Complete topology inversion can be part of normal membrane protein biogenesis.

Science.gov (United States)

Woodall, Nicholas B; Hadley, Sarah; Yin, Ying; Bowie, James U

2017-04-01

The topology of helical membrane proteins is generally defined during insertion of the transmembrane helices, yet it is now clear that it is possible for topology to change under unusual circumstances. It remains unclear, however, if topology reorientation is part of normal biogenesis. For dual topology dimer proteins such as the multidrug transporter EmrE, there may be evolutionary pressure to allow topology flipping so that the populations of both orientations can be equalized. We previously demonstrated that when EmrE is forced to insert in a distorted topology, topology flipping of the first transmembrane helix can occur during translation. Here, we show that topological malleability also extends to the C-terminal helix and that even complete topology inversion of the entire EmrE protein can occur after the full protein is translated and inserted. Thus, topology rearrangements are possible during normal biogenesis. Wholesale topology flipping is remarkable given the physical constraints of the membrane and expands the range of possible membrane protein folding pathways, both productive and detrimental. © 2017 The Protein Society.

A concept for global optimization of topology design problems

DEFF Research Database (Denmark)

Stolpe, Mathias; Achtziger, Wolfgang; Kawamoto, Atsushi

2006-01-01

We present a concept for solving topology design problems to proven global optimality. We propose that the problems are modeled using the approach of simultaneous analysis and design with discrete design variables and solved with convergent branch and bound type methods. This concept is illustrated...... on two applications. The first application is the design of stiff truss structures where the bar areas are chosen from a finite set of available areas. The second considered application is simultaneous topology and geometry design of planar articulated mechanisms. For each application we outline...

Topology Optimization for Transient Wave Propagation Problems

DEFF Research Database (Denmark)

Matzen, René

The study of elastic and optical waves together with intensive material research has revolutionized everyday as well as cutting edge technology in very tangible ways within the last century. Therefore it is important to continue the investigative work towards improving existing as well as innovate...... new technology, by designing new materials and their layout. The thesis presents a general framework for applying topology optimization in the design of material layouts for transient wave propagation problems. In contrast to the high level of modeling in the frequency domain, time domain topology...... optimization is still in its infancy. A generic optimization problem is formulated with an objective function that can be field, velocity, and acceleration dependent, as well as it can accommodate the dependency of filtered signals essential in signal shape optimization [P3]. The analytical design gradients...

Mathematical programming methods for large-scale topology optimization problems

DEFF Research Database (Denmark)

Rojas Labanda, Susana

for mechanical problems, but has rapidly extended to many other disciplines, such as fluid dynamics and biomechanical problems. However, the novelty and improvements of optimization methods has been very limited. It is, indeed, necessary to develop of new optimization methods to improve the final designs......, and at the same time, reduce the number of function evaluations. Nonlinear optimization methods, such as sequential quadratic programming and interior point solvers, have almost not been embraced by the topology optimization community. Thus, this work is focused on the introduction of this kind of second...... for the classical minimum compliance problem. Two of the state-of-the-art optimization algorithms are investigated and implemented for this structural topology optimization problem. A Sequential Quadratic Programming (TopSQP) and an interior point method (TopIP) are developed exploiting the specific mathematical...

On some fundamental properties of structural topology optimization problems

DEFF Research Database (Denmark)

Stolpe, Mathias

2010-01-01

We study some fundamental mathematical properties of discretized structural topology optimization problems. Either compliance is minimized with an upper bound on the volume of the structure, or volume is minimized with an upper bound on the compliance. The design variables are either continuous o....... The presented examples can be used as teaching material in graduate and undergraduate courses on structural topology optimization....

PROBLEMS IN TOPOLOGICAL GRAPH THEORY : QUESTIONS I CAN'T ANSWER

OpenAIRE

Archdeacon, Dan

1999-01-01

This paper describes my Problems in Topological Graph Theory, which can be accessed through the world-wide-web at http: //www.emba .uvm.edu/~arcceack/problems/problems.html This list of problems is constantly being revised; the interested reader is encouraged to submit additions and updates.

Newton-type method for the variational discretization of topology optimization problems

DEFF Research Database (Denmark)

Evgrafov, Anton

2013-01-01

We present a locally quadratically convergent optimization algorithm for solving topology optimization problems. The distinguishing feature of the algorithm is to treat the design as a smooth function of the state and not vice versa as in the traditional nested approach to topology optimization, ...

Topology optimization for acoustic-structure interaction problems

DEFF Research Database (Denmark)

Yoon, Gil Ho; Jensen, Jakob Søndergaard; Sigmund, Ole

2006-01-01

We propose a gradient based topology optimization algorithm for acoustic-structure (vibro-acoustic) interaction problems without an explicit interfacing boundary representation. In acoustic-structure interaction problems, the pressure field and the displacement field are governed by the Helmholtz...... to subdomain interfaces evolving during the optimization process. In this paper, we propose to use a mixed finite element formulation with displacements and pressure as primary variables (u/p formulation) which eliminates the need for explicit boundary representation. In order to describe the Helmholtz......-dimensional acoustic-structure interaction problems are optimized to show the validity of the proposed method....

Some problems on selections for hyperspace topologies

Directory of Open Access Journals (Sweden)

Valentin Gutev

2004-04-01

Full Text Available The theory of hyperspaces has attracted the attention of many mathematicians who have found a large variety of its applications during the last decades. The theory has taken also its natural course and has yielded lots of problems which, besides their independent inner beauty, provide ties with numerous classical fields of mathematics. In the present note we are concerned with some open problems about selections for hyperspace topologies which have been in the scope of our recent research interests.

Topology optimization of fluid-structure-interaction problems in poroelasticity

DEFF Research Database (Denmark)

Andreasen, Casper Schousboe; Sigmund, Ole

2013-01-01

This paper presents a method for applying topology optimization to fluid-structure interaction problems in saturated poroelastic media. The method relies on a multiple-scale method applied to periodic media. The resulting model couples the Stokes flow in the pores of the structure with the deform...... by topology optimization in order to optimize the performance of a shock absorber and test the pressure loading capabilities and optimization of an internally pressurized lid. © 2013 Published by Elsevier B.V....

Topology optimization of Channel flow problems

DEFF Research Database (Denmark)

Gersborg-Hansen, Allan; Sigmund, Ole; Haber, R. B.

2005-01-01

function which measures either some local aspect of the velocity field or a global quantity, such as the rate of energy dissipation. We use the finite element method to model the flow, and we solve the optimization problem with a gradient-based math-programming algorithm that is driven by analytical......This paper describes a topology design method for simple two-dimensional flow problems. We consider steady, incompressible laminar viscous flows at low to moderate Reynolds numbers. This makes the flow problem non-linear and hence a non-trivial extension of the work of [Borrvall&Petersson 2002......]. Further, the inclusion of inertia effects significantly alters the physics, enabling solutions of new classes of optimization problems, such as velocity--driven switches, that are not addressed by the earlier method. Specifically, we determine optimal layouts of channel flows that extremize a cost...

Topology optimization of 3D Stokes flow problems

DEFF Research Database (Denmark)

Gersborg-Hansen, Allan; Sigmund, Ole; Bendsøe, Martin P.

fluid mechanics. In future practice a muTAS could be used by doctors, engineers etc. as a hand held device with short reaction time that provides on-site analysis of a flowing substance such as blood, polluted water or similar. Borrvall and Petersson [2] paved the road for using the topology...... particular at micro scales since they are easily manufacturable and maintenance free. Here we consider topology optimization of 3D Stokes flow problems which is a reasonable fluid model to use at small scales. The presentation elaborates on effects caused by 3D fluid modelling on the design. Numerical...

A hierarchical method for structural topology design problems with local stress and displacement constraints

DEFF Research Database (Denmark)

Stolpe, Mathias; Stidsen, Thomas K.

2005-01-01

In this paper we present a hierarchical optimization method for finding feasible true 0-1 solutions to finite element based topology design problems. The topology design problems are initially modeled as non-convex mixed 0-1 programs. The hierarchical optimization method is applied to the problem...... and then successively refined as needed. At each level of design mesh refinement, a neighborhood optimization method is used to solve the problem considered. The non-convex topology design problems are equivalently reformulated as convex all-quadratic mixed 0-1 programs. This reformulation enables the use of methods...... of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively solves a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...

Benefits and Challenges when Performing Robust Topology Optimization for Interior Acoustic Problems

OpenAIRE

Christiansen, Rasmus Ellebæk; Jensen, Jakob Søndergaard; Lazarov, Boyan Stefanov; Sigmund, Ole

2014-01-01

The objective of this work is to present benets and challenges of using robust topology optimization techniques for minimizing the sound pressure in interior acoustic problems. The focus is on creating designs which maintain high performance under uniform spatial variations. This work takes offset in previous work considering topology optimization for interior acoustic problems, [1]. However in the previous work the robustness of the designs was not considered.

Benefits and Challenges when Performing Robust Topology Optimization for Interior Acoustic Problems

DEFF Research Database (Denmark)

Christiansen, Rasmus Ellebæk; Jensen, Jakob Søndergaard; Lazarov, Boyan Stefanov

The objective of this work is to present benets and challenges of using robust topology optimization techniques for minimizing the sound pressure in interior acoustic problems. The focus is on creating designs which maintain high performance under uniform spatial variations. This work takes offset...... in previous work considering topology optimization for interior acoustic problems, [1]. However in the previous work the robustness of the designs was not considered....

Topology optimization of bounded acoustic problems using the hybrid finite element-wave based method

DEFF Research Database (Denmark)

Goo, Seongyeol; Wang, Semyung; Kook, Junghwan

2017-01-01

This paper presents an alternative topology optimization method for bounded acoustic problems that uses the hybrid finite element-wave based method (FE-WBM). The conventional method for the topology optimization of bounded acoustic problems is based on the finite element method (FEM), which...

Frequency response as a surrogate eigenvalue problem in topology optimization

DEFF Research Database (Denmark)

Andreassen, Erik; Ferrari, Federico; Sigmund, Ole

2018-01-01

This article discusses the use of frequency response surrogates for eigenvalue optimization problems in topology optimization that may be used to avoid solving the eigenvalue problem. The motivation is to avoid complications that arise from multiple eigenvalues and the computational complexity as...

A hierarchical method for discrete structural topology design problems with local stress and displacement constraints

DEFF Research Database (Denmark)

Stolpe, Mathias; Stidsen, Thomas K.

2007-01-01

In this paper, we present a hierarchical optimization method for finding feasible true 0-1 solutions to finite-element-based topology design problems. The topology design problems are initially modelled as non-convex mixed 0-1 programs. The hierarchical optimization method is applied to the problem...... and then successively refined as needed. At each level of design mesh refinement, a neighbourhood optimization method is used to treat the problem considered. The non-convex topology design problems are equivalently reformulated as convex all-quadratic mixed 0-1 programs. This reformulation enables the use of methods...... of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively treats a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...

