumulation from sites and with a discrete analysis based on the presence of mainstem river confluences (i.e., basin area >250 km2) within 20 fluvial km (fkm) from sites. Continuous variation in stream network topology was related to local species richness within a distance of ???10 fkm, suggesting an influence of fish dispersal within this spatial grain. This effect was explained largely by catostomid species, cyprinid species, and riverine species, but was not explained by zoogeographic regions, ecoregions, sampling period, or spatial autocorrelation. Sites near mainstem river confluences supported greater species richness and abundance of catostomid, cyprinid, and ictalurid fishes than did sites >20 fkm from such confluences. Assemblages at sites on the smallest streams were not related to stream network topology, consistent with the hypothesis that local stream size regulates the influence of regional dispersal. These results demonstrate that the size and proximity of connected streams influence the spatial distribution of fish and suggest that these influences can be incorporated into the designs of stream bioassessments and reserves to enhance management efficacy. ?? 2008 by The North American Benthological Society.

Dirac state in a centrosymmetric superconductor α -PdBi2

NASA Astrophysics Data System (ADS)

Dimitri, Klauss; Hosen, M. Mofazzel; Dhakal, Gyanendra; Choi, Hongchul; Kabir, Firoza; Sims, Christopher; Kaczorowski, Dariusz; Durakiewicz, Tomasz; Zhu, Jian-Xin; Neupane, Madhab

2018-04-01

Topological superconductor (TSC) hosting Majorana fermions has been established as a milestone that may shift our scientific trajectory from research to applications in topological quantum computing. Recently, superconducting Pd-Bi binaries have attracted great attention as a possible medium for the TSC phase as a result of their large spin-orbit coupling strength. Here, we report a systematic high-resolution angle-resolved photoemission spectroscopy (ARPES) study on the normal state electronic structure of superconducting α -PdBi2 (Tc=1.7 K). Our results show the presence of Dirac states at higher-binding energy with the location of the Dirac point at 1.26 eV below the chemical potential at the zone center. Furthermore, the ARPES data indicate multiple band crossings at the chemical potential, consistent with the metallic behavior of α -PdBi2 . Our detailed experimental studies are complemented by first-principles calculations, which reveal the presence of surface Rashba states residing in the vicinity of the chemical potential. The obtained results provide an opportunity to investigate the relationship between superconductivity, topology, and the Majorana fermion, as well as explore pathways to possible future platforms for topological quantum computing.

Effect of exercise on patient specific abdominal aortic aneurysm flow topology and mixing

PubMed Central

Arzani, Amirhossein; Les, Andrea S.; Dalman, Ronald L.; Shadden, Shawn C.

2014-01-01

SUMMARY Computational fluid dynamics modeling was used to investigate changes in blood transport topology between rest and exercise conditions in five patient-specific abdominal aortic aneurysm models. Magnetic resonance imaging was used to provide the vascular anatomy and necessary boundary conditions for simulating blood velocity and pressure fields inside each model. Finite-time Lyapunov exponent fields, and associated Lagrangian coherent structures, were computed from blood velocity data, and used to compare features of the transport topology between rest and exercise both mechanistically and qualitatively. A mix-norm and mix-variance measure based on fresh blood distribution throughout the aneurysm over time were implemented to quantitatively compare mixing between rest and exercise. Exercise conditions resulted in higher and more uniform mixing, and reduced the overall residence time in all aneurysms. Separated regions of recirculating flow were commonly observed in rest, and these regions were either reduced or removed by attached and unidirectional flow during exercise, or replaced with regional chaotic and transiently turbulent mixing, or persisted and even extended during exercise. The main factor that dictated the change in flow topology from rest to exercise was the behavior of the jet of blood penetrating into the aneurysm during systole. PMID:24493404

High-Threshold Fault-Tolerant Quantum Computation with Analog Quantum Error Correction

NASA Astrophysics Data System (ADS)

Fukui, Kosuke; Tomita, Akihisa; Okamoto, Atsushi; Fujii, Keisuke

2018-04-01

To implement fault-tolerant quantum computation with continuous variables, the Gottesman-Kitaev-Preskill (GKP) qubit has been recognized as an important technological element. However, it is still challenging to experimentally generate the GKP qubit with the required squeezing level, 14.8 dB, of the existing fault-tolerant quantum computation. To reduce this requirement, we propose a high-threshold fault-tolerant quantum computation with GKP qubits using topologically protected measurement-based quantum computation with the surface code. By harnessing analog information contained in the GKP qubits, we apply analog quantum error correction to the surface code. Furthermore, we develop a method to prevent the squeezing level from decreasing during the construction of the large-scale cluster states for the topologically protected, measurement-based, quantum computation. We numerically show that the required squeezing level can be relaxed to less than 10 dB, which is within the reach of the current experimental technology. Hence, this work can considerably alleviate this experimental requirement and take a step closer to the realization of large-scale quantum computation.

A Whirlwind Tour of Computational Geometry.

ERIC Educational Resources Information Center

Graham, Ron; Yao, Frances

1990-01-01

Described is computational geometry which used concepts and results from classical geometry, topology, combinatorics, as well as standard algorithmic techniques such as sorting and searching, graph manipulations, and linear programing. Also included are special techniques and paradigms. (KR)

Walking or Waiting? Topologies of the Breeding Ground in Malaria Control

PubMed Central

Lezaun, Javier

2013-01-01

Few places bear as much historical and scientific significance as the breeding ground, the accumulation of stagnant water where disease-carrying insects lay their eggs. Since the turn of the twentieth century, when mosquitoes of the Anopheles genus were identified as the vector of malaria transmission, these aquatic habitats have been a key object of epidemiological research and public health intervention against the disease. Yet the breeding ground can be incorporated into a number of different topologies, each implying a different spatialization of malaria and a distinct imagination of what kind of mosquito control is ‘doable'. A contemporary example of malaria control in Dar es Salaam, Tanzania, illuminates an essential tension between what we characterize as territorial and bionomic approaches to the breeding ground—that is, between control strategies premised on treating all mosquito habitats within a given region, and those that prioritize certain sites on the basis of their position within ecological networks. Each topology localizes the breeding ground by reference to a distinct set of relations, and thus advances an idiosyncratic understanding of what sort of research is worthwhile conducting and what kinds of intervention are sustainable. The multiple ways in which the breeding ground can become an object of research and action clarifies the role of topology as an infra-logic of public health, and makes explicit the politics implicit in efforts to bring different orders of the local to scale. PMID:25937707

Quantum computation on the edge of a symmetry-protected topological order.

PubMed

Miyake, Akimasa

2010-07-23

We elaborate the idea of quantum computation through measuring the correlation of a gapped ground state, while the bulk Hamiltonian is utilized to stabilize the resource. A simple computational primitive, by pulling out a single spin adiabatically from the bulk followed by its measurement, is shown to make any ground state of the one-dimensional isotropic Haldane phase useful ubiquitously as a quantum logical wire. The primitive is compatible with certain discrete symmetries that protect this topological order, and the antiferromagnetic Heisenberg spin-1 finite chain is practically available. Our approach manifests a holographic principle in that the logical information of a universal quantum computer can be written and processed perfectly on the edge state (i.e., boundary) of the system, supported by the persistent entanglement from the bulk even when the ground state and its evolution cannot be exactly analyzed.

Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.

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

PubMed

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

2015-12-01

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

Explicit time integration of finite element models on a vectorized, concurrent computer with shared memory

NASA Technical Reports Server (NTRS)

Gilbertsen, Noreen D.; Belytschko, Ted

1990-01-01

The implementation of a nonlinear explicit program on a vectorized, concurrent computer with shared memory is described and studied. The conflict between vectorization and concurrency is described and some guidelines are given for optimal block sizes. Several example problems are summarized to illustrate the types of speed-ups which can be achieved by reprogramming as compared to compiler optimization.

Topology-optimized dual-polarization Dirac cones

NASA Astrophysics Data System (ADS)

Lin, Zin; Christakis, Lysander; Li, Yang; Mazur, Eric; Rodriguez, Alejandro W.; Lončar, Marko

2018-02-01

We apply a large-scale computational technique, known as topology optimization, to the inverse design of photonic Dirac cones. In particular, we report on a variety of photonic crystal geometries, realizable in simple isotropic dielectric materials, which exhibit dual-polarization Dirac cones. We present photonic crystals of different symmetry types, such as fourfold and sixfold rotational symmetries, with Dirac cones at different points within the Brillouin zone. The demonstrated and related optimization techniques open avenues to band-structure engineering and manipulating the propagation of light in periodic media, with possible applications to exotic optical phenomena such as effective zero-index media and topological photonics.

Fivebranes and 3-manifold homology

DOE PAGES

Gukov, Sergei; Putrov, Pavel; Vafa, Cumrun

2017-07-14

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

MAX - An advanced parallel computer for space applications

NASA Technical Reports Server (NTRS)

Lewis, Blair F.; Bunker, Robert L.

1991-01-01

MAX is a fault-tolerant multicomputer hardware and software architecture designed to meet the needs of NASA spacecraft systems. It consists of conventional computing modules (computers) connected via a dual network topology. One network is used to transfer data among the computers and between computers and I/O devices. This network's topology is arbitrary. The second network operates as a broadcast medium for operating system synchronization messages and supports the operating system's Byzantine resilience. A fully distributed operating system supports multitasking in an asynchronous event and data driven environment. A large grain dataflow paradigm is used to coordinate the multitasking and provide easy control of concurrency. It is the basis of the system's fault tolerance and allows both static and dynamical location of tasks. Redundant execution of tasks with software voting of results may be specified for critical tasks. The dataflow paradigm also supports simplified software design, test and maintenance. A unique feature is a method for reliably patching code in an executing dataflow application.

Global regularizing flows with topology preservation for active contours and polygons.

PubMed

Sundaramoorthi, Ganesh; Yezzi, Anthony

2007-03-01

Active contour and active polygon models have been used widely for image segmentation. In some applications, the topology of the object(s) to be detected from an image is known a priori, despite a complex unknown geometry, and it is important that the active contour or polygon maintain the desired topology. In this work, we construct a novel geometric flow that can be added to image-based evolutions of active contours and polygons in order to preserve the topology of the initial contour or polygon. We emphasize that, unlike other methods for topology preservation, the proposed geometric flow continually adjusts the geometry of the original evolution in a gradual and graceful manner so as to prevent a topology change long before the curve or polygon becomes close to topology change. The flow also serves as a global regularity term for the evolving contour, and has smoothness properties similar to curvature flow. These properties of gradually adjusting the original flow and global regularization prevent geometrical inaccuracies common with simple discrete topology preservation schemes. The proposed topology preserving geometric flow is the gradient flow arising from an energy that is based on electrostatic principles. The evolution of a single point on the contour depends on all other points of the contour, which is different from traditional curve evolutions in the computer vision literature.

On Spatially Explicit Models of Cholera Epidemics: Hydrologic controls, environmental drivers, human-mediated transmissions (Invited)

NASA Astrophysics Data System (ADS)

Rinaldo, A.; Bertuzzo, E.; Mari, L.; Righetto, L.; Gatto, M.; Casagrandi, R.; Rodriguez-Iturbe, I.

2010-12-01

A recently proposed model for cholera epidemics is examined. The model accounts for local communities of susceptibles and infectives in a spatially explicit arrangement of nodes linked by networks having different topologies. The vehicle of infection (Vibrio cholerae) is transported through the network links which are thought of as hydrological connections among susceptible communities. The mathematical tools used are borrowed from general schemes of reactive transport on river networks acting as the environmental matrix for the circulation and mixing of water-borne pathogens. The results of a large-scale application to the Kwa Zulu (Natal) epidemics of 2001-2002 will be discussed. Useful theoretical results derived in the spatially-explicit context will also be reviewed (like e.g. the exact derivation of the speed of propagation for traveling fronts of epidemics on regular lattices endowed with uniform population density). Network effects will be discussed. The analysis of the limit case of uniformly distributed population density proves instrumental in establishing the overall conditions for the relevance of spatially explicit models. To that extent, it is shown that the ratio between spreading and disease outbreak timescales proves the crucial parameter. The relevance of our results lies in the major differences potentially arising between the predictions of spatially explicit models and traditional compartmental models of the SIR-like type. Our results suggest that in many cases of real-life epidemiological interest timescales of disease dynamics may trigger outbreaks that significantly depart from the predictions of compartmental models. Finally, a view on further developments includes: hydrologically improved aquatic reservoir models for pathogens; human mobility patterns affecting disease propagation; double-peak emergence and seasonality in the spatially explicit epidemic context.

A computational study of the topology of vortex breakdown

NASA Technical Reports Server (NTRS)

Spall, Robert E.; Gatski, Thomas B.