On topological derivatives for contact problems in elasticity

Czech Academy of Sciences Publication Activity Database

Giusti, S.M.; Sokolowski, S.; Stebel, Jan

2015-01-01

Roč. 165, č. 1 (2015), s. 279-294 ISSN 0022-3239 R&D Projects: GA ČR GA201/09/0917 Institutional support: RVO:67985840 Keywords : topological derivative * static frictionless contact problem * asymptotic analysis Subject RIV: BA - General Mathematics Impact factor: 1.160, year: 2015 http://link.springer.com/article/10.1007%2Fs10957-014-0594-7

Topological regularizations of the triple collision singularity in the 3-vortex problem

International Nuclear Information System (INIS)

Hiraoka, Yasuaki

2008-01-01

The triple collision singularity in the 3-vortex problem is studied in this paper. Under the necessary condition k 1 -1 +k 2 -1 +k 3 -1 =0 for vorticities to have the triple collision, the main results are summarized as follows: (i) For k 1 = k 2 , the triple collision singularity is topologically regularizable. (ii) For 0 1 − k 2 | < ε with a sufficiently small ε, the triple collision singularity is not topologically regularizable. First of all, in order to prove these statements, all singularities in the 3-vortex problem are classified. Then, we introduce a dynamical system by blowing up the triple collision singularity with an appropriate time scaling. Roughly speaking, it corresponds to pasting an invariant manifold at the triple collision singularity on the original phase space. This technique is well known as McGehee's collision manifold (1974 Inventions Math. 27 191–227) in the N-body problem of celestial mechanics. Finally, by adopting the viewpoint of Easton (1971 J. Diff. Eqns 10 92–9), topological regularizations of the triple collision singularity are studied in detail

Industrial Application of Topology Optimization for Combined Conductive and Convective Heat Transfer Problems

DEFF Research Database (Denmark)

Zhou, Mingdong; Alexandersen, Joe; Sigmund, Ole

2016-01-01

This paper presents an industrial application of topology optimization for combined conductive and convective heat transfer problems. The solution is based on a synergy of computer aided design and engineering software tools from Dassault Systemes. The considered physical problem of steady......-state heat transfer under convection is simulated using SIMULIA-Abaqus. A corresponding topology optimization feature is provided by SIMULIA-Tosca. By following a standard workflow of design optimization, the proposed solution is able to accommodate practical design scenarios and results in efficient...

Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen.

Science.gov (United States)

Al-Abdul-Wahid, M Sameer; Verardi, Raffaello; Veglia, Gianluigi; Prosser, R Scott

2011-09-01

In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.

Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen

International Nuclear Information System (INIS)

Al-Abdul-Wahid, M. Sameer; Verardi, Raffaello; Veglia, Gianluigi; Prosser, R. Scott

2011-01-01

In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.

Topology optimization for transient heat transfer problems

DEFF Research Database (Denmark)

Zeidan, Said; Sigmund, Ole; Lazarov, Boyan Stefanov

The focus of this work is on passive control of transient heat transfer problems using the topology optimization (TopOpt) method [1]. The goal is to find distributions of a limited amount of phase change material (PCM), within a given design domain, which optimizes the heat energy storage [2]. Our......, TopOpt has later been extended to transient problems in mechanics and photonics (e.g. [5], [6] and [7]). In the presented approach, the optimization is gradient-based, where in each iteration the non-steady heat conduction equation is solved,using the finite element method and an appropriate time......-stepping scheme. A PCM can efficiently absorb heat while keeping its temperature nearly unchanged [8]. The use of PCM ine.g. electronics [9] and mechanics [10], yields improved performance and lower costs depending on a.o., the spatial distribution of PCM.The considered problem consists in optimizing...

Topology optimization of coated structures and material interface problems

DEFF Research Database (Denmark)

Clausen, Anders; Aage, Niels; Sigmund, Ole

2015-01-01

This paper presents a novel method for including coated structures and prescribed material interface properties into the minimum compliance topology optimization problem. Several elements of the method are applicable to a broader range of interface problems. The approach extends the standard SIMP......-step filtering/projection approach. The modeled coating thickness is derived analytically, and the coating is shown to be accurately controlled and applied in a highly uniform manner over the structure. An alternative interpretation of the model is to perform single-material design for additive manufacturing...

DNA topology and transcription

Science.gov (United States)

Kouzine, Fedor; Levens, David; Baranello, Laura

2014-01-01

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

Global optimization of discrete truss topology design problems using a parallel cut-and-branch method

DEFF Research Database (Denmark)

Rasmussen, Marie-Louise Højlund; Stolpe, Mathias

2008-01-01

the physics, and the cuts (Combinatorial Benders’ and projected Chvátal–Gomory) come from an understanding of the particular mathematical structure of the reformulation. The impact of a stronger representation is investigated on several truss topology optimization problems in two and three dimensions.......The subject of this article is solving discrete truss topology optimization problems with local stress and displacement constraints to global optimum. We consider a formulation based on the Simultaneous ANalysis and Design (SAND) approach. This intrinsically non-convex problem is reformulated...

High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

Science.gov (United States)

Doherty, Tim; Su, Yongchao; Hong, Mei

2010-08-27

The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Linux software for large topology optimization problems

DEFF Research Database (Denmark)

evolving product, which allows a parallel solution of the PDE, it lacks the important feature that the matrix-generation part of the computations is localized to each processor. This is well-known to be critical for obtaining a useful speedup on a Linux cluster and it motivates the search for a COMSOL......-like package for large topology optimization problems. One candidate for such software is developed for Linux by Sandia Nat’l Lab in the USA being the Sundance system. Sundance also uses a symbolic representation of the PDE and a scalable numerical solution is achieved by employing the underlying Trilinos...

Random matrix analysis of the QCD sign problem for general topology

International Nuclear Information System (INIS)

Bloch, Jacques; Wettig, Tilo

2009-01-01

Motivated by the important role played by the phase of the fermion determinant in the investigation of the sign problem in lattice QCD at nonzero baryon density, we derive an analytical formula for the average phase factor of the fermion determinant for general topology in the microscopic limit of chiral random matrix theory at nonzero chemical potential, for both the quenched and the unquenched case. The formula is a nontrivial extension of the expression for zero topology derived earlier by Splittorff and Verbaarschot. Our analytical predictions are verified by detailed numerical random matrix simulations of the quenched theory.

Topology optimization of unsteady flow problems using the lattice Boltzmann method

DEFF Research Database (Denmark)

Nørgaard, Sebastian Arlund; Sigmund, Ole; Lazarov, Boyan Stefanov

2016-01-01

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...

Topology Optimization for Wave Propagation Problems with Experimental Validation

DEFF Research Database (Denmark)

Christiansen, Rasmus Ellebæk

designed using the proposed method is provided. A novel approach for designing meta material slabs with selectively tuned negative refractive behavior is outlined. Numerical examples demonstrating the behavior of a slab under different conditions is provided. Results from an experimental studydemonstrating...... agreement with numerical predictions are presented. Finally an approach for designing acoustic wave shaping devices is treated. Three examples of applications are presented, a directional sound emission device, a wave splitting device and a flat focusing lens. Experimental results for the first two devices......This Thesis treats the development and experimental validation of density-based topology optimization methods for wave propagation problems. Problems in the frequency regime where design dimensions are between approximately one fourth and ten wavelengths are considered. All examples treat problems...

Relativized problems with abelian phase group in topological dynamics.

Science.gov (United States)

McMahon, D

1976-04-01

Let (X, T) be the equicontinuous minimal transformation group with X = pi(infinity)Z(2), the Cantor group, and S = [unk](infinity)Z(2) endowed with the discrete topology acting on X by right multiplication. For any countable group T we construct a function F:X x S --> T such that if (Y, T) is a minimal transformation group, then (X x Y, S) is a minimal transformation group with the action defined by (x, y)s = [xs, yF(x, s)]. If (W, T) is a minimal transformation group and varphi:(Y, T) --> (W, T) is a homomorphism, then identity x varphi:(X x Y, S) --> (X x W, S) is a homomorphism and has many of the same properties that varphi has. For this reason, one may assume that the phase group is abelian (or S) without loss of generality for many relativized problems in topological dynamics.

Triple Helix going abroad?

DEFF Research Database (Denmark)

Sørensen, Olav Jull; Hu, Yimei

2014-01-01

The aim of the article is to explore to what extent the Tripple helix is being internationalized. Each of the helixes have their own internationalization rationale but the article show by small example that the helix itself is being internationalized and integrated with the host country tripple h...

Topological insulators and topological superconductors

CERN Document Server

Bernevig, Andrei B

2013-01-01

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

General topology

CERN Document Server

Willard, Stephen

2004-01-01

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

A note on the consensus finding problem in communication networks with switching topologies

KAUST Repository

Haskovec, Jan

2014-01-01

In this note, we discuss the problem of consensus finding in communication networks of agents with dynamically switching topologies. In particular, we consider the case of directed networks with unbalanced matrices of communication rates. We

Wavelet approach to accelerator problems. 3: Melnikov functions and symplectic topology

International Nuclear Information System (INIS)

Fedorova, A.; Zeitlin, M.; Parsa, Z.

1997-05-01

This is the third part of a series of talks in which the authors present applications of methods of wavelet analysis to polynomial approximations for a number of accelerator physics problems. They consider the generalization of the variational wavelet approach to nonlinear polynomial problems to the case of Hamiltonian systems for which they need to preserve underlying symplectic or Poissonian or quasicomplex structures in any type of calculations. They use the approach for the problem of explicit calculations of Arnold-Weinstein curves via Floer variational approach from symplectic topology. The loop solutions are parameterized by the solutions of reduced algebraical problem--matrix Quadratic Mirror Filters equations. Also they consider wavelet approach to the calculations of Melnikov functions in the theory of homoclinic chaos in perturbed Hamiltonian systems

Intrinsic optical conductivity of a {{\\rm{C}}}_{2v} symmetric topological insulator

Science.gov (United States)

Sengupta, Parijat; Matsubara, Masahiko; Bellotti, Enrico; Shi, Junxia

2017-07-01

In this work we analytically investigate the longitudinal optical conductivity of the {{{C}}}2v symmetric topological insulator. The conductivity expressions at T = 0 are derived using the Kubo formula and expressed as a function of the ratio of the Dresselhaus and Rashba parameters that characterize the low-energy Hamiltonian. We find that the longitudinal inter-band conductivity vanishes when Dresselhaus and Rashba parameters are equal in strength, also called the persistent spin helix state. The calculations are extended to obtain the frequency-dependent real and imaginary components of the optical conductivity for the topological Kondo insulator SmB6 which exhibits {{{C}}}2v symmetric and anisotropic Dirac cones hosting topological states at \\overline{X} point on the surface Brillouin zone.

Broadband and high-efficiency vortex beam generator based on a hybrid helix array.

Science.gov (United States)

Fang, Chaoqun; Wu, Chao; Gong, Zhijie; Zhao, Song; Sun, Anqi; Wei, Zeyong; Li, Hongqiang

2018-04-01

The vortex beam which carries the orbital angular momentum has versatile applications, such as high-resolution imaging, optical communications, and particle manipulation. Generating vortex beams with the Pancharatnam-Berry (PB) phase has drawn considerable attention for its unique spin-to-orbital conversion features. Despite the PB phase being frequency independent, an optical element with broadband high-efficiency circular polarization conversion feature is still needed for the broadband high-efficiency vortex beam generation. In this work, a broadband and high-efficiency vortex beam generator based on the PB phase is built with a hybrid helix array. Such devices can generate vortex beams with arbitrary topological charge. Moreover, vortex beams with opposite topological charge can be generated with an opposite handedness incident beam that propagates backward. The measured efficiency of our device is above 65% for a wide frequency range, with the relative bandwidth of 46.5%.

Multiple helix ecosystems for sustainable competitiveness

CERN Document Server

Ferreira, João; Farinha, Luís; Fernandes, Nuno

2016-01-01

This book discusses the main issues, challenges, opportunities, and trends involving the interactions between academia, industry, government and society. Specifically, it aims to explore how these interactions enhance the ways in which companies deliver products and services in order to achieve sustainable competitiveness in the marketplace. Sustainable competitiveness has been widely discussed by academics and practitioners, considering the importance of protecting the environment while sustaining the economic goals of organizations. The Quintuple Helix innovation model is a framework for facilitating knowledge, innovation and sustainable competitive advantage. It embeds the Triple and the Quadruple Helix models by adding a fifth helix, the “natural environment.” The Triple Helix model focuses on the university-industry-government triad, while the Quadruple adds civil society (the media- and culture-driven public) as a fourth helix. The Quintuple Helix model facilitates research, public policy, and pract...

Generating structured light with phase helix and intensity helix using reflection-enhanced plasmonic metasurface at 2 μm

Science.gov (United States)

Zhao, Yifan; Du, Jing; Zhang, Jinrun; Shen, Li; Wang, Jian

2018-04-01

Mid-infrared (2-20 μm) light has been attracting great attention in many areas of science and technology. Beyond the extended wavelength range from visible and near-infrared to mid-infrared, shaping spatial structures may add opportunities to grooming applications of mid-infrared photonics. Here, we design and fabricate a reflection-enhanced plasmonic metasurface and demonstrate efficient generation of structured light with the phase helix and intensity helix at 2 μm. This work includes two distinct aspects. First, structured light (phase helix, intensity helix) generation at 2 μm, which is far beyond the ability of conventional spatial light modulators, is enabled by the metasurface with sub-wavelength engineered structures. Second, the self-referenced intensity helix against environmental noise is generated without using a spatially separated light. The demonstrations may open up advanced perspectives to structured light applications at 2 μm, such as phase helix for communications and non-communications (imaging, sensing) and intensity helix for enhanced microscopy and advanced metrology.

A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

Directory of Open Access Journals (Sweden)

Karen A. Hudson

2015-01-01

Full Text Available The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281 of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

OpenAIRE

Pires, Nuno; Dolan, Liam

2009-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

Topological Classification of Morse Functions and Generalisations of Hilbert's 16-th Problem

International Nuclear Information System (INIS)

Arnold, Vladimir I.

2007-01-01

The topological structures of the generic smooth functions on a smooth manifold belong to the small quantity of the most fundamental objects of study both in pure and applied mathematics. The problem of their study has been formulated by A. Cayley in 1868, who required the classification of the possible configurations of the horizontal lines on the topographical maps of mountain regions, and created the first elements of what is called today 'Morse Theory' and 'Catastrophes Theory'. In the paper we describe this problem, and in particular describe the classification of Morse functions on the 2 sphere and on the torus

Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

Science.gov (United States)

Lignell, Martin; Becker, Hans-Christian

2010-01-01

Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

Science.gov (United States)

Zhang, Qi-Yi

2017-02-01

Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations. © 2016 Wiley Periodicals, Inc.

The role of a topologically conserved isoleucine in glutathione transferase structure, stability and function

International Nuclear Information System (INIS)

Achilonu, Ikechukwu; Gildenhuys, Samantha; Fisher, Loren; Burke, Jonathan; Fanucchi, Sylvia; Sewell, B. Trevor; Fernandes, Manuel; Dirr, Heini W.

2010-01-01

The role of a topologically conserved isoleucine in the structure of glutathione transferase was investigated by replacing the Ile71 residue in human GSTA1-1 by alanine or valine. The common fold shared by members of the glutathione-transferase (GST) family has a topologically conserved isoleucine residue at the N-terminus of helix 3 which is involved in the packing of helix 3 against two β-strands in domain 1. The role of the isoleucine residue in the structure, function and stability of GST was investigated by replacing the Ile71 residue in human GSTA1-1 by alanine or valine. The X-ray structures of the I71A and I71V mutants resolved at 1.75 and 2.51 Å, respectively, revealed that the mutations do not alter the overall structure of the protein compared with the wild type. Urea-induced equilibrium unfolding studies using circular dichroism and tryptophan fluorescence suggest that the mutation of Ile71 to alanine or valine reduces the stability of the protein. A functional assay with 1-chloro-2,4-dinitrobenzene shows that the mutation does not significantly alter the function of the protein relative to the wild type. Overall, the results suggest that conservation of the topologically conserved Ile71 maintains the structural stability of the protein but does not play a significant role in catalysis and substrate binding

Topology optimization for acoustic problems

DEFF Research Database (Denmark)

Dühring, Maria Bayard

2006-01-01

In this paper a method to control acoustic properties in a room with topology optimization is presented. It is shown how the squared sound pressure amplitude in a certain part of a room can be minimized by distribution of material in a design domain along the ceiling in 2D and 3D. Nice 0-1 designs...

Creating geometrically robust designs for highly sensitive problems using topology optimization: Acoustic cavity design

DEFF Research Database (Denmark)

Christiansen, Rasmus E.; Lazarov, Boyan S.; Jensen, Jakob S.

2015-01-01

Resonance and wave-propagation problems are known to be highly sensitive towards parameter variations. This paper discusses topology optimization formulations for creating designs that perform robustly under spatial variations for acoustic cavity problems. For several structural problems, robust...... and limitations are discussed. In addition, a known explicit penalization approach is considered for comparison. For near-uniform spatial variations it is shown that highly robust designs can be obtained using the double filter approach. It is finally demonstrated that taking non-uniform variations into account...... further improves the robustness of the designs....

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

Science.gov (United States)

Best, Robert B; Hummer, Gerhard

2009-07-02

Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

Helix-Hopes on Finite Hyperfields

Directory of Open Access Journals (Sweden)

Thomas Vougiouklis

2016-12-01

Full Text Available Hyperstructure theory can overcome restrictions which ordinary algebraic structures have. A hyperproduct on non-square ordinary matrices can be defined by using the so called helix-hyperoperations. We study the helix-hyperstructures on the representations using ordinary fields. The related theory can be faced by defining the hyperproduct on the set of non square matrices. The main tools of the Hyperstructure Theory are the fundamental relations which connect the largest class of hyperstructures, the Hv-structures, with the corresponding classical ones. We focus on finite dimensional helix-hyperstructures and on small Hv-fields, as well.

Efficient methods for solving discrete topology design problems in the PLATO-N project

DEFF Research Database (Denmark)

Canh, Nam Nguyen; Stolpe, Mathias

This paper considers the general multiple load structural topology design problems in the framework of the PLATO-N project. The problems involve a large number of discrete design variables and were modeled as a non-convex mixed 0–1 program. For the class of problems considered, a global...... optimization method based on the branch-and-cut concept was developed and implemented. In the method a large number of continuous relaxations were solved. We also present an algorithm for generating cuts to strengthen the quality of the relaxations. Several heuristics were also investigated to obtain efficient...... algorithms. The branch and cut method is used to solve benchmark examples which can be used to validate other methods and heuristics....

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

Science.gov (United States)

Komatsu, Setsuko; Takasaki, Hironori

2009-07-01

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

A Branch and Bound Approach for Truss Topology Design Problems with Valid Inequalities

International Nuclear Information System (INIS)

Cerveira, Adelaide; Agra, Agostinho; Bastos, Fernando; Varum, Humberto

2010-01-01

One of the classical problems in the structural optimization field is the Truss Topology Design Problem (TTDP) which deals with the selection of optimal configuration for structural systems for applications in mechanical, civil, aerospace engineering, among others. In this paper we consider a TTDP where the goal is to find the stiffest truss, under a given load and with a bound on the total volume. The design variables are the cross-section areas of the truss bars that must be chosen from a given finite set. This results in a large-scale non-convex problem with discrete variables. This problem can be formulated as a Semidefinite Programming Problem (SDP problem) with binary variables. We propose a branch and bound algorithm to solve this problem. In this paper it is considered a binary formulation of the problem, to take advantage of its structure, which admits a Knapsack problem as subproblem. Thus, trying to improve the performance of the Branch and Bound, at each step, some valid inequalities for the Knapsack problem are included.

Topology optimization for coated structures

DEFF Research Database (Denmark)

Clausen, Anders; Andreassen, Erik; Sigmund, Ole

2015-01-01

This paper presents new results within the design of three-dimensional (3D) coated structures using topology optimization.The work is an extension of a recently published two-dimensional (2D) method for including coatedstructures into the minimum compliance topology optimization problem. The high...... level of control over key parameters demonstrated for the 2D model can likewise be achieved in 3D. The effectiveness of the approach isdemonstrated with numerical examples, which for the 3D problems have been solved using a parallel topology optimization implementation based on the PETSc toolkit....

Double-helix stellarator

International Nuclear Information System (INIS)

Moroz, P.E.

1997-09-01

A new stellarator configuration, the Double-Helix Stellarator (DHS), is introduced. This novel configuration features a double-helix center post as the only helical element of the stellarator coil system. The DHS configuration has many unique characteristics. One of them is the extreme low plasma aspect ratio, A ∼ 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-β MHD equilibria. Moreover, the DHS features improved transport characteristics caused by the absence of the magnetic field ripple on the outboard of the torus. Compactness, simplicity and modularity of the coil system add to the DHS advantages for fusion applications

Analysis of eco-innovation with triple helix approach: case-study of biofloc catfish farming in Yogyakarta

Science.gov (United States)

Purwadi, D.; Nurlaily, I.

2018-03-01

Concerning environmental into focus of innovation process will expand the number of actor involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concern are integrated in innovation process and how different stakeholder groups are having inter relation. Case study from biofloc catfish farming in Yogyakarta is presented to demonstrate a possible approach for researching the success of triple helix frameworks. This case is considered on basic of the result of a survey among farmers, academician and government. The paper concludes the creating of full triple helix encounters problem in practice. It also includes suggestion for further research on fisheries development.