1991-01-01

A fully three-dimensional numerical simulation of vortex breakdown using the unsteady, incompressible Navier-Stokes equations has been performed. Solutions to four distinct types of breakdown are identified and compared with experimental results. The computed solutions include weak helical, double helix, spiral, and bubble-type breakdowns. The topological structure of the various breakdowns as well as their interrelationship are studied. The data reveal that the asymmetric modes of breakdown may be subject to additional breakdowns as the vortex core evolves in the streamwise direction. The solutions also show that the freestream axial velocity distribution has a significant effect on the position and type of vortex breakdown.

Modeling and distributed gain scheduling strategy for load frequency control in smart grids with communication topology changes.

PubMed

Liu, Shichao; Liu, Xiaoping P; El Saddik, Abdulmotaleb

2014-03-01

In this paper, we investigate the modeling and distributed control problems for the load frequency control (LFC) in a smart grid. In contrast with existing works, we consider more practical and real scenarios, where the communication topology of the smart grid changes because of either link failures or packet losses. These topology changes are modeled as a time-varying communication topology matrix. By using this matrix, a new closed-loop power system model is proposed to integrate the communication topology changes into the dynamics of a physical power system. The globally asymptotical stability of this closed-loop power system is analyzed. A distributed gain scheduling LFC strategy is proposed to compensate for the potential degradation of dynamic performance (mean square errors of state vectors) of the power system under communication topology changes. In comparison to conventional centralized control approaches, the proposed method can improve the robustness of the smart grid to the variation of the communication network as well as to reduce computation load. Simulation results show that the proposed distributed gain scheduling approach is capable to improve the robustness of the smart grid to communication topology changes. © 2013 ISA. Published by ISA. All rights reserved.

A general multiblock Euler code for propulsion integration. Volume 1: Theory document

NASA Technical Reports Server (NTRS)

Chen, H. C.; Su, T. Y.; Kao, T. J.

1991-01-01

A general multiblock Euler solver was developed for the analysis of flow fields over geometrically complex configurations either in free air or in a wind tunnel. In this approach, the external space around a complex configuration was divided into a number of topologically simple blocks, so that surface-fitted grids and an efficient flow solution algorithm could be easily applied in each block. The computational grid in each block is generated using a combination of algebraic and elliptic methods. A grid generation/flow solver interface program was developed to facilitate the establishment of block-to-block relations and the boundary conditions for each block. The flow solver utilizes a finite volume formulation and an explicit time stepping scheme to solve the Euler equations. A multiblock version of the multigrid method was developed to accelerate the convergence of the calculations. The generality of the method was demonstrated through the analysis of two complex configurations at various flow conditions. Results were compared to available test data. Two accompanying volumes, user manuals for the preparation of multi-block grids (vol. 2) and for the Euler flow solver (vol. 3), provide information on input data format and program execution.

Understanding regulatory networks requires more than computing a multitude of graph statistics. Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O.C. Martin et al.

NASA Astrophysics Data System (ADS)

Tkačik, Gašper

2016-07-01

The article by O. Martin and colleagues provides a much needed systematic review of a body of work that relates the topological structure of genetic regulatory networks to evolutionary selection for function. This connection is very important. Using the current wealth of genomic data, statistical features of regulatory networks (e.g., degree distributions, motif composition, etc.) can be quantified rather easily; it is, however, often unclear how to interpret the results. On a graph theoretic level the statistical significance of the results can be evaluated by comparing observed graphs to ;randomized; ones (bravely ignoring the issue of how precisely to randomize!) and comparing the frequency of appearance of a particular network structure relative to a randomized null expectation. While this is a convenient operational test for statistical significance, its biological meaning is questionable. In contrast, an in-silico genotype-to-phenotype model makes explicit the assumptions about the network function, and thus clearly defines the expected network structures that can be compared to the case of no selection for function and, ultimately, to data.

Knowledge-based automated technique for measuring total lung volume from CT

NASA Astrophysics Data System (ADS)

Brown, Matthew S.; McNitt-Gray, Michael F.; Mankovich, Nicholas J.; Goldin, Jonathan G.; Aberle, Denise R.

1996-04-01

A robust, automated technique has been developed for estimating total lung volumes from chest computed tomography (CT) images. The technique includes a method for segmenting major chest anatomy. A knowledge-based approach automates the calculation of separate volumes of the whole thorax, lungs, and central tracheo-bronchial tree from volumetric CT data sets. A simple, explicit 3D model describes properties such as shape, topology and X-ray attenuation, of the relevant anatomy, which constrain the segmentation of these anatomic structures. Total lung volume is estimated as the sum of the right and left lungs and excludes the central airways. The method requires no operator intervention. In preliminary testing, the system was applied to image data from two healthy subjects and four patients with emphysema who underwent both helical CT and pulmonary function tests. To obtain single breath-hold scans, the healthy subjects were scanned with a collimation of 5 mm and a pitch of 1.5, while the emphysema patients were scanned with collimation of 10 mm at a pitch of 2.0. CT data were reconstructed as contiguous image sets. Automatically calculated volumes were consistent with body plethysmography results (< 10% difference).

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

PubMed Central

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

2001-01-01

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

SCOUT: simultaneous time segmentation and community detection in dynamic networks

PubMed Central

Hulovatyy, Yuriy; Milenković, Tijana

2016-01-01

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

A comparison of two central difference schemes for solving the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Maksymiuk, C. M.; Swanson, R. C.; Pulliam, T. H.

1990-01-01

Five viscous transonic airfoil cases were computed by two significantly different computational fluid dynamics codes: An explicit finite-volume algorithm with multigrid, and an implicit finite-difference approximate-factorization method with Eigenvector diagonalization. Both methods are described in detail, and their performance on the test cases is compared. The codes utilized the same grids, turbulence model, and computer to provide the truest test of the algorithms. The two approaches produce very similar results, which, for attached flows, also agree well with experimental results; however, the explicit code is considerably faster.

Application of the Hughes-LIU algorithm to the 2-dimensional heat equation

NASA Technical Reports Server (NTRS)

Malkus, D. S.; Reichmann, P. I.; Haftka, R. T.

1982-01-01

An implicit explicit algorithm for the solution of transient problems in structural dynamics is described. The method involved dividing the finite elements into implicit and explicit groups while automatically satisfying the conditions. This algorithm is applied to the solution of the linear, transient, two dimensional heat equation subject to an initial condition derived from the soluton of a steady state problem over an L-shaped region made up of a good conductor and an insulating material. Using the IIT/PRIME computer with virtual memory, a FORTRAN computer program code was developed to make accuracy, stability, and cost comparisons among the fully explicit Euler, the Hughes-Liu, and the fully implicit Crank-Nicholson algorithms. The Hughes-Liu claim that the explicit group governs the stability of the entire region while maintaining the unconditional stability of the implicit group is illustrated.

Finite-size and asymptotic behaviors of the gyration radius of knotted cylindrical self-avoiding polygons.

PubMed

Shimamura, Miyuki K; Deguchi, Tetsuo

2002-05-01

Several nontrivial properties are shown for the mean-square radius of gyration R2(K) of ring polymers with a fixed knot type K. Through computer simulation, we discuss both finite size and asymptotic behaviors of the gyration radius under the topological constraint for self-avoiding polygons consisting of N cylindrical segments with radius r. We find that the average size of ring polymers with the knot K can be much larger than that of no topological constraint. The effective expansion due to the topological constraint depends strongly on the parameter r that is related to the excluded volume. The topological expansion is particularly significant for the small r case, where the simulation result is associated with that of random polygons with the knot K.

Multi-Scale Hierarchical and Topological Design of Structures for Failure Resistance

DTIC Science & Technology

2013-10-04

materials, simulation, 3D printing , advanced manufacturing, design, fracture Markus J. Buehler Massachusetts Institute of Technology (MIT) 77...by Mineralized Natural Materials: Computation, 3D printing , and Testing, Advanced Functional Materials, (09 2013): 0. doi: 10.1002/adfm.201300215 10...have made substantial progress. Recent work focuses on the analysis of topological effects of composite design, 3D printing of bioinspired and

Automated Slicing for a Multi-Axis Metal Deposition System (Preprint)

DTIC Science & Technology

2006-09-01

experimented with different materials like H13 tool steel to build the part. Following the same slicing and scanning toolpath result, there is a geometric...and analysis tool -centroidal axis. Similar to medial axis, it contains geometry and topological information but is significantly computationally...geometry reasoning and analysis tool -centroidal axis. Similar to medial axis, it contains geometry and topological information but is significantly

Topology synthesis and size optimization of morphing wing structures

NASA Astrophysics Data System (ADS)

Inoyama, Daisaku

This research demonstrates a novel topology and size optimization methodology for synthesis of distributed actuation systems with specific applications to morphing air vehicle structures. The main emphasis is placed on the topology and size optimization problem formulations and the development of computational modeling concepts. The analysis model is developed to meet several important criteria: It must allow a rigid-body displacement, as well as a variation in planform area, with minimum strain on structural members while retaining acceptable numerical stability for finite element analysis. Topology optimization is performed on a semi-ground structure with design variables that control the system configuration. In effect, the optimization process assigns morphing members as "soft" elements, non-morphing load-bearing members as "stiff' elements, and non-existent members as "voids." The optimization process also determines the optimum actuator placement, where each actuator is represented computationally by equal and opposite nodal forces with soft axial stiffness. In addition, the configuration of attachments that connect the morphing structure to a non-morphing structure is determined simultaneously. Several different optimization problem formulations are investigated to understand their potential benefits in solution quality, as well as meaningfulness of the formulations. Extensions and enhancements to the initial concept and problem formulations are made to accommodate multiple-configuration definitions. In addition, the principal issues on the external-load dependency and the reversibility of a design, as well as the appropriate selection of a reference configuration, are addressed in the research. The methodology to control actuator distributions and concentrations is also discussed. Finally, the strategy to transfer the topology solution to the sizing optimization is developed and cross-sectional areas of existent structural members are optimized under applied aerodynamic loads. That is, the optimization process is implemented in sequential order: The actuation system layout is first determined through multi-disciplinary topology optimization process, and then the thickness or cross-sectional area of each existent member is optimized under given constraints and boundary conditions. Sample problems are solved to demonstrate the potential capabilities of the presented methodology. The research demonstrates an innovative structural design procedure from a computational perspective and opens new insights into the potential design requirements and characteristics of morphing structures.

A structural topological optimization method for multi-displacement constraints and any initial topology configuration

NASA Astrophysics Data System (ADS)

Rong, J. H.; Yi, J. H.

2010-10-01

In density-based topological design, one expects that the final result consists of elements either black (solid material) or white (void), without any grey areas. Moreover, one also expects that the optimal topology can be obtained by starting from any initial topology configuration. An improved structural topological optimization method for multi- displacement constraints is proposed in this paper. In the proposed method, the whole optimization process is divided into two optimization adjustment phases and a phase transferring step. Firstly, an optimization model is built to deal with the varied displacement limits, design space adjustments, and reasonable relations between the element stiffness matrix and mass and its element topology variable. Secondly, a procedure is proposed to solve the optimization problem formulated in the first optimization adjustment phase, by starting with a small design space and advancing to a larger deign space. The design space adjustments are automatic when the design domain needs expansions, in which the convergence of the proposed method will not be affected. The final topology obtained by the proposed procedure in the first optimization phase, can approach to the vicinity of the optimum topology. Then, a heuristic algorithm is given to improve the efficiency and make the designed structural topology black/white in both the phase transferring step and the second optimization adjustment phase. And the optimum topology can finally be obtained by the second phase optimization adjustments. Two examples are presented to show that the topologies obtained by the proposed method are of very good 0/1 design distribution property, and the computational efficiency is enhanced by reducing the element number of the design structural finite model during two optimization adjustment phases. And the examples also show that this method is robust and practicable.

A hybrid computational model to explore the topological characteristics of epithelial tissues.

PubMed

González-Valverde, Ismael; García-Aznar, José Manuel

2017-11-01

Epithelial tissues show a particular topology where cells resemble a polygon-like shape, but some biological processes can alter this tissue topology. During cell proliferation, mitotic cell dilation deforms the tissue and modifies the tissue topology. Additionally, cells are reorganized in the epithelial layer and these rearrangements also alter the polygon distribution. We present here a computer-based hybrid framework focused on the simulation of epithelial layer dynamics that combines discrete and continuum numerical models. In this framework, we consider topological and mechanical aspects of the epithelial tissue. Individual cells in the tissue are simulated by an off-lattice agent-based model, which keeps the information of each cell. In addition, we model the cell-cell interaction forces and the cell cycle. Otherwise, we simulate the passive mechanical behaviour of the cell monolayer using a material that approximates the mechanical properties of the cell. This continuum approach is solved by the finite element method, which uses a dynamic mesh generated by the triangulation of cell polygons. Forces generated by cell-cell interaction in the agent-based model are also applied on the finite element mesh. Cell movement in the agent-based model is driven by the displacements obtained from the deformed finite element mesh of the continuum mechanical approach. We successfully compare the results of our simulations with some experiments about the topology of proliferating epithelial tissues in Drosophila. Our framework is able to model the emergent behaviour of the cell monolayer that is due to local cell-cell interactions, which have a direct influence on the dynamics of the epithelial tissue. Copyright © 2017 John Wiley & Sons, Ltd.