Band connectivity for topological quantum chemistry: Band structures as a graph theory problem

Science.gov (United States)

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

2018-01-01

The conventional theory of solids is well suited to describing band structures locally near isolated points in momentum space, but struggles to capture the full, global picture necessary for understanding topological phenomena. In part of a recent paper [B. Bradlyn et al., Nature (London) 547, 298 (2017), 10.1038/nature23268], we have introduced the way to overcome this difficulty by formulating the problem of sewing together many disconnected local k .p band structures across the Brillouin zone in terms of graph theory. In this paper, we give the details of our full theoretical construction. We show that crystal symmetries strongly constrain the allowed connectivities of energy bands, and we employ graph theoretic techniques such as graph connectivity to enumerate all the solutions to these constraints. The tools of graph theory allow us to identify disconnected groups of bands in these solutions, and so identify topologically distinct insulating phases.

Stretched versus compressed exponential kinetics in α-helix folding

International Nuclear Information System (INIS)

Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

2006-01-01

In a recent paper (J. Bredenbeck, J. Helbing, J.R. Kumita, G.A. Woolley, P. Hamm, α-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy, Proc. Natl. Acad. Sci USA 102 (2005) 2379), we have investigated the folding of a photo-switchable α-helix with a kinetics that could be fit by a stretched exponential function exp(-(t/τ) β ). The stretching factor β became smaller as the temperature was lowered, a result which has been interpreted in terms of activated diffusion on a rugged energy surface. In the present paper, we discuss under which conditions diffusion problems occur with stretched exponential kinetics (β 1). We show that diffusion problems do have a strong tendency to yield stretched exponential kinetics, yet, that there are conditions (strong perturbation from equilibrium, performing the experiment in the folding direction) under which compressed exponential kinetics would be expected instead. We discuss the kinetics on free energy surfaces predicted by simple initiation-propagation models (zipper models) of α-helix folding, as well as by folding funnel models. We show that our recent experiment has been performed under condition for which models with strong downhill driving force, such as the zipper model, would predict compressed, rather than stretched exponential kinetics, in disagreement with the experimental observation. We therefore propose that the free energy surface along a reaction coordinate that governs the folding kinetics must be relatively flat and has a shape similar to a 1D golf course. We discuss how this conclusion can be unified with the thermodynamically well established zipper model by introducing an additional kinetic reaction coordinate

Topology optimization of acoustic-structure interaction problems using a mixed finite element formulation

DEFF Research Database (Denmark)

Yoon, Gil Ho; Jensen, Jens Stissing; Sigmund, Ole

2007-01-01

given during the optimization process. In this paper we circumvent the explicit boundary representation by using a mixed finite element formulation with displacements and pressure as primary variables (a u/p-formulation). The Helmholtz equation is obtained as a special case of the mixed formulation...... for the elastic shear modulus equating to zero. Hence, by spatial variation of the mass density, shear and bulk moduli we are able to solve the coupled problem by the mixed formulation. Using this modelling approach, the topology optimization procedure is simply implemented as a standard density approach. Several...... two-dimensional acoustic-structure problems are optimized in order to verify the proposed method....

Topological Rankings in Communication Networks

DEFF Research Database (Denmark)

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

2015-01-01

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

Relational topology

CERN Document Server

Schmidt, Gunther

2018-01-01

This book introduces and develops new algebraic methods to work with relations, often conceived as Boolean matrices, and applies them to topology. Although these objects mirror the matrices that appear throughout mathematics, numerics, statistics, engineering, and elsewhere, the methods used to work with them are much less well known. In addition to their purely topological applications, the volume also details how the techniques may be successfully applied to spatial reasoning and to logics of computer science. Topologists will find several familiar concepts presented in a concise and algebraically manipulable form which is far more condensed than usual, but visualized via represented relations and thus readily graspable. This approach also offers the possibility of handling topological problems using proof assistants.

On the Hardness of Topology Inference

Science.gov (United States)

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

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

Topology optimization based on the harmony search method

International Nuclear Information System (INIS)

Lee, Seung-Min; Han, Seog-Young

2017-01-01

A new topology optimization scheme based on a Harmony search (HS) as a metaheuristic method was proposed and applied to static stiffness topology optimization problems. To apply the HS to topology optimization, the variables in HS were transformed to those in topology optimization. Compliance was used as an objective function, and harmony memory was defined as the set of the optimized topology. Also, a parametric study for Harmony memory considering rate (HMCR), Pitch adjusting rate (PAR), and Bandwidth (BW) was performed to find the appropriate range for topology optimization. Various techniques were employed such as a filtering scheme, simple average scheme and harmony rate. To provide a robust optimized topology, the concept of the harmony rate update rule was also implemented. Numerical examples are provided to verify the effectiveness of the HS by comparing the optimal layouts of the HS with those of Bidirectional evolutionary structural optimization (BESO) and Artificial bee colony algorithm (ABCA). The following conclu- sions could be made: (1) The proposed topology scheme is very effective for static stiffness topology optimization problems in terms of stability, robustness and convergence rate. (2) The suggested method provides a symmetric optimized topology despite the fact that the HS is a stochastic method like the ABCA. (3) The proposed scheme is applicable and practical in manufacturing since it produces a solid-void design of the optimized topology. (4) The suggested method appears to be very effective for large scale problems like topology optimization.

Topology optimization based on the harmony search method

Energy Technology Data Exchange (ETDEWEB)

Lee, Seung-Min; Han, Seog-Young [Hanyang University, Seoul (Korea, Republic of)

2017-06-15

A new topology optimization scheme based on a Harmony search (HS) as a metaheuristic method was proposed and applied to static stiffness topology optimization problems. To apply the HS to topology optimization, the variables in HS were transformed to those in topology optimization. Compliance was used as an objective function, and harmony memory was defined as the set of the optimized topology. Also, a parametric study for Harmony memory considering rate (HMCR), Pitch adjusting rate (PAR), and Bandwidth (BW) was performed to find the appropriate range for topology optimization. Various techniques were employed such as a filtering scheme, simple average scheme and harmony rate. To provide a robust optimized topology, the concept of the harmony rate update rule was also implemented. Numerical examples are provided to verify the effectiveness of the HS by comparing the optimal layouts of the HS with those of Bidirectional evolutionary structural optimization (BESO) and Artificial bee colony algorithm (ABCA). The following conclu- sions could be made: (1) The proposed topology scheme is very effective for static stiffness topology optimization problems in terms of stability, robustness and convergence rate. (2) The suggested method provides a symmetric optimized topology despite the fact that the HS is a stochastic method like the ABCA. (3) The proposed scheme is applicable and practical in manufacturing since it produces a solid-void design of the optimized topology. (4) The suggested method appears to be very effective for large scale problems like topology optimization.

The swimming of a perfect deforming helix

Science.gov (United States)

Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

2017-11-01

Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

Duality and topology

Science.gov (United States)

Sacramento, P. D.; Vieira, V. R.

2018-04-01

Mappings between models may be obtained by unitary transformations with preservation of the spectra but in general a change in the states. Non-canonical transformations in general also change the statistics of the operators involved. In these cases one may expect a change of topological properties as a consequence of the mapping. Here we consider some dualities resulting from mappings, by systematically using a Majorana fermion representation of spin and fermionic problems. We focus on the change of topological invariants that results from unitary transformations taking as examples the mapping between a spin system and a topological superconductor, and between different fermionic systems.

Topology optimization based on spline-based meshfree method using topological derivatives

International Nuclear Information System (INIS)

Hur, Junyoung; Youn, Sung-Kie; Kang, Pilseong

2017-01-01

Spline-based meshfree method (SBMFM) is originated from the Isogeometric analysis (IGA) which integrates design and analysis through Non-uniform rational B-spline (NURBS) basis functions. SBMFM utilizes trimming technique of CAD system by representing the domain using NURBS curves. In this work, an explicit boundary topology optimization using SBMFM is presented with an effective boundary update scheme. There have been similar works in this subject. However unlike the previous works where semi-analytic method for calculating design sensitivities is employed, the design update is done by using topological derivatives. In this research, the topological derivative is used to derive the sensitivity of boundary curves and for the creation of new holes. Based on the values of topological derivatives, the shape of boundary curves is updated. Also, the topological change is achieved by insertion and removal of the inner holes. The presented approach is validated through several compliance minimization problems.

Topology optimization based on spline-based meshfree method using topological derivatives

Energy Technology Data Exchange (ETDEWEB)

Hur, Junyoung; Youn, Sung-Kie [KAIST, Daejeon (Korea, Republic of); Kang, Pilseong [Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of)

2017-05-15

Spline-based meshfree method (SBMFM) is originated from the Isogeometric analysis (IGA) which integrates design and analysis through Non-uniform rational B-spline (NURBS) basis functions. SBMFM utilizes trimming technique of CAD system by representing the domain using NURBS curves. In this work, an explicit boundary topology optimization using SBMFM is presented with an effective boundary update scheme. There have been similar works in this subject. However unlike the previous works where semi-analytic method for calculating design sensitivities is employed, the design update is done by using topological derivatives. In this research, the topological derivative is used to derive the sensitivity of boundary curves and for the creation of new holes. Based on the values of topological derivatives, the shape of boundary curves is updated. Also, the topological change is achieved by insertion and removal of the inner holes. The presented approach is validated through several compliance minimization problems.

Topology Discovery Using Cisco Discovery Protocol

OpenAIRE

Rodriguez, Sergio R.

2009-01-01

In this paper we address the problem of discovering network topology in proprietary networks. Namely, we investigate topology discovery in Cisco-based networks. Cisco devices run Cisco Discovery Protocol (CDP) which holds information about these devices. We first compare properties of topologies that can be obtained from networks deploying CDP versus Spanning Tree Protocol (STP) and Management Information Base (MIB) Forwarding Database (FDB). Then we describe a method of discovering topology ...

Reduced order modeling in topology optimization of vibroacoustic problems

DEFF Research Database (Denmark)

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

2017-01-01

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

Explorations in topology map coloring, surfaces and knots

CERN Document Server

Gay, David

2013-01-01

Explorations in Topology, Second Edition, provides students a rich experience with low-dimensional topology (map coloring, surfaces, and knots), enhances their geometrical and topological intuition, empowers them with new approaches to solving problems, and provides them with experiences that will help them make sense of future, more formal topology courses. The book's innovative story-line style models the problem-solving process, presents the development of concepts in a natural way, and engages students in meaningful encounters with the material. The updated end-of-chapter investigation

Optimal Topology Design of Discrete Structures Resisting Degradation Effects

DEFF Research Database (Denmark)

Achtziger, W.; Bendsøe, Martin P.

1999-01-01

In this technical note we treat the problem of finding the optimal topology of a truss, so that stiffness after degradation is maximized. It is shown that for the problem setting at hand, the optimal topology has uniform relative degradation in all bars and the topology is unchanged from the topo...

Topological inversion for solution of geodesy-constrained geophysical problems

Science.gov (United States)

Saltogianni, Vasso; Stiros, Stathis

2015-04-01

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

Manufacturing tolerant topology optimization

DEFF Research Database (Denmark)

Sigmund, Ole

2009-01-01

In this paper we present an extension of the topology optimization method to include uncertainties during the fabrication of macro, micro and nano structures. More specifically, we consider devices that are manufactured using processes which may result in (uniformly) too thin (eroded) or too thick...... (dilated) structures compared to the intended topology. Examples are MEMS devices manufactured using etching processes, nano-devices manufactured using e-beam lithography or laser micro-machining and macro structures manufactured using milling processes. In the suggested robust topology optimization...... approach, under- and over-etching is modelled by image processing-based "erode" and "dilate" operators and the optimization problem is formulated as a worst case design problem. Applications of the method to the design of macro structures for minimum compliance and micro compliant mechanisms show...

Topology optimization under stochastic stiffness

Science.gov (United States)

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

Optimization-based topology identification of complex networks

International Nuclear Information System (INIS)

Tang Sheng-Xue; Chen Li; He Yi-Gang

2011-01-01

In many cases, the topological structures of a complex network are unknown or uncertain, and it is of significance to identify the exact topological structure. An optimization-based method of identifying the topological structure of a complex network is proposed in this paper. Identification of the exact network topological structure is converted into a minimal optimization problem by using the estimated network. Then, an improved quantum-behaved particle swarm optimization algorithm is used to solve the optimization problem. Compared with the previous adaptive synchronization-based method, the proposed method is simple and effective and is particularly valid to identify the topological structure of synchronization complex networks. In some cases where the states of a complex network are only partially observable, the exact topological structure of a network can also be identified by using the proposed method. Finally, numerical simulations are provided to show the effectiveness of the proposed method. (general)

Filters in topology optimization

DEFF Research Database (Denmark)

Bourdin, Blaise

1999-01-01

In this article, a modified (``filtered'') version of the minimum compliance topology optimization problem is studied. The direct dependence of the material properties on its pointwise density is replaced by a regularization of the density field using a convolution operator. In this setting...... it is possible to establish the existence of solutions. Moreover, convergence of an approximation by means of finite elements can be obtained. This is illustrated through some numerical experiments. The ``filtering'' technique is also shown to cope with two important numerical problems in topology optimization...

Designing cooperatively folded abiotic uni- and multimolecular helix bundles

Science.gov (United States)

de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

2018-01-01

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

A computational study of the topology of vortex breakdown

Science.gov (United States)

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.

A note on the consensus finding problem in communication networks with switching topologies

KAUST Repository

Haskovec, Jan

2014-05-07

In this note, we discuss the problem of consensus finding in communication networks of agents with dynamically switching topologies. In particular, we consider the case of directed networks with unbalanced matrices of communication rates. We formulate sufficient conditions for consensus finding in terms of strong connectivity of the underlying directed graphs and prove that, given these conditions, consensus is found asymptotically. Moreover, we show that this consensus is an emergent property of the system, being encoded in its dynamics and not just an invariant of its initial configuration. © 2014 © 2014 Taylor & Francis.

First Meeting in Topology and Functional Analysis

CERN Document Server

López-Pellicer, Manuel

2014-01-01

Descriptive topology and functional analysis, with extensive material demonstrating new connections between them, are the subject of the first section of this work. Applications to spaces of continuous functions, topological Abelian groups, linear topological equivalence and to the separable quotient problem are included and are presented as open problems. The second section is devoted to Banach spaces, Banach algebras and operator theory. Each chapter presents a lot of worthwhile and important recent theorems with an abstract discussing the material in the chapter. Each chapter can almost be seen as a survey covering a particular area.

Influence of semisynthetic modification of the scaffold of a contact domain of HbS on polymerization: role of flexible surface topology in polymerization inhibition.

Science.gov (United States)

Sonati, Srinivasulu; Bhutoria, Savita; Prabhakaran, Muthuchidambaran; Acharya, Seetharama A

2018-02-01

A new variant of HbS, HbS-Einstein with a deletion of segment α 23-26 in the B-helix, has been assembled by semisynthetic approach. B-helix of the α chain of cis αβ-dimer of HbS plays dominant role in the quinary interactions of deoxy HbS dimer. This B-helix is the primary scaffold that provides the orientation for the side chains of contact residues of this intermolecular contact domain. The design of HbS-Einstein has been undertaken to map the influence of perturbation of molecular surface topology and the flexibility of surface residues in the polymerization. The internal deletion exerts a strong inhibitory influence on Val-6 (β)-dependent polymerization, comparable to single contact site mutations and not for complete neutralization of Val-6(β)-dependent polymerization. The scaffold modification in cis-dimer is inhibitory, and is without any effect when present on the trans dimer. The flexibility changes in the surface topology in the region of scaffold modification apparently counteracts the intrinsic polymerization potential of the molecule. The inhibition is close to that of Le Lamentin mutation [His-20 (α) → Gln] wherein a mutation engineered without much change in flexibility of the contact domain. Interestingly, the chimeric HbS with swine-human chimeric α chain with multiple non-conservative mutations completely inhibits the Val-6(β)-dependent polymerization. The deformabilities of surface topology of chimeric HbS are comparable to HbS in spite of the multiple contact site mutations in the α-chain. We conclude that the design of antisickling Hbs for gene therapy of sickle cell disease should involve multiple mutations of intermolecular contact sites.

On Equivalence between Optimality Criteria and Projected Gradient Methods with Application to Topology Optimization Problem

OpenAIRE

Ananiev, Sergey

2006-01-01

The paper demonstrates the equivalence between the optimality criteria (OC) method, initially proposed by Bendsoe & Kikuchi for topology optimization problem, and the projected gradient method. The equivalence is shown using Hestenes definition of Lagrange multipliers. Based on this development, an alternative formulation of the Karush-Kuhn-Tucker (KKT) condition is suggested. Such reformulation has some advantages, which will be also discussed in the paper. For verification purposes the modi...

Helix probe areas for the utilization of geothermal power. A practical example; Helix-Sondenfelder zur Nutzung von Erdwaerme. Ein Praxisbeispiel

Energy Technology Data Exchange (ETDEWEB)

Kuebert, Markus; Walker-Hertkorn, Simone [tewag Technologie - Erdwaermeanlagen - Umweltschutz GmbH, Starzach (Germany); Tietz, Jan [REHAU AG und Co., Erlangen-Eltersdorf (Germany); Riepold, Markus; Gloeckl, Andreas [MR Tiefbau GmbH, Brunnen (Germany)

2013-02-01

Thanks to their spiral shape so-called helix probes with a tube length of 40 meter have a height of only three meter: A lot of heat exchange area in a small space. Thus, helix probes are an ideal solution for the utilization of geothermal energy at places at which one cannot drill deeply due to geothermal reasons. Under this aspect, the contribution under consideration reports on the planning of a helix probe area being sustainably adapted to the user requirements for the new construction of a production facility.

Topology for analysis

CERN Document Server

Wilansky, Albert

2008-01-01

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

QCD as a topologically ordered system

International Nuclear Information System (INIS)

Zhitnitsky, Ariel R.

2013-01-01

We argue that QCD belongs to a topologically ordered phase similar to many well-known condensed matter systems with a gap such as topological insulators or superconductors. Our arguments are based on an analysis of the so-called “deformed QCD” which is a weakly coupled gauge theory, but nevertheless preserves all the crucial elements of strongly interacting QCD, including confinement, nontrivial θ dependence, degeneracy of the topological sectors, etc. Specifically, we construct the so-called topological “BF” action which reproduces the well known infrared features of the theory such as non-dispersive contribution to the topological susceptibility which cannot be associated with any propagating degrees of freedom. Furthermore, we interpret the well known resolution of the celebrated U(1) A problem where the would be η ′ Goldstone boson generates its mass as a result of mixing of the Goldstone field with a topological auxiliary field characterizing the system. We then identify the non-propagating auxiliary topological field of the BF formulation in deformed QCD with the Veneziano ghost (which plays the crucial role in resolution of the U(1) A problem). Finally, we elaborate on relation between “string-net” condensation in topologically ordered condensed matter systems and long range coherent configurations, the “skeletons”, studied in QCD lattice simulations. -- Highlights: •QCD may belong to a topologically ordered phase similar to condensed matter (CM) systems. •We identify the non-propagating topological field in deformed QCD with the Veneziano ghost. •Relation between “string-net” condensates in CM systems and the “skeletons” in QCD lattice simulations is studied

Topology optimization for nano-photonics

DEFF Research Database (Denmark)

Jensen, Jakob Søndergaard; Sigmund, Ole

2011-01-01

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

Topology Optimization

DEFF Research Database (Denmark)

A. Kristensen, Anders Schmidt; Damkilde, Lars

2007-01-01

. A way to solve the initial design problem namely finding a form can be solved by so-called topology optimization. The idea is to define a design region and an amount of material. The loads and supports are also fidefined, and the algorithm finds the optimal material distribution. The objective function...... dictates the form, and the designer can choose e.g. maximum stiness, maximum allowable stresses or maximum lowest eigenfrequency. The result of the topology optimization is a relatively coarse map of material layout. This design can be transferred to a CAD system and given the necessary geometrically...... refinements, and then remeshed and reanalysed in other to secure that the design requirements are met correctly. The output of standard topology optimization has seldom well-defined, sharp contours leaving the designer with a tedious interpretation, which often results in less optimal structures. In the paper...

Topology mapping to characterize cyanobacterial bicarbonate transporters: BicA (SulP/SLC26 family) and SbtA.

Science.gov (United States)

Price, G Dean; Howitt, Susan M

2014-09-01

This mini-review addresses advances in understanding the transmembrane topologies of two unrelated, single-subunit bicarbonate transporters from cyanobacteria, namely BicA and SbtA. BicA is a Na(+)-dependent bicarbonate transporter that belongs to the SulP/SLC26 family that is widespread in both eukaryotes and prokaryotes. Topology mapping of BicA via the phoA/lacZ fusion reporter method identified 12 transmembrane helices with an unresolved hydrophobic region just beyond helix 8. Re-interpreting this data in the light of a recent topology study on rat prestin leads to a consensus topology of 14 transmembrane domains with a 7+7 inverted repeat structure. SbtA is also a Na(+)-dependent bicarbonate transporter, but of considerably higher affinity (Km 2-5 μM versus >100 μM for BicA). Whilst SbtA is widespread in cyanobacteria and a few bacteria, it appears to be absent from eukaryotes. Topology mapping of SbtA via the phoA/lacZ fusion reporter method identified 10 transmembrane helices. The topology consists of a 5+5 inverted repeat, with the two repeats separated by a large intracellular loop. The unusual location of the N and C-termini outside the cell raises the possibility that SbtA forms a novel fold, not so far identified by structural and topological studies on transport proteins.

Constraint interface preconditioning for topology optimization problems

Czech Academy of Sciences Publication Activity Database

Kočvara, Michal; Loghin, D.; Turner, J.

2016-01-01

Roč. 38, č. 1 (2016), A128-A145 ISSN 1064-8275 R&D Projects: GA AV ČR IAA100750802 Grant - others:European Commission - EC(XE) 313781 Institutional support: RVO:67985556 Keywords : topology optimization * domain decomposition * Newton-Krylov Subject RIV: BA - General Mathematics Impact factor: 2.195, year: 2016 http://library.utia.cas.cz/separaty/2016/MTR/kocvara-0460325.pdf

Interactions between the mixotrophic dinoflagellate Takayama helix and common heterotrophic protists.