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

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

PubMed

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

2011-03-01

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

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.

Critical phenomena in communication/computation networks with various topologies and suboptimal to optimal resource allocation

NASA Astrophysics Data System (ADS)

Cogoni, Marco; Busonera, Giovanni; Anedda, Paolo; Zanetti, Gianluigi

2015-01-01

We generalize previous studies on critical phenomena in communication networks [1,2] by adding computational capabilities to the nodes. In our model, a set of tasks with random origin, destination and computational structure is distributed on a computational network, modeled as a graph. By varying the temperature of a Metropolis Montecarlo, we explore the global latency for an optimal to suboptimal resource assignment at a given time instant. By computing the two-point correlation function for the local overload, we study the behavior of the correlation distance (both for links and nodes) while approaching the congested phase: a transition from peaked to spread g(r) is seen above a critical (Montecarlo) temperature Tc. The average latency trend of the system is predicted by averaging over several network traffic realizations while maintaining a spatially detailed information for each node: a sharp decrease of performance is found over Tc independently of the workload. The globally optimized computational resource allocation and network routing defines a baseline for a future comparison of the transition behavior with respect to existing routing strategies [3,4] for different network topologies.

Area collapse algorithm computing new curve of 2D geometric objects

NASA Astrophysics Data System (ADS)

Buczek, Michał Mateusz

2017-06-01

The processing of cartographic data demands human involvement. Up-to-date algorithms try to automate a part of this process. The goal is to obtain a digital model, or additional information about shape and topology of input geometric objects. A topological skeleton is one of the most important tools in the branch of science called shape analysis. It represents topological and geometrical characteristics of input data. Its plot depends on using algorithms such as medial axis, skeletonization, erosion, thinning, area collapse and many others. Area collapse, also known as dimension change, replaces input data with lower-dimensional geometric objects like, for example, a polygon with a polygonal chain, a line segment with a point. The goal of this paper is to introduce a new algorithm for the automatic calculation of polygonal chains representing a 2D polygon. The output is entirely contained within the area of the input polygon, and it has a linear plot without branches. The computational process is automatic and repeatable. The requirements of input data are discussed. The author analyzes results based on the method of computing ends of output polygonal chains. Additional methods to improve results are explored. The algorithm was tested on real-world cartographic data received from BDOT/GESUT databases, and on point clouds from laser scanning. An implementation for computing hatching of embankment is described.

Majorana fermions and orthogonal complex structures

NASA Astrophysics Data System (ADS)

Calderón-García, J. S.; Reyes-Lega, A. F.

2018-05-01

Ground states of quadratic Hamiltonians for fermionic systems can be characterized in terms of orthogonal complex structures. The standard way in which such Hamiltonians are diagonalized makes use of a certain “doubling” of the Hilbert space. In this work, we show that this redundancy in the Hilbert space can be completely lifted if the relevant orthogonal structure is taken into account. Such an approach allows for a treatment of Majorana fermions which is both physically and mathematically transparent. Furthermore, an explicit connection between orthogonal complex structures and the topological ℤ2-invariant is given.

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.

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors

PubMed Central

Thorwart, Michael

2018-01-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing. PMID:29756034

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors.

PubMed

Kim, Howon; Palacio-Morales, Alexandra; Posske, Thore; Rózsa, Levente; Palotás, Krisztián; Szunyogh, László; Thorwart, Michael; Wiesendanger, Roland

2018-05-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.

A System for Modelling Cell–Cell Interactions during Plant Morphogenesis

PubMed Central

Dupuy, Lionel; Mackenzie, Jonathan; Rudge, Tim; Haseloff, Jim

2008-01-01

Background and aims During the development of multicellular organisms, cells are capable of interacting with each other through a range of biological and physical mechanisms. A description of these networks of cell–cell interactions is essential for an understanding of how cellular activity is co-ordinated in regionalized functional entities such as tissues or organs. The difficulty of experimenting on living tissues has been a major limitation to describing such systems, and computer modelling appears particularly helpful to characterize the behaviour of multicellular systems. The experimental difficulties inherent to the multitude of parallel interactions that underlie cellular morphogenesis have led to the need for computer models. Methods A new generic model of plant cellular morphogenesis is described that expresses interactions amongst cellular entities explicitly: the plant is described as a multi-scale structure, and interactions between distinct entities is established through a topological neighbourhood. Tissues are represented as 2D biphasic systems where the cell wall responds to turgor pressure through a viscous yielding of the cell wall. Key Results This principle was used in the development of the CellModeller software, a generic tool dedicated to the analysis and modelling of plant morphogenesis. The system was applied to three contrasting study cases illustrating genetic, hormonal and mechanical factors involved in plant morphogenesis. Conclusions Plant morphogenesis is fundamentally a cellular process and the CellModeller software, through its underlying generic model, provides an advanced research tool to analyse coupled physical and biological morphogenetic mechanisms. PMID:17921524

Amplitude-dependent topological edge states in nonlinear phononic lattices

NASA Astrophysics Data System (ADS)

Pal, Raj Kumar; Vila, Javier; Leamy, Michael; Ruzzene, Massimo

2018-03-01

This work investigates the effect of nonlinearities on topologically protected edge states in one- and two-dimensional phononic lattices. We first show that localized modes arise at the interface between two spring-mass chains that are inverted copies of each other. Explicit expressions derived for the frequencies of the localized modes guide the study of the effect of cubic nonlinearities on the resonant characteristics of the interface, which are shown to be described by a Duffing-like equation. Nonlinearities produce amplitude-dependent frequency shifts, which in the case of a softening nonlinearity cause the localized mode to migrate to the bulk spectrum. The case of a hexagonal lattice implementing a phononic analog of a crystal exhibiting the quantum spin Hall effect is also investigated in the presence of weakly nonlinear cubic springs. An asymptotic analysis provides estimates of the amplitude dependence of the localized modes, while numerical simulations illustrate how the lattice response transitions from bulk-to-edge mode-dominated by varying the excitation amplitude. In contrast with the interface mode of the first example studies, this occurs both for hardening and softening springs. The results of this study provide a theoretical framework for the investigation of nonlinear effects that induce and control topologically protected wave modes through nonlinear interactions and amplitude tuning.

The impact of network characteristics on the diffusion of innovations

NASA Astrophysics Data System (ADS)

Peres, Renana

2014-05-01

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

Topological Phases in the Real World

NASA Astrophysics Data System (ADS)

Hsu, Yi-Ting

The experimental discovery and subsequent theoretical understanding of the integer quantum Hall effect, the first known topological phase, has started a revolutionary breakthrough in understanding states of matter since its discovery four decades ago. Topological phases are predicted to have many generic signatures resulting from their underlying topological nature, such as quantized Hall transport, robust boundary states, and possible fractional excitations. The intriguing nature of these signatures and their potential applications in quantum computation has intensely fueled the efforts of the physics community to materialize topological phases. Among various topological phases initially predicted on theoretical grounds, chiral topological superconductors and time-reversal symmetric topological insulators (TI) in three dimension (3D) are two promising candidates for experimental realization and application. The family of materials, Bi2X3 (X = Se, Te), has been predicted and shown experimentally to be time-reversal symmetric 3D TIs through the observation of robust Dirac surface states with Rashba-type spin-winding. Due to their robust surface states with spin-windings, these 3D TIs are expected to be promising materials for producing large spin-transfer torques which are advantageous for spintronics application. As for topological superconductors, despite the exotic excitations that have been extensively proposed as qubits for topological quantum computing, materials hosting topological superconductivity are rare to date and the leading candidate in two dimensions (2D), Sr 2RuO4, has a low transition temperature (Tc ). The goal of my phd study is to push forward the current status of realization of topological phases by materializing higher Tc topological superconductors and investigating the stability of Dirac surface states in 3D TIs. In the first part of this thesis, I will discuss our double-pronged objective for topological superconductors: to propose how to enhance the T c of the existing leading candidate Sr2RuO 4 and to propose new material candidates for topological superconductors. First, by carrying out perturbative renormalization group (RG) analysis, we predicted that straining the ruthenate films will maximize the T c for triplet pairing channel when the Fermi surface is close to van Hove singularities without tuning on to the singularity. Then with a similar RG approach and a self-consistent calculation for the gap equations, we investigated the repulsion-mediated intrinsic and proximity-induced superconductivity in a family of lightly hole-doped noncentrosymmetric semiconductors, monolayer transition metal dichalcogenides (TMDs). We found that thanks to the spin-valley locking in lightly hole-doped TMDs, two distinct topological pairing states are favored for the intrinsically superconducting case: an interpocket paired state with Chern number 2 and an intrapocket paired state with finite pair momentum. Moreover, nematic odd-parity pairing with a possibly high Tc can be induced when proximitized by a cuprate. A confirmation of our predictions will open up possibilities for manipulating unconventional and topological superconductivity at a higher temperature on the device-friendly platform of strained ruthenate films and monolayer TMDs. In the second part, I will discuss our studies on the stability of the Dirac surface states in 3D TIs in the presence of bulk states and in TI-ferromagnetic metal heterostructures. We constructed simple microscopic models with Fano-type couplings between localized and extended states for each situation. Then with ab initio calculations we investigated the fate of the Dirac surface states in terms of the spectrum, the spatial profile and the spin-texture. Based on our results, we proposed explanations for existing experimental spectroscopic and spin-torque results.

Implicit Runge-Kutta Methods with Explicit Internal Stages

NASA Astrophysics Data System (ADS)

Skvortsov, L. M.

2018-03-01

The main computational costs of implicit Runge-Kutta methods are caused by solving a system of algebraic equations at every step. By introducing explicit stages, it is possible to increase the stage (or pseudo-stage) order of the method, which makes it possible to increase the accuracy and avoid reducing the order in solving stiff problems, without additional costs of solving algebraic equations. The paper presents implicit methods with an explicit first stage and one or two explicit internal stages. The results of solving test problems are compared with similar methods having no explicit internal stages.

Automatic discovery of the communication network topology for building a supercomputer model

NASA Astrophysics Data System (ADS)

Sobolev, Sergey; Stefanov, Konstantin; Voevodin, Vadim

2016-10-01

The Research Computing Center of Lomonosov Moscow State University is developing the Octotron software suite for automatic monitoring and mitigation of emergency situations in supercomputers so as to maximize hardware reliability. The suite is based on a software model of the supercomputer. The model uses a graph to describe the computing system components and their interconnections. One of the most complex components of a supercomputer that needs to be included in the model is its communication network. This work describes the proposed approach for automatically discovering the Ethernet communication network topology in a supercomputer and its description in terms of the Octotron model. This suite automatically detects computing nodes and switches, collects information about them and identifies their interconnections. The application of this approach is demonstrated on the "Lomonosov" and "Lomonosov-2" supercomputers.

Explicit Computations of Instantons and Large Deviations in Beta-Plane Turbulence

NASA Astrophysics Data System (ADS)

Laurie, J.; Bouchet, F.; Zaboronski, O.

2012-12-01

We use a path integral formalism and instanton theory in order to make explicit analytical predictions about large deviations and rare events in beta-plane turbulence. The path integral formalism is a concise way to get large deviation results in dynamical systems forced by random noise. In the most simple cases, it leads to the same results as the Freidlin-Wentzell theory, but it has a wider range of applicability. This approach is however usually extremely limited, due to the complexity of the theoretical problems. As a consequence it provides explicit results in a fairly limited number of models, often extremely simple ones with only a few degrees of freedom. Few exception exist outside the realm of equilibrium statistical physics. We will show that the barotropic model of beta-plane turbulence is one of these non-equilibrium exceptions. We describe sets of explicit solutions to the instanton equation, and precise derivations of the action functional (or large deviation rate function). The reason why such exact computations are possible is related to the existence of hidden symmetries and conservation laws for the instanton dynamics. We outline several applications of this apporach. For instance, we compute explicitly the very low probability to observe flows with an energy much larger or smaller than the typical one. Moreover, we consider regimes for which the system has multiple attractors (corresponding to different numbers of alternating jets), and discuss the computation of transition probabilities between two such attractors. These extremely rare events are of the utmost importance as the dynamics undergo qualitative macroscopic changes during such transitions.

Advances in the treatment of explicit water molecules in docking and binding free energy calculations.

PubMed

Hu, Xiao; Maffucci, Irene; Contini, Alessandro

2018-05-13

The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Here, we analyse software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

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

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Thermally Driven Electronic Topological Transition in FeTi

NASA Astrophysics Data System (ADS)

Yang, F. C.; Muñoz, J. A.; Hellman, O.; Mauger, L.; Lucas, M. S.; Tracy, S. J.; Stone, M. B.; Abernathy, D. L.; Xiao, Yuming; Fultz, B.

2016-08-01

Ab initio molecular dynamics, supported by inelastic neutron scattering and nuclear resonant inelastic x-ray scattering, showed an anomalous thermal softening of the M5- phonon mode in B 2 -ordered FeTi that could not be explained by phonon-phonon interactions or electron-phonon interactions calculated at low temperatures. A computational investigation showed that the Fermi surface undergoes a novel thermally driven electronic topological transition, in which new features of the Fermi surface arise at elevated temperatures. The thermally induced electronic topological transition causes an increased electronic screening for the atom displacements in the M5- phonon mode and an adiabatic electron-phonon interaction with an unusual temperature dependence.

Topology optimization of unsteady flow problems using the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Nørgaard, Sebastian; Sigmund, Ole; Lazarov, Boyan

2016-02-01

This article demonstrates and discusses topology optimization for unsteady incompressible fluid flows. The fluid flows are simulated using the lattice Boltzmann method, and a partial bounceback model is implemented to model the transition between fluid and solid phases in the optimization problems. The optimization problem is solved with a gradient based method, and the design sensitivities are computed by solving the discrete adjoint problem. For moderate Reynolds number flows, it is demonstrated that topology optimization can successfully account for unsteady effects such as vortex shedding and time-varying boundary conditions. Such effects are relevant in several engineering applications, i.e. fluid pumps and control valves.

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

DOE PAGES

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

2014-06-19

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Recoverable information and emergent conservation laws in fracton stabilizer codes

NASA Astrophysics Data System (ADS)

Schmitz, A. T.; Ma, Han; Nandkishore, Rahul M.; Parameswaran, S. A.

2018-04-01

We introduce a new quantity that we term recoverable information, defined for stabilizer Hamiltonians. For such models, the recoverable information provides a measure of the topological information as well as a physical interpretation, which is complementary to topological entanglement entropy. We discuss three different ways to calculate the recoverable information and prove their equivalence. To demonstrate its utility, we compute recoverable information for fracton models using all three methods where appropriate. From the recoverable information, we deduce the existence of emergent Z2 Gauss-law-type constraints, which in turn imply emergent Z2 conservation laws for pointlike quasiparticle excitations of an underlying topologically ordered phase.

HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots

NASA Astrophysics Data System (ADS)

Ricca, Renzo L.; Liu, Xin

2018-02-01

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

PubMed Central

Minh, Bui Quang; von Haeseler, Arndt

2015-01-01

Abstract In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original “full” terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference. PMID:26448206

High-order computer-assisted estimates of topological entropy

NASA Astrophysics Data System (ADS)

Grote, Johannes

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

Sketch Matching on Topology Product Graph.

PubMed

Liang, Shuang; Luo, Jun; Liu, Wenyin; Wei, Yichen

2015-08-01

Sketch matching is the fundamental problem in sketch based interfaces. After years of study, it remains challenging when there exists large irregularity and variations in the hand drawn sketch shapes. While most existing works exploit topology relations and graph representations for this problem, they are usually limited by the coarse topology exploration and heuristic (thus suboptimal) similarity metrics between graphs. We present a new sketch matching method with two novel contributions. We introduce a comprehensive definition of topology relations, which results in a rich and informative graph representation of sketches. For graph matching, we propose topology product graph that retains the full correspondence for matching two graphs. Based on it, we derive an intuitive sketch similarity metric whose exact solution is easy to compute. In addition, the graph representation and new metric naturally support partial matching, an important practical problem that received less attention in the literature. Extensive experimental results on a real challenging dataset and the superior performance of our method show that it outperforms the state-of-the-art.

Personalized anticancer therapy selection using molecular landscape topology and thermodynamics.

PubMed

Rietman, Edward A; Scott, Jacob G; Tuszynski, Jack A; Klement, Giannoula Lakka

2017-03-21

Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG). We show that while these three histologically distinct tumor types (astrocytoma, oligoastrocytoma, and oligodendroglioma) may share potential therapeutic targets, the majority of patients would benefit from more individualized therapies. The method involves computing Gibbs free energy of the protein-protein interaction network and applying a topological filtration on the energy landscape to produce a subnetwork known as persistent homology. We then determine the most likely best target for therapeutic intervention using a topological measure of the network known as Betti number. We describe the algorithm and discuss its application to several patients.

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.

Interplay between topology and disorder in a two-dimensional semi-Dirac material

NASA Astrophysics Data System (ADS)

Sriluckshmy, P. V.; Saha, Kush; Moessner, Roderich

2018-01-01

We investigate the role of disorder in a two-dimensional semi-Dirac material characterized by a linear dispersion in one direction and a parabolic dispersion in the orthogonal direction. Using the self-consistent Born approximation, we show that disorder can drive a topological Lifshitz transition from an insulator to a semimetal, as it generates a momentum-independent off-diagonal contribution to the self-energy. Breaking time-reversal symmetry enriches the topological phase diagram with three distinct regimes—single-node trivial, two-node trivial, and two-node Chern. We find that disorder can drive topological transitions from both the single- and two-node trivial to the two-node Chern regime. We further analyze these transitions in an appropriate tight-binding Hamiltonian of an anisotropic hexagonal lattice by calculating the real-space Chern number. Additionally, we compute the disorder-averaged entanglement entropy which signals both the topological Lifshitz and Chern transition as a function of the anisotropy of the hexagonal lattice. Finally, we discuss experimental aspects of our results.

Topology, structures, and energy landscapes of human chromosomes

PubMed Central

Zhang, Bin; Wolynes, Peter G.

2015-01-01

Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward “ideal” chromosome structures that represent hierarchical fibrils of fibrils. PMID:25918364

Gapless Andreev bound states in the quantum spin Hall insulator HgTe.

PubMed

Bocquillon, Erwann; Deacon, Russell S; Wiedenmann, Jonas; Leubner, Philipp; Klapwijk, Teunis M; Brüne, Christoph; Ishibashi, Koji; Buhmann, Hartmut; Molenkamp, Laurens W

2017-02-01

In recent years, Majorana physics has attracted considerable attention because of exotic new phenomena and its prospects for fault-tolerant topological quantum computation. To this end, one needs to engineer the interplay between superconductivity and electronic properties in a topological insulator, but experimental work remains scarce and ambiguous. Here, we report experimental evidence for topological superconductivity induced in a HgTe quantum well, a 2D topological insulator that exhibits the quantum spin Hall (QSH) effect. The a.c. Josephson effect demonstrates that the supercurrent has a 4π periodicity in the superconducting phase difference, as indicated by a doubling of the voltage step for multiple Shapiro steps. In addition, this response like that of a superconducting quantum interference device to a perpendicular magnetic field shows that the 4π-periodic supercurrent originates from states located on the edges of the junction. Both features appear strongest towards the QSH regime, and thus provide evidence for induced topological superconductivity in the QSH edge states.

GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

NASA Astrophysics Data System (ADS)

Hong, Pengyu; Sun, Hui; Sha, Long; Pu, Yi; Khatri, Kshitij; Yu, Xiang; Tang, Yang; Lin, Cheng

2017-08-01

A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. [Figure not available: see fulltext.

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.

Effect of exercise on patient specific abdominal aortic aneurysm flow topology and mixing.

PubMed

Arzani, Amirhossein; Les, Andrea S; Dalman, Ronald L; Shadden, Shawn C

2014-02-01

Computational fluid dynamics modeling was used to investigate changes in blood transport topology between rest and exercise conditions in five patient-specific abdominal aortic aneurysm models. MRI was used to provide the vascular anatomy and necessary boundary conditions for simulating blood velocity and pressure fields inside each model. Finite-time Lyapunov exponent fields and associated Lagrangian coherent structures were computed from blood velocity data and were used to compare features of the transport topology between rest and exercise both mechanistically and qualitatively. A mix-norm and mix-variance measure based on fresh blood distribution throughout the aneurysm over time were implemented to quantitatively compare mixing between rest and exercise. Exercise conditions resulted in higher and more uniform mixing and reduced the overall residence time in all aneurysms. Separated regions of recirculating flow were commonly observed in rest, and these regions were either reduced or removed by attached and unidirectional flow during exercise, or replaced with regional chaotic and transiently turbulent mixing, or persisted and even extended during exercise. The main factor that dictated the change in flow topology from rest to exercise was the behavior of the jet of blood penetrating into the aneurysm during systole. Copyright © 2013 John Wiley & Sons, Ltd.

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.

Tunable Intrinsic Spin Hall Conductivities in Bi2(Se,Te)3 Topological Insulators

NASA Astrophysics Data System (ADS)

Şahin, Cüneyt; Flatté, Michael E.

2015-03-01

It has been recently shown by spin-transfer torque measurements that Bi2Se3 exhibits a very large spin Hall conductivity (SHC). It is expected that Bi2Te3, a topological insulator with similar crystal and band structures as well as large spin-orbit coupling, would also exhibit a giant SHC. In this study we have calculated intrinsic spin Hall conductivities of Bi2Se3andBi2Te3 topological insulators from a tight-binding Hamiltonian including two nearest-neighbor interactions. We have calculated the Berry curvature, used the Kubo formula in the static, clean limit and shown that both materials exhibit giant spin Hall conductivities, consistent with the results of Ref. 1 and larger than previously reported Bi1-xSbx alloys. The density of Berry curvature has also been computed from the full Brillouin zone in order to compute the dependence of the SHC in these materials on the Fermi energy. Finally we report the intrinsic SHC for Bi2(Se,Te)3 topological insulators, which changes dramatically with doping or gate voltage. This work was supported in part by C-SPIN, one of six centers of STARnet, a Semiconductor Research Corporation program, sponsored by MARCO and DARPA.

Overcoming Geometry-Induced Stiffness with IMplicit-Explicit (IMEX) Runge-Kutta Algorithms on Unstructured Grids with Applications to CEM, CFD, and CAA

NASA Technical Reports Server (NTRS)

Kanevsky, Alex

2004-01-01

My goal is to develop and implement efficient, accurate, and robust Implicit-Explicit Runge-Kutta (IMEX RK) methods [9] for overcoming geometry-induced stiffness with applications to computational electromagnetics (CEM), computational fluid dynamics (CFD) and computational aeroacoustics (CAA). IMEX algorithms solve the non-stiff portions of the domain using explicit methods, and isolate and solve the more expensive stiff portions using implicit methods. Current algorithms in CEM can only simulate purely harmonic (up to lOGHz plane wave) EM scattering by fighter aircraft, which are assumed to be pure metallic shells, and cannot handle the inclusion of coatings, penetration into and radiation out of the aircraft. Efficient MEX RK methods could potentially increase current CEM capabilities by 1-2 orders of magnitude, allowing scientists and engineers to attack more challenging and realistic problems.

Resonant UPS topologies for the emerging hybrid fiber-coaxial networks

NASA Astrophysics Data System (ADS)

Pinheiro, Humberto

Uninterruptible power supply (UPS) systems have been extensively applied to feed critical loads in many areas. Typical examples of critical loads include life-support equipment, computers and telecommunication systems. Although all UPS systems have a common purpose to provide continuous power-to critical loads, the emerging hybrid fiber-coaxial networks have created the need for specific types of UPS topologies. For example, galvanic isolation for the load and the battery, small size, high input power factor, and trapezoidal output voltage waveforms are among the required features of UPS topologies for hybrid fiber-coaxial networks. None of the conventional UPS topologies meet all these requirements. Consequently. this thesis is directed towards the design and analysis of UPS topologies for this new application. Novel UPS topologies are proposed and control techniques are developed to allow operation at high switching frequencies without penalizing the converter efficiency. By the use of resonant converters in the proposed UPS topologies. a high input power factor is achieved without requiring a dedicated power factor correction stage. In addition, a self-sustained oscillation control method is proposed to ensure soft switching under all operating conditions. A detailed analytical treatment of the resonant converters in the proposed UPS topologies is presented and design procedures illustrated. Simulation and experimental results are presented to validate the analyses and to demonstrate the feasibility of the proposed schemes.