Science.gov (United States)

Ok, Jin Hee; Jeong, Hae Jin; Lim, An Suk; Lee, Kyung Ha

2017-09-01

The phototrophic dinoflagellate Takayama helix that is known to be harmful to abalone larvae has recently been revealed to be mixotrophic. Although mixotrophy elevates the growth rate of T. helix by 79%-185%, its absolute growth rate is still as low as 0.3d -1 . Thus, if the mortality rate of T. helix due to predation is high, this dinoflagellate may not easily prevail. To investigate potential effective protistan grazers on T. helix, feeding by diverse heterotrophic dinoflagellates such as engulfment-feeding Oxyrrhis marina, Gyrodinium dominans, Gyrodinium moestrupii, Polykrikos kofoidii, and Noctiluca scintillans, peduncle-feeding Aduncodinium glandula, Gyrodiniellum shiwhaense, Luciella masanensis, and Pfiesteria piscicida, pallium-feeding Oblea rotunda and Protoperidinium pellucidum, and the naked ciliates Pelagostrobilidium sp. (ca. 40μm in cell length) and Strombidinopsis sp. (ca. 150μm in cell length) on T. helix was explored. Among the tested heterotrophic protists, O. marina, G. dominans, G. moestrupii, A. glandula, L. masanensis, P. kofoidii, P. piscicida, and Strombidinopsis sp. were able to feed on T. helix. The growth rates of all these predators except Strombidinopsis sp. with T. helix prey were lower than those without the prey. The growth rate of Strombidinopsis sp. on T. helix was almost zero although the growth rate of Strombidinopsis sp. with T. helix prey was higher than those without the prey. Moreover, T. helix fed on O. marina and P. pellucidum and lysed the cells of P. kofoidii and G. shiwhaense. With increasing the concentrations of T. helix, the growth rates of O. marina and P. kofoidii decreased, but those of G. dominans and L. masanensis largely did not change. Therefore, reciprocal predation, lysis, no feeding, and the low ingestion rates of the common protists preying on T. helix may result in a low mortality rate due to predation, thereby compensating for this species' low growth rate. Copyright © 2017 Elsevier B.V. All rights

Comparative Study on the Adaptation and Growth Dynamics of the Helix pomatia and Helix aspersa Muller Terrestrial Snails Under Different Feeding Regimes

Directory of Open Access Journals (Sweden)

Adrian Toader-Williams

2010-05-01

Full Text Available We used Helix pomatia and Helix aspersa species and measure their growth as the snails were approaching the hibernation season. Helix pomatia 2yo shown a decrease in weight while being raised in enclosed parcels of 4sqm the younger Helix pomatia 1yo as well as Helix aspersa Muller demonstrated the ability to adapt relatively fast to the same conditions. We established 5 experimental lots in a Helix pomatia farm, GPS coordinates N46.606040 E23.599950. Control lot contained Taraxacum officinales, Sonchus oleraceus, Equisetum arvense and Atriplex hortensis, wild flora found within the farm. The other lots contained the same plants as the control lot plus different combinations of imported plants from other areals. The H. pomatia 2yo weight decreased in the control lot by a mean of -3.86% while H. aspersa 1yo marked an increase of +16.89% in the same lot during the same period. The lot containing lupinus polyphyllus delivered snails with weight gain of +24.66% for H. pomatia 2yo and an increase of only +1.98% for H. aspersa 1yo. As a contrast, H. pomatia 2yo gained only +7.72% while H. aspersa 1yo gained +28.89%, in the lot containing Lavanda officinalis, Foeniculum vulgare and Hyssopus officinalis among the other plants.

Robust Topology Optimization Based on Stochastic Collocation Methods under Loading Uncertainties

Directory of Open Access Journals (Sweden)

Qinghai Zhao

2015-01-01

Full Text Available A robust topology optimization (RTO approach with consideration of loading uncertainties is developed in this paper. The stochastic collocation method combined with full tensor product grid and Smolyak sparse grid transforms the robust formulation into a weighted multiple loading deterministic problem at the collocation points. The proposed approach is amenable to implementation in existing commercial topology optimization software package and thus feasible to practical engineering problems. Numerical examples of two- and three-dimensional topology optimization problems are provided to demonstrate the proposed RTO approach and its applications. The optimal topologies obtained from deterministic and robust topology optimization designs under tensor product grid and sparse grid with different levels are compared with one another to investigate the pros and cons of optimization algorithm on final topologies, and an extensive Monte Carlo simulation is also performed to verify the proposed approach.

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

Science.gov (United States)

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.

Ring-array processor distribution topology for optical interconnects

Science.gov (United States)

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.

Topological visual mapping in robotics.

Science.gov (United States)

Romero, Anna; Cazorla, Miguel

2012-08-01

A key problem in robotics is the construction of a map from its environment. This map could be used in different tasks, like localization, recognition, obstacle avoidance, etc. Besides, the simultaneous location and mapping (SLAM) problem has had a lot of interest in the robotics community. This paper presents a new method for visual mapping, using topological instead of metric information. For that purpose, we propose prior image segmentation into regions in order to group the extracted invariant features in a graph so that each graph defines a single region of the image. Although others methods have been proposed for visual SLAM, our method is complete, in the sense that it makes all the process: it presents a new method for image matching; it defines a way to build the topological map; and it also defines a matching criterion for loop-closing. The matching process will take into account visual features and their structure using the graph transformation matching (GTM) algorithm, which allows us to process the matching and to remove out the outliers. Then, using this image comparison method, we propose an algorithm for constructing topological maps. During the experimentation phase, we will test the robustness of the method and its ability constructing topological maps. We have also introduced new hysteresis behavior in order to solve some problems found building the graph.

Government and Governance of Regional Triple Helix Interactions

Science.gov (United States)

Danson, Mike; Todeva, Emanuela

2016-01-01

This conceptual paper contributes to the discussion of the role of regional government and regional Triple Helix constellations driving economic development and growth within regional boundaries. The impact of regionalism and subsidiarity on regional Triple Helix constellations, and the questions of governmentality, governance and institutional…

A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia

Science.gov (United States)

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during...

Double helix vortex breakdown in a turbulent swirling annular jet flow

Science.gov (United States)

Vanierschot, M.; Percin, M.; van Oudheusden, B. W.

2018-03-01

In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is investigated experimentally by means of time-resolved tomographic particle image velocimetry. Notwithstanding the axisymmetric nature of the time-averaged flow, analysis of the instantaneous three-dimensional (3D) vortical structures shows the existence of a vortex core along the central axis which breaks up into a double helix downstream. The winding sense of this double helix is opposite to the swirl direction (m =-2 ) and it is wrapped around a central vortex breakdown bubble. This structure is quite different from double helix breakdown found in laminar flows where the helix is formed in the wake of the bubble and not upstream. The double helix precesses around the central axis of the jet with a precessing frequency corresponding to a Strouhal number of 0.27.

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

Science.gov (United States)

Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

2016-09-05

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

IFITM3 requires an amphipathic helix for antiviral activity.

Science.gov (United States)

Chesarino, Nicholas M; Compton, Alex A; McMichael, Temet M; Kenney, Adam D; Zhang, Lizhi; Soewarna, Victoria; Davis, Matthew; Schwartz, Olivier; Yount, Jacob S

2017-10-01

Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion. © 2017 The Authors.

Topology optimization

DEFF Research Database (Denmark)

Bendsøe, Martin P.; Sigmund, Ole

2007-01-01

Taking as a starting point a design case for a compliant mechanism (a force inverter), the fundamental elements of topology optimization are described. The basis for the developments is a FEM format for this design problem and emphasis is given to the parameterization of design as a raster image...

Effect of Hedera helix on lung histopathology in chronic asthma.

Science.gov (United States)

Hocaoglu, Arzu Babayigit; Karaman, Ozkan; Erge, Duygu Olmez; Erbil, Guven; Yilmaz, Osman; Kivcak, Bijen; Bagriyanik, H Alper; Uzuner, Nevin

2012-12-01

Hedera helix is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c mice were divided into four groups; I (Placebo), II (Hedera helix), III (Dexamethasone) and IV (Control). All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group I received saline, group II 100 mg/kg Hedera helix and group III 1 mg/kg dexamethasone via orogastic gavage once daily for one week. Airway histopathology was evaluated by using light and electron microscopy in all groups.Goblet cell numbers and thicknesses of basement membrane were found significantly lower in group II, but there was no statistically significant difference in terms of number of mast cells, thicknesses of epithelium and subepithelial smooth muscle layers between group I and II. When Hedera helix and dexamethasone groups were compared with each other, thickness of epithelium, subepithelial muscle layers, number of mast cells and goblet cells of group III were significantly ameliorated when compared with the group II. Although Hedera helix administration reduced only goblet cell counts and the thicknesses of basement membrane in the asthmatic airways, dexamethasone ameliorated all histopathologic parameters except thickness of basement membrane better than Hedera helix.

Topological Derivatives in Shape Optimization

CERN Document Server

Novotny, Antonio André

2013-01-01

The topological derivative is defined as the first term (correction) of the asymptotic expansion of a given shape functional with respect to a small parameter that measures the size of singular domain perturbations, such as holes, inclusions, defects, source-terms and cracks. Over the last decade, topological asymptotic analysis has become a broad, rich and fascinating research area from both theoretical and numerical standpoints. It has applications in many different fields such as shape and topology optimization, inverse problems, imaging processing and mechanical modeling including synthesis and/or optimal design of microstructures, sensitivity analysis in fracture mechanics and damage evolution modeling. Since there is no monograph on the subject at present, the authors provide here the first account of the theory which combines classical sensitivity analysis in shape optimization with asymptotic analysis by means of compound asymptotic expansions for elliptic boundary value problems. This book is intende...

Reconfigurable topological photonic crystal

Science.gov (United States)

Shalaev, Mikhail I.; Desnavi, Sameerah; Walasik, Wiktor; Litchinitser, Natalia M.

2018-02-01

Topological insulators are materials that conduct on the surface and insulate in their interior due to non-trivial topology of the band structure. The edge states on the interface between topological (non-trivial) and conventional (trivial) insulators are topologically protected from scattering due to structural defects and disorders. Recently, it was shown that photonic crystals (PCs) can serve as a platform for realizing a scatter-free propagation of light waves. In conventional PCs, imperfections, structural disorders, and surface roughness lead to significant losses. The breakthrough in overcoming these problems is likely to come from the synergy of the topological PCs and silicon-based photonics technology that enables high integration density, lossless propagation, and immunity to fabrication imperfections. For many applications, reconfigurability and capability to control the propagation of these non-trivial photonic edge states is essential. One way to facilitate such dynamic control is to use liquid crystals (LCs), which allow to modify the refractive index with external electric field. Here, we demonstrate dynamic control of topological edge states by modifying the refractive index of a LC background medium. Background index is changed depending on the orientation of a LC, while preserving the topology of the system. This results in a change of the spectral position of the photonic bandgap and the topological edge states. The proposed concept might be implemented using conventional semiconductor technology, and can be used for robust energy transport in integrated photonic devices, all-optical circuity, and optical communication systems.

Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

Science.gov (United States)

Law, S F; Zhang, Y Z; Fashena, S J; Toby, G; Estojak, J; Golemis, E A

1999-10-10

HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation. Copyright 1999 Academic Press.

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA

NARCIS (Netherlands)

Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

2014-01-01

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an

Mode conversions by a discontinuous junction of two helix loaded waveguides

International Nuclear Information System (INIS)

Choe, J.Y.; Ahn, S.; Ganquly, A.K.; Uhm, H.S.

1983-01-01

For various reasons, it is desirable to vary the primary propagating mode from one section of the waveguide to another. We choose the base structure to be the sheath helix loaded waveguide. Specifically, we join two physically different helix loaded waveguides axisymmetrically, thereby providing the required discontinuities at the junction (Z = 0). The helix loaded waveguide is more advantageous to the simple waveguide in that the helix mode that exists uniquely in the helix waveguide in addition to the usual fast wave hybrid modes, is without cutoff and thus behaves like a transmission line. In order to obtain the mode conversion rates, we expand the waves in the both sides of the junction with its own eigenmodes including the evanescent modes, and by matching fields at the junction (Z = 0) obtain the matrix equation for the coefficients for the eigenmodes in both sides. By choosing the propagating incident wave (Z = 0) the resulting outgoing waves in the other end (Z > 0) will be computed from the matrix equation. A computer program is devised to solve the suitably truncated matrix equation, and the numerical examples for the mode conversion rates with the parameter variations will be presented. The relevant physical parameters to yield discontinuities at the junction are the radii of the outer conductor and the helix wire and the pitch angle of the helix. Special emphases are on the conversion rates from the helix mode (Z 0) for the application to the tapered gyrotron amplifier

Topological transitions in the theory of spacetime

International Nuclear Information System (INIS)

Konstantinov, M.Y.; Melnikov, V.N.

1986-01-01

Results of a realisation of the topological transitions hypothesis are presented. The basic difficulties in the construction of quantum topological transition theory are connected with a necessity to introduce a new non-local interaction defined on a space of topological states. So the general method of construction and study of topological transitions classical models is formulated as a necessary step towards a corresponding quantum description. Their local properties, including an asymptotic behaviour in the neighbourhood of the transition, are studied and applications to problems of gravitation and cosmology are given. The method used is shown to lead to a scalar-tensor theory of topological transitions. Different variants of this theory and its main features are discussed. (author)

Topology Optimization of Nanophotonic Devices

DEFF Research Database (Denmark)

Yang, Lirong

This thesis explores the various aspects of utilizing topology optimization in designing nanophotonic devices. Either frequency-domain or time-domain methods is used in combination with the optimization algorithms, depending on various aims of the designing problems. The frequency-domain methods...... lengthscale and flexible pulse delay are addressed to demonstrate time-domain based topology optimization’s potential in designing complicated photonic structures with specifications on the time characteristics of pulses....

Topological effects in QCD and the problem of short-distance singularities

International Nuclear Information System (INIS)

Luescher, Martin

2004-01-01

The topological susceptibility and the higher moments of the topological charge distribution in QCD are expressed through certain n-point functions of the scalar and pseudo-scalar quark densities at vanishing momenta, which are free of short-distance singularities. Since the normalization of the correlation functions is determined by the non-singlet chiral Ward identities, these formulae provide an unambiguous regularization-independent definition of the moments and thus of the charge distribution

Topological strength of magnetic skyrmions

Energy Technology Data Exchange (ETDEWEB)

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

2017-02-01

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

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

Directory of Open Access Journals (Sweden)

Vasyl V Mykuliak

2018-04-01

Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

Efficient Reanalysis Procedures in Structural Topology Optimization

DEFF Research Database (Denmark)

Amir, Oded

This thesis examines efficient solution procedures for the structural analysis problem within topology optimization. The research is motivated by the observation that when the nested approach to structural optimization is applied, most of the computational effort is invested in repeated solutions...... on approximate reanalysis. For cases where memory limitations require the utilization of iterative equation solvers, we suggest efficient procedures based on alternative termination criteria for such solvers. These approaches are tested on two- and three-dimensional topology optimization problems including...

Self-consistent adjoint analysis for topology optimization of electromagnetic waves

Science.gov (United States)

Deng, Yongbo; Korvink, Jan G.

2018-05-01

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

DNA-like double helix formed by peptide nucleic acid

DEFF Research Database (Denmark)

Wittung, P; Nielsen, Peter E.; Buchardt, O

1994-01-01

Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...

The Topology of Three-Dimensional Symmetric Tensor Fields

Science.gov (United States)

Lavin, Yingmei; Levy, Yuval; Hesselink, Lambertus

1994-01-01

We study the topology of 3-D symmetric tensor fields. The goal is to represent their complex structure by a simple set of carefully chosen points and lines analogous to vector field topology. The basic constituents of tensor topology are the degenerate points, or points where eigenvalues are equal to each other. First, we introduce a new method for locating 3-D degenerate points. We then extract the topological skeletons of the eigenvector fields and use them for a compact, comprehensive description of the tensor field. Finally, we demonstrate the use of tensor field topology for the interpretation of the two-force Boussinesq problem.

Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

Science.gov (United States)

Ying Chow, W.; Bihan, Dominique; Forman, Chris J.; Slatter, David A.; Reid, David G.; Wales, David J.; Farndale, Richard W.; Duer, Melinda J.

2015-07-01

Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

Inferring network topology from complex dynamics

International Nuclear Information System (INIS)

Shandilya, Srinivas Gorur; Timme, Marc

2011-01-01

Inferring the network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method for inferring the structural connection topology of a network, given an observation of one collective dynamical trajectory. The general theoretical framework is applicable to arbitrary network dynamical systems described by ordinary differential equations. No interference (external driving) is required and the type of dynamics is hardly restricted in any way. In particular, the observed dynamics may be arbitrarily complex; stationary, invariant or transient; synchronous or asynchronous and chaotic or periodic. Presupposing a knowledge of the functional form of the dynamical units and of the coupling functions between them, we present an analytical solution to the inverse problem of finding the network topology from observing a time series of state variables only. Robust reconstruction is achieved in any sufficiently long generic observation of the system. We extend our method to simultaneously reconstructing both the entire network topology and all parameters appearing linear in the system's equations of motion. Reconstruction of network topology and system parameters is viable even in the presence of external noise that distorts the original dynamics substantially. The method provides a conceptually new step towards reconstructing a variety of real-world networks, including gene and protein interaction networks and neuronal circuits.

Nature of the Charged-Group Effect on the Stability of the C-Peptide Helix

Science.gov (United States)

Shoemaker, Kevin R.; Kim, Peter S.; Brems, David N.; Marqusee, Susan; York, Eunice J.; Chaiken, Irwin M.; Stewart, John M.; Baldwin, Robert L.

1985-04-01

The residues responsible for the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A) have been identified by chemical synthesis of analogues and measurement of their helix-forming properties. Each of the residues ionizing between pH 2 and pH 8 has been replaced separately by an uncharged residue. Protonation of Glu-2- is responsible for the sharp decrease in helix stability between pH 5 and pH 2, and deprotonation of His-12+ causes a similar decrease between pH 5 and pH 8. Glu-9- is not needed for helix stability. The results cannot be explained by the Zimm-Bragg model and host-guest data for α -helix formation, which predict that the stability of the C-peptide helix should increase when Glu-2- is protonated or when His-12+ is deprotonated. Moreover, histidine+ is a strong helix-breaker in host-guest studies. In proteins, acidic and basic residues tend to occur at opposite ends of α -helices: acidic residues occur preferentially near the NH2-terminal end and basic residues near the COOH-terminal end. A possible explanation, based on a helix dipole model, has been given [Blagdon, D. E. & Goodman, M. (1975) Biopolymers 14, 241-245]. Our results are consistent with the helix dipole model and they support the suggestion that the distribution of charged residues in protein helices reflects the helix-stabilizing propensity of those residues. Because Glu-9 is not needed for helix stability, a possible Glu-9-\\cdots His-12+ salt bridge does not contribute significantly to helix stability. The role of a possible Glu-2-\\cdots Arg-10+ salt bridge has not yet been evaluated. A charged-group effect on α -helix stability in water has also been observed in a different peptide system [Ihara, S., Ooi, T. & Takahashi, S. (1982) Biopolymers 21, 131-145]: block copolymers containing (Ala)20 and (Glu)20 show partial helix formation at low temperatures, pH 7.5, where the glutamic acid residues are ionized. (Glu)20(Ala)20Phe forms a

Quark-parton model from dual topological unitarization

International Nuclear Information System (INIS)

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

1979-01-01

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 to the confinement problem

Topology-Based Methods in Visualization 2015

CERN Document Server

Garth, Christoph; Weinkauf, Tino

2017-01-01

This book presents contributions on topics ranging from novel applications of topological analysis for particular problems, through studies of the effectiveness of modern topological methods, algorithmic improvements on existing methods, and parallel computation of topological structures, all the way to mathematical topologies not previously applied to data analysis. Topological methods are broadly recognized as valuable tools for analyzing the ever-increasing flood of data generated by simulation or acquisition. This is particularly the case in scientific visualization, where the data sets have long since surpassed the ability of the human mind to absorb every single byte of data. The biannual TopoInVis workshop has supported researchers in this area for a decade, and continues to serve as a vital forum for the presentation and discussion of novel results in applications in the area, creating a platform to disseminate knowledge about such implementations throughout and beyond the community. The present volum...

"Special Issue": Regional Dimensions of the Triple Helix Model

Science.gov (United States)

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

Directory of Open Access Journals (Sweden)

Yu Wei-Hsuan

2012-05-01

Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6�

Topological theory of dynamical systems recent advances

CERN Document Server

Aoki, N

1994-01-01

This monograph aims to provide an advanced account of some aspects of dynamical systems in the framework of general topology, and is intended for use by interested graduate students and working mathematicians. Although some of the topics discussed are relatively new, others are not: this book is not a collection of research papers, but a textbook to present recent developments of the theory that could be the foundations for future developments. This book contains a new theory developed by the authors to deal with problems occurring in diffentiable dynamics that are within the scope of general topology. To follow it, the book provides an adequate foundation for topological theory of dynamical systems, and contains tools which are sufficiently powerful throughout the book. Graduate students (and some undergraduates) with sufficient knowledge of basic general topology, basic topological dynamics, and basic algebraic topology will find little difficulty in reading this book.