An efficient Adaptive Mesh Refinement (AMR) algorithm for the Discontinuous Galerkin method: Applications for the computation of compressible two-phase flows

NASA Astrophysics Data System (ADS)

Papoutsakis, Andreas; Sazhin, Sergei S.; Begg, Steven; Danaila, Ionut; Luddens, Francky

2018-06-01

We present an Adaptive Mesh Refinement (AMR) method suitable for hybrid unstructured meshes that allows for local refinement and de-refinement of the computational grid during the evolution of the flow. The adaptive implementation of the Discontinuous Galerkin (DG) method introduced in this work (ForestDG) is based on a topological representation of the computational mesh by a hierarchical structure consisting of oct- quad- and binary trees. Adaptive mesh refinement (h-refinement) enables us to increase the spatial resolution of the computational mesh in the vicinity of the points of interest such as interfaces, geometrical features, or flow discontinuities. The local increase in the expansion order (p-refinement) at areas of high strain rates or vorticity magnitude results in an increase of the order of accuracy in the region of shear layers and vortices. A graph of unitarian-trees, representing hexahedral, prismatic and tetrahedral elements is used for the representation of the initial domain. The ancestral elements of the mesh can be split into self-similar elements allowing each tree to grow branches to an arbitrary level of refinement. The connectivity of the elements, their genealogy and their partitioning are described by linked lists of pointers. An explicit calculation of these relations, presented in this paper, facilitates the on-the-fly splitting, merging and repartitioning of the computational mesh by rearranging the links of each node of the tree with a minimal computational overhead. The modal basis used in the DG implementation facilitates the mapping of the fluxes across the non conformal faces. The AMR methodology is presented and assessed using a series of inviscid and viscous test cases. Also, the AMR methodology is used for the modelling of the interaction between droplets and the carrier phase in a two-phase flow. This approach is applied to the analysis of a spray injected into a chamber of quiescent air, using the Eulerian-Lagrangian approach. This enables us to refine the computational mesh in the vicinity of the droplet parcels and accurately resolve the coupling between the two phases.

Topological enslavement in evolutionary games on correlated multiplex networks

NASA Astrophysics Data System (ADS)

Kleineberg, Kaj-Kolja; Helbing, Dirk

2018-05-01

Governments and enterprises strongly rely on incentives to generate favorable outcomes from social and strategic interactions between individuals. The incentives are usually modeled by payoffs in evolutionary games, such as the prisoners dilemma or the harmony game, with imitation dynamics. Adjusting the incentives by changing the payoff parameters can favor cooperation, as found in the harmony game, over defection, which prevails in the prisoner’s dilemma. Here, we show that this is not always the case if individuals engage in strategic interactions in multiple domains. In particular, we investigate evolutionary games on multiplex networks where individuals obtain an aggregate payoff. We explicitly control the strength of degree correlations between nodes in the different layers of the multiplex. We find that if the multiplex is composed of many layers and degree correlations are strong, the topology of the system enslaves the dynamics and the final outcome, cooperation or defection, becomes independent of the payoff parameters. The fate of the system is then determined by the initial conditions.

Simplified Design Equations for Class-E Neural Prosthesis Transmitters

PubMed Central

Troyk, Philip; Hu, Zhe

2013-01-01

Extreme miniaturization of implantable electronic devices is recognized as essential for the next generation of neural prostheses, owing to the need for minimizing the damage and disruption of the surrounding neural tissue. Transcutaneous power and data transmission via a magnetic link remains the most effective means of powering and controlling implanted neural prostheses. Reduction in the size of the coil, within the neural prosthesis, demands the generation of a high-intensity radio frequency magnetic field from the extracoporeal transmitter. The Class-E power amplifier circuit topology has been recognized as a highly effective means of producing large radio frequency currents within the transmitter coil. Unfortunately, design of a Class-E circuit is most often fraught by the need to solve a complex set of equations so as to implement both the zero-voltage-switching and zero-voltage-derivative-switching conditions that are required for efficient operation. This paper presents simple explicit design equations for designing the Class-E circuit topology. Numerical design examples are presented to illustrate the design procedure. PMID:23292784

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

Generation of structural topologies using efficient technique based on sorted compliances

NASA Astrophysics Data System (ADS)

Mazur, Monika; Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

Topology optimization, although well recognized is still widely developed. It has gained recently more attention since large computational ability become available for designers. This process is stimulated simultaneously by variety of emerging, innovative optimization methods. It is observed that traditional gradient-based mathematical programming algorithms, in many cases, are replaced by novel and e cient heuristic methods inspired by biological, chemical or physical phenomena. These methods become useful tools for structural optimization because of their versatility and easy numerical implementation. In this paper engineering implementation of a novel heuristic algorithm for minimum compliance topology optimization is discussed. The performance of the topology generator is based on implementation of a special function utilizing information of compliance distribution within the design space. With a view to cope with engineering problems the algorithm has been combined with structural analysis system Ansys.

Emergent functions of quantum materials

NASA Astrophysics Data System (ADS)

Tokura, Yoshinori; Kawasaki, Masashi; Nagaosa, Naoto

2017-11-01

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

A New Numerical Method for Z2 Topological Insulators with Strong Disorder

NASA Astrophysics Data System (ADS)

Akagi, Yutaka; Katsura, Hosho; Koma, Tohru

2017-12-01

We propose a new method to numerically compute the Z2 indices for disordered topological insulators in Kitaev's periodic table. All of the Z2 indices are derived from the index formulae which are expressed in terms of a pair of projections introduced by Avron, Seiler, and Simon. For a given pair of projections, the corresponding index is determined by the spectrum of the difference between the two projections. This difference exhibits remarkable and useful properties, as it is compact and has a supersymmetric structure in the spectrum. These properties enable highly efficient numerical calculation of the indices of disordered topological insulators. The method, which we propose, is demonstrated for the Bernevig-Hughes-Zhang and Wilson-Dirac models whose topological phases are characterized by a Z2 index in two and three dimensions, respectively.

Observation of topological superconductivity on the surface of an iron-based superconductor

DOE PAGES

Zhang, Peng; Yaji, Koichiro; Hashimoto, Takahiro; ...

2018-03-08

Topological superconductors are predicted to host exotic Majorana states that obey non-Abelian statistics and can be used to implement a topological quantum computer. Most of the proposed topological superconductors are realized in difficult-to-fabricate heterostructures at very low temperatures. By using high-resolution spin-resolved and angle-resolved photoelectron spectroscopy, we find that the iron-based superconductor FeTe 1–xSe x (x = 0.45; superconducting transition temperature T c = 14.5 kelvin) hosts Dirac-cone–type spin-helical surface states at the Fermi level; the surface states exhibit an s-wave superconducting gap below T c. Thus, our study shows that the surface states of FeTe 0.55Se 0.45 are topologicallymore » superconducting, providing a simple and possibly high-temperature platform for realizing Majorana states.« less

Observation of topological superconductivity on the surface of an iron-based superconductor

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

Zhang, Peng; Yaji, Koichiro; Hashimoto, Takahiro

Topological superconductors are predicted to host exotic Majorana states that obey non-Abelian statistics and can be used to implement a topological quantum computer. Most of the proposed topological superconductors are realized in difficult-to-fabricate heterostructures at very low temperatures. By using high-resolution spin-resolved and angle-resolved photoelectron spectroscopy, we find that the iron-based superconductor FeTe 1–xSe x (x = 0.45; superconducting transition temperature T c = 14.5 kelvin) hosts Dirac-cone–type spin-helical surface states at the Fermi level; the surface states exhibit an s-wave superconducting gap below T c. Thus, our study shows that the surface states of FeTe 0.55Se 0.45 are topologicallymore » superconducting, providing a simple and possibly high-temperature platform for realizing Majorana states.« less

Emergent Topological order from Spin-Orbit Density wave

NASA Astrophysics Data System (ADS)

Gupta, Gaurav; Das, Tanmoy

We study the emergence of a Z2 -type topological order because of Landau type symmetry breaking order parameter. When two Rashba type SOC bands of different chirality become nested by a magic wavevector [(0, ∖pi) or (∖pi,0)], it introduces the inversion of chirality between different lattice sites. Such a density wave state is known as spin-orbit density wave. The resulting quantum order is associated with the topological order which is classified by a Z2 invariant. So, this system can simultaneously be classified by both a symmetry breaking order parameter and the associated Z2 topological invariant. This order parameter can be realized or engineered in two- or quasi-two-dimensional fermionic lattices, quantum wires, with tunable RSOC and correlation strength. The work is facilitated by the computer cluster facility at Department of Physics, Indian Institute of Science.

The entropic boundary law in BF theory

NASA Astrophysics Data System (ADS)

Livine, Etera R.; Terno, Daniel R.

2009-01-01

We compute the entropy of a closed bounded region of space for pure 3d Riemannian gravity formulated as a topological BF theory for the gauge group SU(2) and show its holographic behavior. More precisely, we consider a fixed graph embedded in space and study the flat connection spin network state without and with particle-like topological defects. We regularize and compute exactly the entanglement for a bipartite splitting of the graph and show it scales at leading order with the number of vertices on the boundary (or equivalently with the number of loops crossing the boundary). More generally these results apply to BF theory with any compact gauge group in any space-time dimension.

Dynamics of flexible bodies in tree topology - A computer oriented approach

NASA Technical Reports Server (NTRS)

Singh, R. P.; Vandervoort, R. J.; Likins, P. W.

1984-01-01

An approach suited for automatic generation of the equations of motion for large mechanical systems (i.e., large space structures, mechanisms, robots, etc.) is presented. The system topology is restricted to a tree configuration. The tree is defined as an arbitrary set of rigid and flexible bodies connected by hinges characterizing relative translations and rotations of two adjoining bodies. The equations of motion are derived via Kane's method. The resulting equation set is of minimum dimension. Dynamical equations are imbedded in a computer program called TREETOPS. Extensive control simulation capability is built in the TREETOPS program. The simulation is driven by an interactive set-up program resulting in an easy to use analysis tool.

Synthesis and structure of 1,3-dimethyl-5-(p-sulfonamide-phenylazo)-6-aminouracil and its Ni(II) complex: Topological insights and investigation for noncovalent interactions

NASA Astrophysics Data System (ADS)

Debnath, Diptanu; Roy, Subhadip; Purkayastha, Atanu; Bauzá, Antonio; Choudhury, Rupasree; Ganguly, Rakesh; Frontera, Antonio; Misra, Tarun Kumar

2017-08-01

The azo-derivative, 1,3-dimethyl-5-(p-sulfonamide-phenylazo)-6-aminouracil (HL) containing 6-aminouracil (a biomolecule) and sulfonamide functionality (commonly found in sulfa-drugs), and its Ni(II) complex, NiIIL2 were synthesized. Single-crystal X-ray diffraction studies show that the ligand (HL) consists of an E conformation about the azo-linkage with a nearly planar geometry and the complex possesses distorted square planar geometry. The H-bonded underlying networks of HL and NiIIL2 were topologically classified revealing distinct topological types, namely tts and hxl, respectively. Moreover, topology of molecular packings in HL and NiIIL2 has also been discussed. Density functional theory (DFT) calculations, at the M06-2X/def2TZVP level of theory, are employed to characterize a great variety of non-covalent interactions that explicitly show the importance of antiparallel stacking interactions established by π--π+ interactions and H-bonds in the self-assembled dimmers in HL and lp-π/C-H⋯π interactions in NiIIL2. The results of NMR and UV-vis spectroscopies evidence that the ligand exists in hydrazone-imine-keto (B) tautomeric form in solution. The ligand absorption bands consist of the overlapping bands of π→π* and n→π* transitions. The complex experiences electronic transitions that consist of basically ILCT in character with some sort of participation of the atomic d-orbitals of the nickel. The pKa value of the ligand is found to be 4.09.

Implementation and evaluation of a hypercube-based method for spatiotemporal exploration and analysis

NASA Astrophysics Data System (ADS)

Marchand, Pierre; Brisebois, Alexandre; Bédard, Yvan; Edwards, Geoffrey

This paper presents the results obtained with a new type of spatiotemporal topological dimension implemented within a hypercube, i.e., within a multidimensional database (MDDB) structure formed by the conjunction of several thematic, spatial and temporal dimensions. Our goal is to support efficient SpatioTemporal Exploration and Analysis (STEA) in the context of Automatic Position Reporting System (APRS), the worldwide amateur radio system for position report transmission. Mobile APRS stations are equipped with GPS navigation systems to provide real-time positioning reports. Previous research about the multidimensional approach has proved good potential for spatiotemporal exploration and analysis despite a lack of explicit topological operators (spatial, temporal and spatiotemporal). Our project implemented such operators through a hierarchy of operators that are applied to pairs of instances of objects. At the top of the hierarchy, users can use simple operators such as "same place", "same time" or "same time, same place". As they drill down into the hierarchy, more detailed topological operators are made available such as "adjacent immediately after", "touch during" or more detailed operators. This hierarchy is structured according to four levels of granularity based on cognitive models, generalized relationships and formal models of topological relationships. In this paper, we also describe the generic approach which allows efficient STEA within the multidimensional approach. Finally, we demonstrate that such an implementation offers query run times which permit to maintain a "train-of-thought" during exploration and analysis operations as they are compatible with Newell's cognitive band (query runtime<10 s) (Newell, A., 1990. Unified theories of cognition. Harvard University Press, Cambridge MA, 549 p.).

Multiresolution persistent homology for excessively large biomolecular datasets

NASA Astrophysics Data System (ADS)

Xia, Kelin; Zhao, Zhixiong; Wei, Guo-Wei

2015-10-01

Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

Decoherence of Topological Qubit in Linear Motions: Decoherence Impedance, Anti-Unruh and Information Backflow

NASA Astrophysics Data System (ADS)

Liu, Pei-Hua; Lin, Feng-Li

2017-08-01

In this work we study the decoherence of topological qubits in linear motions. The topological qubit is made of two spatially-separated Majorana zero modes which are the edge excitations of Kitaev chain [1]. In a previous work [2], it was shown by one of us and his collaborators that the decoherence of topological qubit is exactly solvable, moreover, topological qubit is robust against decoherence in the super-Ohmic environments. We extend the setup of [2] to consider the effect of motions on the decoherence of the topological qubits. Our results show the thermalization as expected by Unruh effect. Besides, we also find the so-called “anti-Unruh” phenomena which shows the rate of decoherence is anti-correlated with the acceleration in short-time scale. Moreover, we modulate the motion patterns of each Majorana modes and find information backflow and the preservation of coherence even with nonzero accelerations. This is the characteristics of the underlying non-Markovian reduced dynamics. We conclude that he topological qubit is in general more robust against decoherence than the usual qubits, and can be take into serious consideration for realistic implementation to have robust quantum computation and communication. This talk is based on our work in [3].

Low-storage implicit/explicit Runge-Kutta schemes for the simulation of stiff high-dimensional ODE systems

NASA Astrophysics Data System (ADS)

Cavaglieri, Daniele; Bewley, Thomas

2015-04-01

Implicit/explicit (IMEX) Runge-Kutta (RK) schemes are effective for time-marching ODE systems with both stiff and nonstiff terms on the RHS; such schemes implement an (often A-stable or better) implicit RK scheme for the stiff part of the ODE, which is often linear, and, simultaneously, a (more convenient) explicit RK scheme for the nonstiff part of the ODE, which is often nonlinear. Low-storage RK schemes are especially effective for time-marching high-dimensional ODE discretizations of PDE systems on modern (cache-based) computational hardware, in which memory management is often the most significant computational bottleneck. In this paper, we develop and characterize eight new low-storage implicit/explicit RK schemes which have higher accuracy and better stability properties than the only low-storage implicit/explicit RK scheme available previously, the venerable second-order Crank-Nicolson/Runge-Kutta-Wray (CN/RKW3) algorithm that has dominated the DNS/LES literature for the last 25 years, while requiring similar storage (two, three, or four registers of length N) and comparable floating-point operations per timestep.

Impact of pore space topology on permeability, cut-off frequencies and validity of wave propagation theories

NASA Astrophysics Data System (ADS)

Sarout, Joël.

2012-04-01

For the first time, a comprehensive and quantitative analysis of the domains of validity of popular wave propagation theories for porous/cracked media is provided. The case of a simple, yet versatile rock microstructure is detailed. The microstructural parameters controlling the applicability of the scattering theories, the effective medium theories, the quasi-static (Gassmann limit) and dynamic (inertial) poroelasticity are analysed in terms of pores/cracks characteristic size, geometry and connectivity. To this end, a new permeability model is devised combining the hydraulic radius and percolation concepts. The predictions of this model are compared to published micromechanical models of permeability for the limiting cases of capillary tubes and penny-shaped cracks. It is also compared to published experimental data on natural rocks in these limiting cases. It explicitly accounts for pore space topology around the percolation threshold and far above it. Thanks to this permeability model, the scattering, squirt-flow and Biot cut-off frequencies are quantitatively compared. This comparison leads to an explicit mapping of the domains of validity of these wave propagation theories as a function of the rock's actual microstructure. How this mapping impacts seismic, geophysical and ultrasonic wave velocity data interpretation is discussed. The methodology demonstrated here and the outcomes of this analysis are meant to constitute a quantitative guide for the selection of the most suitable modelling strategy to be employed for prediction and/or interpretation of rocks elastic properties in laboratory-or field-scale applications when information regarding the rock's microstructure is available.

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.

PubMed

Ho, Hsiang; Milenković, Tijana; Memisević, Vesna; Aruri, Jayavani; Przulj, Natasa; Ganesan, Anand K

2010-06-15

RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis. In this study, we utilize a PPI network topology-based approach to identify targets within our RNAi dataset that may be components of known melanogenesis regulatory pathways. Our computational approach identifies a set of screen targets that cluster topologically in a human PPI network with the known pigment regulator Endothelin receptor type B (EDNRB). Validation studies reveal that these genes impact pigment production and EDNRB signaling in pigmented melanoma cells (MNT-1) and normal melanocytes. We present an approach that identifies novel components of well-characterized biological pathways from functional genomics datasets that could not have been identified by existing statistical and computational approaches.

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

PubMed Central

2010-01-01

Background RNA-mediated interference (RNAi)-based functional genomics is a systems-level approach to identify novel genes that control biological phenotypes. Existing computational approaches can identify individual genes from RNAi datasets that regulate a given biological process. However, currently available methods cannot identify which RNAi screen "hits" are novel components of well-characterized biological pathways known to regulate the interrogated phenotype. In this study, we describe a method to identify genes from RNAi datasets that are novel components of known biological pathways. We experimentally validate our approach in the context of a recently completed RNAi screen to identify novel regulators of melanogenesis. Results In this study, we utilize a PPI network topology-based approach to identify targets within our RNAi dataset that may be components of known melanogenesis regulatory pathways. Our computational approach identifies a set of screen targets that cluster topologically in a human PPI network with the known pigment regulator Endothelin receptor type B (EDNRB). Validation studies reveal that these genes impact pigment production and EDNRB signaling in pigmented melanoma cells (MNT-1) and normal melanocytes. Conclusions We present an approach that identifies novel components of well-characterized biological pathways from functional genomics datasets that could not have been identified by existing statistical and computational approaches. PMID:20550706

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

PubMed

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

2017-12-01

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

Algorithms for the explicit computation of Penrose diagrams

NASA Astrophysics Data System (ADS)

Schindler, J. C.; Aguirre, A.

2018-05-01

An algorithm is given for explicitly computing Penrose diagrams for spacetimes of the form . The resulting diagram coordinates are shown to extend the metric continuously and nondegenerately across an arbitrary number of horizons. The method is extended to include piecewise approximations to dynamically evolving spacetimes using a standard hypersurface junction procedure. Examples generated by an implementation of the algorithm are shown for standard and new cases. In the appendix, this algorithm is compared to existing methods.

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.

Topological charge number multiplexing for JTC multiple-image encryption

NASA Astrophysics Data System (ADS)

Chen, Qi; Shen, Xueju; Dou, Shuaifeng; Lin, Chao; Wang, Long

2018-04-01

We propose a method of topological charge number multiplexing based on the JTC encryption system to achieve multiple-image encryption. Using this method, multi-image can be encrypted into single ciphertext, and the original images can be recovered according to the authority level. The number of encrypted images is increased, moreover, the quality of decrypted images is improved. Results of computer simulation and initial experiment identify the validity of our proposed method.

Robust Airborne Networking Extensions (RANGE)

DTIC Science & Technology

2008-02-01

IMUNES [13] project, which provides an entire network stack virtualization and topology control inside a single FreeBSD machine . The emulated topology...Multicast versus broadcast in a manet.” in ADHOC-NOW, 2004, pp. 14–27. [9] J. Mukherjee, R. Atwood , “ Rendezvous point relocation in protocol independent...computer with an Ethernet connection, or a Linux virtual machine on some other (e.g., Windows) operating system, should work. 2.1 Patching the source code

THE EFFECT OF MAGNETIC TOPOLOGY ON THERMALLY DRIVEN WIND: TOWARD A GENERAL FORMULATION OF THE BRAKING LAW

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

Réville, Victor; Brun, Allan Sacha; Strugarek, Antoine

Stellar wind is thought to be the main process responsible for the spin down of main-sequence stars. The extraction of angular momentum by a magnetized wind has been studied for decades, leading to several formulations for the resulting torque. However, previous studies generally consider simple dipole or split monopole stellar magnetic topologies. Here we consider, in addition to a dipolar stellar magnetic field, both quadrupolar and octupolar configurations, while also varying the rotation rate and the magnetic field strength. Sixty simulations made with a 2.5D cylindrical and axisymmetric set-up, and computed with the PLUTO code, were used to find torquemore » formulations for each topology. We further succeed to give a unique law that fits the data for every topology by formulating the torque in terms of the amount of open magnetic flux in the wind. We also show that our formulation can be applied to even more realistic magnetic topologies, with examples of the Sun in its minimum and maximum phases as observed at the Wilcox Solar Observatory, and of a young K-star (TYC-0486-4943-1) whose topology has been obtained by Zeeman-Doppler Imaging.« less

The influence of the magnetic topology on the wind braking of sun-like stars.

NASA Astrophysics Data System (ADS)

Réville, V.; Brun, A. S.; Matt, S. P.; Strugarek, A.; Pinto, R.

2014-12-01

Stellar winds are thought to be the main process responsible for the spin down of main-sequence stars. The extraction of angular momentum by a magnetized wind has been studied for decades, leading to several formulations for the resulting torque. However, previous studies generally consider simple dipole or split monopole stellar magnetic topologies. Here we consider in addition to a dipolar stellar magnetic field, both quadrupolar and octupolar configurations, while also varying the rotation rate and the magnetic field strength. 60 simulations made with a 2.5D, cylindrical and axisymmetric set-up and computed with the PLUTO code were used to find torque formulations for each topology. We further succeed to give a unique law that fits the data for every topology by formulating the torque in terms of the amount of open magnetic flux in the wind. We also show that our formulation can be applied to even more realistic magnetic topologies, with examples of the Sun in its minimum and maximum phase as observed at the Wilcox Solar Observatory, and of a young K-star (TYC-0486-4943-1) whose topology has been obtained by Zeeman-Doppler Imaging (ZDI).

Solutions of the Taylor-Green Vortex Problem Using High-Resolution Explicit Finite Difference Methods

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2013-01-01

A computational fluid dynamics code that solves the compressible Navier-Stokes equations was applied to the Taylor-Green vortex problem to examine the code s ability to accurately simulate the vortex decay and subsequent turbulence. The code, WRLES (Wave Resolving Large-Eddy Simulation), uses explicit central-differencing to compute the spatial derivatives and explicit Low Dispersion Runge-Kutta methods for the temporal discretization. The flow was first studied and characterized using Bogey & Bailley s 13-point dispersion relation preserving (DRP) scheme. The kinetic energy dissipation rate, computed both directly and from the enstrophy field, vorticity contours, and the energy spectra are examined. Results are in excellent agreement with a reference solution obtained using a spectral method and provide insight into computations of turbulent flows. In addition the following studies were performed: a comparison of 4th-, 8th-, 12th- and DRP spatial differencing schemes, the effect of the solution filtering on the results, the effect of large-eddy simulation sub-grid scale models, and the effect of high-order discretization of the viscous terms.

Reconfigurable Analog PDE computation for Baseband and RFComputation

DTIC Science & Technology

2017-03-01

waveguiding PDEs. One-dimensional ladder topologies enable linear delays, linear-phase analog filters , as well as analog beamforming, potentially at RF...performance. This discussion focuses on ODE / PDE analog computation available in SoC FPAA structures. One such computation is a ladder filter (Fig...Implementation of a one-dimensional ladder filter for computing inductor (L) and capacitor (C) lines. These components can be implemented in CABs or as

Investigation of upwind, multigrid, multiblock numerical schemes for three dimensional flows. Volume 1: Runge-Kutta methods for a thin layer Navier-Stokes solver

NASA Technical Reports Server (NTRS)

Cannizzaro, Frank E.; Ash, Robert L.

1992-01-01

A state-of-the-art computer code has been developed that incorporates a modified Runge-Kutta time integration scheme, upwind numerical techniques, multigrid acceleration, and multi-block capabilities (RUMM). A three-dimensional thin-layer formulation of the Navier-Stokes equations is employed. For turbulent flow cases, the Baldwin-Lomax algebraic turbulence model is used. Two different upwind techniques are available: van Leer's flux-vector splitting and Roe's flux-difference splitting. Full approximation multi-grid plus implicit residual and corrector smoothing were implemented to enhance the rate of convergence. Multi-block capabilities were developed to provide geometric flexibility. This feature allows the developed computer code to accommodate any grid topology or grid configuration with multiple topologies. The results shown in this dissertation were chosen to validate the computer code and display its geometric flexibility, which is provided by the multi-block structure.

Braid group representation on quantum computation

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

Aziz, Ryan Kasyfil, E-mail: kasyfilryan@gmail.com; Muchtadi-Alamsyah, Intan, E-mail: ntan@math.itb.ac.id

2015-09-30

There are many studies about topological representation of quantum computation recently. One of diagram representation of quantum computation is by using ZX-Calculus. In this paper we will make a diagrammatical scheme of Dense Coding. We also proved that ZX-Calculus diagram of maximally entangle state satisfies Yang-Baxter Equation and therefore, we can construct a Braid Group representation of set of maximally entangle state.

On Topological Indices of Certain Dendrimer Structures

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Bashir, Yasir; Ahmad, Safyan; Gao, Wei

2017-05-01

A topological index can be considered as transformation of chemical structure in to real number. In QSAR/QSPR study, physicochemical properties and topological indices such as Randić, Zagreb, atom-bond connectivity ABC, and geometric-arithmetic GA index are used to predict the bioactivity of chemical compounds. Dendrimers are highly branched, star-shaped macromolecules with nanometer-scale dimensions. Dendrimers are defined by three components: a central core, an interior dendritic structure (the branches), and an exterior surface with functional surface groups. In this paper we determine generalised Randić, general Zagreb, general sum-connectivity indices of poly(propyl) ether imine, porphyrin, and zinc-Porphyrin dendrimers. We also compute ABC and GA indices of these families of dendrimers.

Thermally Driven Electronic Topological Transition in FeTi

DOE PAGES

Yang, F. C.; Muñoz, J. A.; Hellman, O.; ...

2016-08-08

In this paper, ab initio molecular dynamics, supported by inelastic neutron scattering and nuclear resonant inelastic x-ray scattering, showed an anomalous thermal softening of the M 5 - phonon mode in B2-ordered FeTi that could not be explained by phonon-phonon interactions or electron-phonon interactions calculated at low temperatures. A computational investigation showed that the Fermi surface undergoes a novel thermally driven electronic topological transition, in which new features of the Fermi surface arise at elevated temperatures. Finally, the thermally induced electronic topological transition causes an increased electronic screening for the atom displacements in the M 5 - phonon mode andmore » an adiabatic electron-phonon interaction with an unusual temperature dependence.« less

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.

Topological T-duality for torus bundles with monodromy

NASA Astrophysics Data System (ADS)

Baraglia, David

2015-05-01

We give a simplified definition of topological T-duality that applies to arbitrary torus bundles. The new definition does not involve Chern classes or spectral sequences, only gerbes and morphisms between them. All the familiar topological conditions for T-duals are shown to follow. We determine necessary and sufficient conditions for existence of a T-dual in the case of affine torus bundles. This is general enough to include all principal torus bundles as well as torus bundles with arbitrary monodromy representations. We show that isomorphisms in twisted cohomology, twisted K-theory and of Courant algebroids persist in this general setting. We also give an example where twisted K-theory groups can be computed by iterating T-duality.

Physical realization of topological quantum walks on IBM-Q and beyond

NASA Astrophysics Data System (ADS)

Balu, Radhakrishnan; Castillo, Daniel; Siopsis, George

2018-07-01

We discuss an efficient physical realization of topological quantum walks on a one-dimensional finite lattice with periodic boundary conditions (circle). The N-point lattice is realized with {log}}2N qubits, and the quantum circuit utilizes a number of quantum gates that are polynomial in the number of qubits. In a certain scaling limit, we show that a large number of steps are implemented with a number of quantum gates which are independent of the number of steps. We ran the quantum algorithm on the IBM-Q five-qubit quantum computer, thus experimentally demonstrating topological features, such as boundary bound states, on a one-dimensional lattice with N = 4 points.

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.

Numerosity as a topological invariant.

PubMed

Kluth, Tobias; Zetzsche, Christoph

2016-01-01

The ability to quickly recognize the number of objects in our environment is a fundamental cognitive function. However, it is far from clear which computations and which actual neural processing mechanisms are used to provide us with such a skill. Here we try to provide a detailed and comprehensive analysis of this issue, which comprises both the basic mathematical foundations and the peculiarities imposed by the structure of the visual system and by the neural computations provided by the visual cortex. We suggest that numerosity should be considered as a mathematical invariant. Making use of concepts from mathematical topology--like connectedness, Betti numbers, and the Gauss-Bonnet theorem--we derive the basic computations suited for the computation of this invariant. We show that the computation of numerosity is possible in a neurophysiologically plausible fashion using only computational elements which are known to exist in the visual cortex. We further show that a fundamental feature of numerosity perception, its Weber property, arises naturally, assuming noise in the basic neural operations. The model is tested on an extended data set (made publicly available). It is hoped that our results can provide a general framework for future research on the invariance properties of the numerosity system.

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs

PubMed Central

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C.; Hütt, Marc-Thorsten

2017-01-01

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience. PMID:28186182

Experimental and theoretical study of topology and electronic correlations in PuB4

NASA Astrophysics Data System (ADS)

Choi, Hongchul; Zhu, Wei; Cary, S. K.; Winter, L. E.; Huang, Zhoushen; McDonald, R. D.; Mocko, V.; Scott, B. L.; Tobash, P. H.; Thompson, J. D.; Kozimor, S. A.; Bauer, E. D.; Zhu, Jian-Xin; Ronning, F.

2018-05-01

We synthesize single crystals of PuB4 using an Al-flux technique. Single-crystal diffraction data provide structural parameters for first-principles density functional theory (DFT) calculations. By computing the density of states, the Z2 topological invariant using the Wilson loop method, and the surface electronic structure from slab calculations, we find that PuB4 is a nonmagnetic strong topological insulator with a band gap of 254 meV. Our magnetic susceptibility, heat capacity, and resistivity measurements are consistent with this analysis, albeit with a smaller gap of 35 meV. DFT plus dynamical mean-field theory calculations show that electronic correlations reduce the size of the band gap, and provide better agreement with the value determined by resistivity. These results demonstrate that PuB4 is a promising actinide material to investigate the interplay of electronic correlations and nontrivial topology.

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs.

PubMed

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C; Hütt, Marc-Thorsten

2017-02-10

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience.

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

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

Witman, Matthew; Ling, Sanliang; Anderson, Samantha

Here, we present the in silico design of metal-organic frameworks (MOFs) exhibiting 1-dimensional rod topologies. We then introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type analogs. Furthermore, we perform a broad search for new linkers that satisfy the topological requirements of MOF-74 and consider the largest database of known chemical space for organic compounds, the PubChem database. Our in silico crystal assembly, when combined with dispersion-corrected density functional theory (DFT) calculations, is demonstrated to generate a hypothetical library of open-metal site containing MOF-74 analogs in the 1-D rod topology frommore » which we can simulate the adsorption behavior of CO 2 . We conclude that these hypothetical structures have synthesizable potential through computational identification and experimental validation of a novel MOF-74 analog, Mg 2 (olsalazine).« less

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

DOE PAGES

Witman, Matthew; Ling, Sanliang; Anderson, Samantha; ...

2016-06-21

Here, we present the in silico design of metal-organic frameworks (MOFs) exhibiting 1-dimensional rod topologies. We then introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type analogs. Furthermore, we perform a broad search for new linkers that satisfy the topological requirements of MOF-74 and consider the largest database of known chemical space for organic compounds, the PubChem database. Our in silico crystal assembly, when combined with dispersion-corrected density functional theory (DFT) calculations, is demonstrated to generate a hypothetical library of open-metal site containing MOF-74 analogs in the 1-D rod topology frommore » which we can simulate the adsorption behavior of CO 2 . We conclude that these hypothetical structures have synthesizable potential through computational identification and experimental validation of a novel MOF-74 analog, Mg 2 (olsalazine).« less

Experimental Study of Saddle Point of Attachment in Laminar Juncture Flow

NASA Technical Reports Server (NTRS)

Coon, Michael D.; Tobak, Murray

1995-01-01

An experimental study of laminar horseshoe vortex flows upstream of a cylinder/flat plate juncture has been conducted to verify the existence of saddle-point-of-attachment topologies. In the classical depiction of this flowfield, a saddle point of separation exists on the flat plate upstream of the cylinder, and the boundary layer separates from the surface. Recent computations have indicated that the topology may actually involve a saddle point of attachment on the surface and additional singular points in the flow. Laser light sheet flow visualizations have been performed on the symmetry plane and crossflow planes to identify the saddle-point-of-attachment flowfields. The visualizations reveal that saddle-point-of-attachment topologies occur over a range of Reynolds numbers in both single and multiple vortex regimes. An analysis of the flow topologies is presented that describes the existence and evolution of the singular points in the flowfield.

3D Topology Preserving Flows for Viewpoint-Based Cortical Unfolding

PubMed Central

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

2009-01-01

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

Topological superfluids with finite-momentum pairing and Majorana fermions.

PubMed

Qu, Chunlei; Zheng, Zhen; Gong, Ming; Xu, Yong; Mao, Li; Zou, Xubo; Guo, Guangcan; Zhang, Chuanwei

2013-01-01

Majorana fermions (MFs), quantum particles that are their own antiparticles, are not only of fundamental importance in elementary particle physics and dark matter, but also building blocks for fault-tolerant quantum computation. Recently MFs have been intensively studied in solid state and cold atomic systems. These studies are generally based on superconducting pairing with zero total momentum. On the other hand, finite total momentum Cooper pairings, known as Fulde-Ferrell (FF) Larkin-Ovchinnikov (LO) states, were widely studied in many branches of physics. However, whether FF and LO superconductors can support MFs has not been explored. Here we show that MFs can exist in certain types of gapped FF states, yielding a new quantum matter: topological FF superfluids/superconductors. We demonstrate the existence of such topological FF superfluids and the associated MFs using spin-orbit-coupled degenerate Fermi gases and derive their parameter regions. The implementation of topological FF superconductors in semiconductor/superconductor heterostructures is also discussed.

Manipulating Topological Edge Spins in One-Dimensional Optical Lattice

NASA Astrophysics Data System (ADS)

Liu, Xiong-Jun; Liu, Zheng-Xin; Cheng, Meng

2013-03-01

We propose to observe and manipulate topological edge spins in 1D optical lattice based on currently available experimental platforms. Coupling the atomic spin states to a laser-induced periodic Zeeman field, the lattice system can be driven into a symmetry protected topological (SPT) phase, which belongs to the chiral unitary (AIII) class protected by particle number conservation and chiral symmetries. In free-fermion case the SPT phase is classified by a Z invariant which reduces to Z4 with interactions. The zero edge modes of the SPT phase are spin-polarized, with left and right edge spins polarized to opposite directions and forming a topological spin-qubit (TSQ). We demonstrate a novel scheme to manipulate the zero modes and realize single spin control in optical lattice. The manipulation of TSQs has potential applications to quantum computation. We acknowledge the support from JQI-NSF-PFC, Microsoft-Q, and DARPA- QuEST.

The sponge-like topology of large-scale structure in the universe

NASA Technical Reports Server (NTRS)

Gott, J. R., III; Dickinson, M.; Melott, A. L.

1986-01-01

The relative connectedness of the high- and low-density regions in the universe is studied using a median density contour which divides space into two equal volumes. The CfA data are found to show a sponge-like topology where the highand low-density regions are both interlocking and equivalent. The boundary surface between the two regions has a general negative curvature, and is characterized by a large number of holes. In the initial conditions the connectedness of the two regions must be identical because a change of sign in the random quantum fluctuations would reverse their roles. It is noted that in the cold dark matter and neutrino scenarios the hole sizes are typically of the order of the smoothing diameter or the damping length, whichever is larger. The sponge-like topology is consistent with the universe having a frothy appearance without being divided neatly into cells. A computer algorithm for measuring topology is discussed.

Spectral identification of topological domains

PubMed Central

Chen, Jie; Hero, Alfred O.; Rajapakse, Indika

2016-01-01

Motivation: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy. Results: An efficient algorithm is presented to identify topological domains from the Hi-C matrix. Availability and Implementation: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/ Contact: indikar@med.umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153657

On the Topologic Properties of River Networks

NASA Astrophysics Data System (ADS)

Sarker, S.; Singh, A.

2017-12-01

River network is an important landscape feature and has been studied extensively from a range of geomorphological and hydrological perspective. However, quantifying topologic dynamics and reorganization of river networks is becoming more and more challenging under changing natural and anthropogenic forcings. Here, we use a graph-theoretical approach to study topologic properties of natural and simulated river networks for a range of climatic and tectonic conditions. Among other metrics, we use betweeness and eigenvector centrality distributions computed using adjacency matrix of river networks and show their dependence on energy exponent γ that characterizes mechanism of erosional processes on a landscape. We further compare these topologic characteristics of landscape to geomorphic features such as slope-area curve and drainage density. Furthermore, we identify locations of critical nodes and links on a network as a function of energy exponent γ to understand network robustness and vulnerability under external attacks.

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs

NASA Astrophysics Data System (ADS)

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C.; Hütt, Marc-Thorsten

2017-02-01

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience.

pmx: Automated protein structure and topology generation for alchemical perturbations

PubMed Central

Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

2015-01-01

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36. PMID:25487359

Computers and Play.

ERIC Educational Resources Information Center

Colker, Larry

Viewing computers in various forms as developmentally appropriate objects for children, this discussion provides a framework for integrating conceptions of computers and conceptions of play. Several instances are cited from the literature in which explicit analogies have been made between computers and playthings or play environments.…

Lattice-matched heterojunctions between topological and normal insulators: A first-principles study

NASA Astrophysics Data System (ADS)

Lee, Hyungjun; Yazyev, Oleg V.

2017-02-01

Gapless boundary modes at the interface between topologically distinct regions are one of the most salient manifestations of topology in physics. Metallic boundary states of time-reversal-invariant topological insulators (TIs), a realization of topological order in condensed matter, have been of much interest not only due to such a fundamental nature, but also due to their practical significance. These boundary states are immune to backscattering and localization owing to their topological origin, thereby opening up the possibility to tailor them for potential uses in spintronics and quantum computing. The heterojunction between a TI and a normal insulator (NI) is a representative playground for exploring such a topologically protected metallic boundary state and expected to constitute a building block for future electronic and spintronic solid-state devices based on TIs. Here, we report a first-principles study of two experimentally realized lattice-matched heterojunctions between TIs and NIs, Bi2Se3 (0001)/InP(111) and Bi2Te3 (0001)/BaF2(111). We evaluate the band offsets at these interfaces from many-body perturbation theory within the G W approximation as well as density-functional theory. Furthermore, we investigate the topological interface states, demonstrating that at these lattice-matched heterointerfaces, they are strictly localized and their helical spin textures are as well preserved as those at the vacuum-facing surfaces. These results taken together may help in designing devices relying on spin-helical metallic boundary states of TIs.

Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

PubMed Central

Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

2009-01-01

We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite-difference methods. PMID:18567005

Implicit schemes and parallel computing in unstructured grid CFD

NASA Technical Reports Server (NTRS)

Venkatakrishnam, V.

1995-01-01

The development of implicit schemes for obtaining steady state solutions to the Euler and Navier-Stokes equations on unstructured grids is outlined. Applications are presented that compare the convergence characteristics of various implicit methods. Next, the development of explicit and implicit schemes to compute unsteady flows on unstructured grids is discussed. Next, the issues involved in parallelizing finite volume schemes on unstructured meshes in an MIMD (multiple instruction/multiple data stream) fashion are outlined. Techniques for partitioning unstructured grids among processors and for extracting parallelism in explicit and implicit solvers are discussed. Finally, some dynamic load balancing ideas, which are useful in adaptive transient computations, are presented.

Network-based statistical comparison of citation topology of bibliographic databases

PubMed Central

Šubelj, Lovro; Fiala, Dalibor; Bajec, Marko

2014-01-01

Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies. PMID:25263231

Spin textures on general surfaces of the correlated topological insulator SmB6

NASA Astrophysics Data System (ADS)

Baruselli, Pier Paolo; Vojta, Matthias

2016-05-01

Employing the k .p expansion for a family of tight-binding models for SmB6, we analytically compute topological surface states on a generic (l m n ) surface. We show how the Dirac-cone spin structure depends on model ingredients and on the angle θ between the surface normal and the main crystal axes. We apply the general theory to (001), (110), (111), and (210) surfaces, for which we provide concrete predictions for the spin pattern of surface states which we also compare with tight-binding results. As shown in previous work, the spin pattern on a (001 ) surface can be related to the value of mirror Chern numbers, and we explore the possibility of topological phase transitions between states with different mirror Chern numbers and the associated change of the spin structure of surface states. Such transitions may be accessed by varying either the hybridization between conduction and f electrons or the crystal-field splitting of the low-energy f multiplets, and we compute corresponding phase diagrams. Experimentally, chemical doping is a promising route to realize such transitions.

Ribbons around Mexican hats

NASA Astrophysics Data System (ADS)

Bachas, C.; Tomaras, T. N.

1994-10-01

We analyze quasi-topological solitons winding around a Mexican-hat potential in two space-time dimensions. They are prototypes for a large number of physical excitations, including skyrmions of the Higgs sector of the standard electroweak model, magnetic bubbles in thin ferromagnetic films, and strings in certain non-trivial backgrounds. We present explicit solutions, derive the conditions for classical stability, and show that contrary to the naive expectation these can be satisfied in the weak-coupling limit. In this limit we can calculate the soliton properties reliably, and estimate their lifetime semiclassically. We explain why gauge interactions destabilize these solitons, unless the scalar sector is extended.

Thermodynamics of Einstein-Born-Infeld black holes with negative cosmological constant

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

Miskovic, Olivera; Olea, Rodrigo; INFN, Sezione di Milano, Via Celoria 16, I-20133, Milano

2008-06-15

We study the thermodynamics associated to topological black hole solutions of AdS gravity coupled to nonlinear electrodynamics (Born-Infeld) in any dimension, using a background-independent regularization prescription for the Euclidean action given by boundary terms, which explicitly depend on the extrinsic curvature (Kounterterms series). A finite action principle leads to the correct definition of thermodynamic variables as Noether charges, which satisfy a Smarr-like relation. In particular, for the odd-dimensional case, a consistent thermodynamic description is achieved if the internal energy of the system includes the vacuum energy for AdS spacetime.

Exact solutions of the Schrödinger equation with a coulomb ring-shaped potential in the cosmic string spacetime

NASA Astrophysics Data System (ADS)

Wang, Zhi; Long, Zheng-wen; Long, Chao-yun; Teng, Jing

2015-05-01

We study the Schrödinger equation with a Coulomb ring-shaped potential in the spacetime of a cosmic string, and the solutions of the system are obtained by using the generalized parametric Nikiforov-Uvarov (NU) method. They show that the quantum dynamics of a physical system depend on the non-trivial topological features of the cosmic string spacetime and the energy levels of the considered quantum system depend explicitly on the angular deficit α which characterizes the global structure of the metric in the cosmic string spacetime.

Topological photonic crystal with equifrequency Weyl points

NASA Astrophysics Data System (ADS)

Wang, Luyang; Jian, Shao-Kai; Yao, Hong

2016-06-01

Weyl points in three-dimensional photonic crystals behave as monopoles of Berry flux in momentum space. Here, based on general symmetry analysis, we show that a minimal number of four symmetry-related (consequently equifrequency) Weyl points can be realized in time-reversal invariant photonic crystals. We further propose an experimentally feasible way to modify double-gyroid photonic crystals to realize four equifrequency Weyl points, which is explicitly confirmed by our first-principle photonic band-structure calculations. Remarkably, photonic crystals with equifrequency Weyl points are qualitatively advantageous in applications including angular selectivity, frequency selectivity, invisibility cloaking, and three-dimensional imaging.

Fast algorithm for automatically computing Strahler stream order

USGS Publications Warehouse

Lanfear, Kenneth J.

1990-01-01

An efficient algorithm was developed to determine Strahler stream order for segments of stream networks represented in a Geographic Information System (GIS). The algorithm correctly assigns Strahler stream order in topologically complex situations such as braided streams and multiple drainage outlets. Execution time varies nearly linearly with the number of stream segments in the network. This technique is expected to be particularly useful for studying the topology of dense stream networks derived from digital elevation model data.

Relationships among the structural topology, bond strength, and mechanical properties of single-walled aluminosilicate nanotubes.

PubMed

Liou, Kai-Hsin; Tsou, Nien-Ti; Kang, Dun-Yen

2015-10-21

Carbon nanotubes (CNTs) are regarded as small but strong due to their nanoscale microstructure and high mechanical strength (Young's modulus exceeds 1000 GPa). A longstanding question has been whether there exist other nanotube materials with mechanical properties as good as those of CNTs. In this study, we investigated the mechanical properties of single-walled aluminosilicate nanotubes (AlSiNTs) using a multiscale computational method and then conducted a comparison with single-walled carbon nanotubes (SWCNTs). By comparing the potential energy estimated from molecular and macroscopic material mechanics, we were able to model the chemical bonds as beam elements for the nanoscale continuum modeling. This method allowed for simulated mechanical tests (tensile, bending, and torsion) with minimum computational resources for deducing their Young's modulus and shear modulus. The proposed approach also enabled the creation of hypothetical nanotubes to elucidate the relative contributions of bond strength and nanotube structural topology to overall nanotube mechanical strength. Our results indicated that it is the structural topology rather than bond strength that dominates the mechanical properties of the nanotubes. Finally, we investigated the relationship between the structural topology and the mechanical properties by analyzing the von Mises stress distribution in the nanotubes. The proposed methodology proved effective in rationalizing differences in the mechanical properties of AlSiNTs and SWCNTs. Furthermore, this approach could be applied to the exploration of new high-strength nanotube materials.

Structural kinetic modeling of metabolic networks.

PubMed

Steuer, Ralf; Gross, Thilo; Selbig, Joachim; Blasius, Bernd

2006-08-08

To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

On common noise-induced synchronization in complex networks with state-dependent noise diffusion processes

NASA Astrophysics Data System (ADS)

Russo, Giovanni; Shorten, Robert

2018-04-01

This paper is concerned with the study of common noise-induced synchronization phenomena in complex networks of diffusively coupled nonlinear systems. We consider the case where common noise propagation depends on the network state and, as a result, the noise diffusion process at the nodes depends on the state of the network. For such networks, we present an algebraic sufficient condition for the onset of synchronization, which depends on the network topology, the dynamics at the nodes, the coupling strength and the noise diffusion. Our result explicitly shows that certain noise diffusion processes can drive an unsynchronized network towards synchronization. In order to illustrate the effectiveness of our result, we consider two applications: collective decision processes and synchronization of chaotic systems. We explicitly show that, in the former application, a sufficiently large noise can drive a population towards a common decision, while, in the latter, we show how common noise can synchronize a network of Lorentz chaotic systems.

Robust spatial memory maps in flickering neuronal networks: a topological model

NASA Astrophysics Data System (ADS)

Dabaghian, Yuri; Babichev, Andrey; Memoli, Facundo; Chowdhury, Samir; Rice University Collaboration; Ohio State University Collaboration

It is widely accepted that the hippocampal place cells provide a substrate of the neuronal representation of the environment--the ``cognitive map''. However, hippocampal network, as any other network in the brain is transient: thousands of hippocampal neurons die every day and the connections formed by these cells constantly change due to various forms of synaptic plasticity. What then explains the remarkable reliability of our spatial memories? We propose a computational approach to answering this question based on a couple of insights. First, we propose that the hippocampal cognitive map is fundamentally topological, and hence it is amenable to analysis by topological methods. We then apply several novel methods from homology theory, to understand how dynamic connections between cells influences the speed and reliability of spatial learning. We simulate the rat's exploratory movements through different environments and study how topological invariants of these environments arise in a network of simulated neurons with ``flickering'' connectivity. We find that despite transient connectivity the network of place cells produces a stable representation of the topology of the environment.

Nonlocal optical response in topological phase transitions in the graphene family

NASA Astrophysics Data System (ADS)

Rodriguez-Lopez, Pablo; Kort-Kamp, Wilton J. M.; Dalvit, Diego A. R.; Woods, Lilia M.

2018-01-01

We investigate the electromagnetic response of staggered two-dimensional materials of the graphene family, including silicene, germanene, and stanene, as they are driven through various topological phase transitions using external fields. Utilizing Kubo formalism, we compute their optical conductivity tensor taking into account the frequency and wave vector of the electromagnetic excitations, and study its behavior over the full electronic phase diagram of the materials. In particular, we find that the resonant behavior of the nonlocal Hall conductivity is strongly affected by the various topological phases present in these materials. We also consider the plasmon excitations in the graphene family and find that nonlocality in the optical response can affect the plasmon dispersion spectra of the various phases. We find a regime of wave vectors for which the plasmon relations for phases with trivial topology are essentially indistinguishable, while those for phases with nontrivial topology are distinct and are redshifted as the corresponding Chern number increases. The expressions for the conductivity components are valid for the entire graphene family and can be readily used by others.

Estimating Bayesian Phylogenetic Information Content

PubMed Central

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

2016-01-01

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

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

PubMed

Ahmad, Sahar; Khan, Muhammad Faisal

2015-12-01

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

Nonlocal optical response in topological phase transitions in the graphene family

DOE PAGES

Rodriguez-Lopez, Pablo; de Melo Kort-Kamp, Wilton Junior; Dalvit, Diego Alejandro Roberto; ...

2018-01-22

We investigate the electromagnetic response of staggered two-dimensional materials of the graphene family, including silicene, germanene, and stanene, as they are driven through various topological phase transitions using external fields. Utilizing Kubo formalism, we compute their optical conductivity tensor taking into account the frequency and wave vector of the electromagnetic excitations, and study its behavior over the full electronic phase diagram of the materials. In particular, we find that the resonant behavior of the nonlocal Hall conductivity is strongly affected by the various topological phases present in these materials. We also consider the plasmon excitations in the graphene family andmore » find that nonlocality in the optical response can affect the plasmon dispersion spectra of the various phases. Here, we find a regime of wave vectors for which the plasmon relations for phases with trivial topology are essentially indistinguishable, while those for phases with nontrivial topology are distinct and are redshifted as the corresponding Chern number increases. Finally, the expressions for the conductivity components are valid for the entire graphene family and can be readily used by others.« less