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

Science.gov (United States)

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

Topology optimization for simplified structural fire safety

DEFF Research Database (Denmark)

Madsen, Søren; Lange, Nis P.; Giuliani, Luisa

2016-01-01

Topology optimization is applied in an idealized structural fire safety model, where the minimum compliance problem is constrained by temperature-controlled structural degradation. The constraint ensures a certain structural stiffness after a prescribed time. As this time period is extended......, resulting optimized topologies tend to become thicker or introduce redundant members that can take over when structural parts near the origin of the fire lose their load carrying capability. Hence, the structural degradation model acts as an erosion operator on the topology and indirectly enforces a minimum...

Topology optimization applied to room acoustic problems and surface acoustic wave devices

DEFF Research Database (Denmark)

Dühring, Maria Bayard; Sigmund, Ole; Jensen, Jakob Søndergaard

can be minimized either by distribution of reflecting material in a design domain along the ceiling or by distribution of absorbing and reflecting material along all the walls for both 2D and 3D problems. It is also shown how the method can be used to design sound barriers. The main part...... in order to optimize more complicated SAW structures such as acoustic horns which focus the SAWs to a small area. [1] M. P. Bendsøe, O. Sigmund, “Topology optimization, theory, methods and applications”, Springer Verlag Berlin Heidelberg New York, 2nd edition, (2003). ISBN 3-540-42992-1. [2] J. S. Jensen......, Berlin, (2000). ISBN 3-540-67232-X. [5] M. M. de Lima Jr and P. V. Santos, “Modulation of photonic structures by surface acoustic waves”, Rep. Prog. Phys., 68 1639-1701 (2005)...

Topological constraints and their breakdown in dynamical evolution

International Nuclear Information System (INIS)

Goldstein, Raymond E; Moffatt, H Keith; Pesci, Adriana I

2012-01-01

A variety of physical and biological systems exhibit dynamical behaviour that has some explicit or implicit topological features. Here, the term ‘topological’ is meant to convey the idea of structures, e.g. physical knots, links or braids, that have some measure of invariance under continuous deformation. Dynamical evolution is then subject to the topological constraints that express this invariance. The simplest problem arising in these systems is the determination of minimum-energy structures (and routes towards these structures) permitted by such constraints, and elucidation of mechanisms by which the constraints may be broken. In more complex nonequilibrium cases there can be recurring singularities associated with topological rearrangements driven by continuous injection of energy. In this brief overview, motivated by an upcoming program on ‘Topological Dynamics in the Physical and Biological Sciences’ at the Isaac Newton Institute for Mathematical Sciences, we present a summary of this class of dynamical systems and discuss examples of important open problems. (invited articles)

Topological insulators/superconductors: Potential future electronic materials

International Nuclear Information System (INIS)

Hor, Y. S.

2014-01-01

A new material called topological insulator has been discovered and becomes one of the fastest growing field in condensed matter physics. Topological insulator is a new quantum phase of matter which has Dirac-like conductivity on its surface, but bulk insulator through its interior. It is considered a challenging problem for the surface transport measurements because of dominant internal conductance due to imperfections of the existing crystals of topological insulators. By a proper method, the internal bulk conduction can be suppressed in a topological insulator, and permit the detection of the surface currents which is necessary for future fault-tolerant quantum computing applications. Doped topological insulators have depicted a large variety of bulk physical properties ranging from magnetic to superconducting behaviors. By chemical doping, a TI can change into a bulk superconductor. Nb x Bi 2 Se 3 is shown to be a superconductor with T c ∼ 3.2 K, which could be a potential candidate for a topological superconductor

The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70

Energy Technology Data Exchange (ETDEWEB)

Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

2005-11-01

The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

CFT and topological recursion

CERN Document Server

Kostov, Ivan

2010-01-01

We study the quasiclassical expansion associated with a complex curve. In a more specific context this is the 1/N expansion in U(N)-invariant matrix integrals. We compare two approaches, the CFT approach and the topological recursion, and show their equivalence. The CFT approach reformulates the problem in terms of a conformal field theory on a Riemann surface, while the topological recursion is based on a recurrence equation for the observables representing symplectic invariants on the complex curve. The two approaches lead to two different graph expansions, one of which can be obtained as a partial resummation of the other.

Contact Stress Analysis for Gears of Different Helix Angle Using Finite Element Method

Directory of Open Access Journals (Sweden)

Patil Santosh

2014-07-01

Full Text Available The gear contact stress problem has been a great point of interest for many years, but still an extensive research is required to understand the various parameters affecting this stress. Among such parameters, helix angle is one which has played a crucial role in variation of contact stress. Numerous studies have been carried out on spur gear for contact stress variation. Hence, the present work is an attempt to study the contact stresses among the helical gear pairs, under static conditions, by using a 3D finite element method. The helical gear pairs on which the analysis is carried are 0, 5, 15, 25 degree helical gear sets. The Lagrange multiplier algorithm has been used between the contacting pairs to determine the stresses. The helical gear contact stress is evaluated using FE model and results have also been found at different coefficient of friction, varying from 0.0 to 0.3. The FE results have been further compared with the analytical calculations. The analytical calculations are based upon Hertz and AGMA equations, which are modified to include helix angle. The commercial finite element software was used in the study and it was shown that this approach can be applied to gear design efficiently. The contact stress results have shown a decreasing trend, with increase in helix angle.

Wave Manipulation by Topology Optimization

DEFF Research Database (Denmark)

Andkjær, Jacob Anders

topology optimization can be used to design structures for manipulation of the electromagnetic and acoustic waves. The wave problems considered here fall within three classes. The first class concerns the design of cloaks, which when wrapped around an object will render the object undetectable...... for the cloak is to delay the waves in regions of higher permittivity than the background and subsequently phase match them to the waves outside. Directional acoustic cloaks can also be designed using the topology optimization method. Aluminum cylinders constitutes the design and their placement and size...... concerns the design of planar Fresnel zone plate lenses for focusing electromagnetic waves. The topology optimized zone plates improve the focusing performance compared to results known from the literature....

Dimensional crossover and cold-atom realization of topological Mott insulators

Science.gov (United States)

Scheurer, Mathias S.; Rachel, Stephan; Orth, Peter P.

2015-02-01

Interacting cold-atomic gases in optical lattices offer an experimental approach to outstanding problems of many body physics. One important example is the interplay of interaction and topology which promises to generate a variety of exotic phases such as the fractionalized Chern insulator or the topological Mott insulator. Both theoretically understanding these states of matter and finding suitable systems that host them have proven to be challenging problems. Here we propose a cold-atom setup where Hubbard on-site interactions give rise to spin liquid-like phases: weak and strong topological Mott insulators. They represent the celebrated paradigm of an interacting and topological quantum state with fractionalized spinon excitations that inherit the topology of the non-interacting system. Our proposal shall help to pave the way for a controlled experimental investigation of this exotic state of matter in optical lattices. Furthermore, it allows for the investigation of a dimensional crossover from a two-dimensional quantum spin Hall insulating phase to a three-dimensional strong topological insulator by tuning the hopping between the layers.

Quantum field theory in topology changing spacetimes; Quantenfeldtheorie auf Raumzeiten mit Topologieaenderungen

Energy Technology Data Exchange (ETDEWEB)

Bauer, W.

2007-03-15

The goal of this diploma thesis is to present an overview of how to reduce the problem of topology change of general spacetimes to the investigation of elementary cobordisms. In the following we investigate the possibility to construct quantum fields on elementary cobordisms, in particular we discuss the trousers topology. Trying to avoid the problems occuring at spacetimes with instant topology change we use a model for simulating topology change. We construct the algebra of observables for a free scalar field with the algebraic approach to quantum field theory. Therefore we determine a fundamental solution of the eld equation. (orig.)

Identification of basic/helix-loop-helix transcription factors reveals candidate genes involved in anthocyanin biosynthesis from the strawberry white-flesh mutant

OpenAIRE

Zhao, Fengli; Li, Gang; Hu, Panpan; Zhao, Xia; Li, Liangjie; Wei, Wei; Feng, Jiayue; Zhou, Houcheng

2018-01-01

As the second largest transcription factor family in plant, the basic helix-loop-helix (bHLH) transcription factor family, characterized by the conserved bHLH domain, plays a central regulatory role in many biological process. However, the bHLH transcription factor family of strawberry has not been systematically identified, especially for the anthocyanin biosynthesis. Here, we identified a total of 113 bHLH transcription factors and described their chromosomal distribution and bioinformatics...

Tensor Network Wavefunctions for Topological Phases

Science.gov (United States)

Ware, Brayden Alexander

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

Slope constrained Topology Optimization

DEFF Research Database (Denmark)

Petersson, J.; Sigmund, Ole

1998-01-01

The problem of minimum compliance topology optimization of an elastic continuum is considered. A general continuous density-energy relation is assumed, including variable thickness sheet models and artificial power laws. To ensure existence of solutions, the design set is restricted by enforcing...

TOWARDS UNDERSTANDING OF HELIX B BASED CONFORMATIONAL DISEASES IN SERPIN

Directory of Open Access Journals (Sweden)

Mohamad Aman Jairajpuri

2012-12-01

Full Text Available Serine protease inhibitors (serpins are a unique family of protease inhibitors that are prone to polymer formation due to their metastable nature and a complex inhibition mechanism that involves large scale conformational change. Helix B is in the shutter region near the strand 2A and strand 3A of �-sheet A, where reactive centre loop inserts during the serpin inhibition mechanism. Helix B region in serpins is a mutation hotspot for naturally occurring variants that result in pathological conditions due to polymerization. Helix B residues are completely buried in the native state and loop inserted latent state but not in the inhibitory loop inserted cleaved conformation. Native to cleaved transition during inhibition forms a large cavity in the shutter region, which invariably is the largest cavity in most serpins in native state. In a recent paper we had for the first time hypothesized that exposure of helix B at the N-terminal end is important for smooth insertion of the reactive center loop during serpin inhibition mechanism. It is therefore possible that natural variant that induces conformational deformation of helix B probably alter the cavity size which increases the rate of loop-sheet interaction between the monomers resulting in increased polymerization.

Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

Directory of Open Access Journals (Sweden)

Vuthy Ea

2015-07-01

Full Text Available Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization.

A new compactness type topological property | Zhao | Quaestiones ...

African Journals Online (AJOL)

By a gauge on a topological space we shall mean a mapping that assigns each element in the space an open neighbourhood. We investigate some topological properties which can be characterized using gauges. The main property we will consider is the gauge compactness. Some problems and possible future work are ...

Topology and condensed matter physics

CERN Document Server

Mj, Mahan; Bandyopadhyay, Abhijit

2017-01-01

This book introduces aspects of topology and applications to problems in condensed matter physics. Basic topics in mathematics have been introduced in a form accessible to physicists, and the use of topology in quantum, statistical and solid state physics has been developed with an emphasis on pedagogy. The aim is to bridge the language barrier between physics and mathematics, as well as the different specializations in physics. Pitched at the level of a graduate student of physics, this book does not assume any additional knowledge of mathematics or physics. It is therefore suited for advanced postgraduate students as well. A collection of selected problems will help the reader learn the topics on one's own, and the broad range of topics covered will make the text a valuable resource for practising researchers in the field.  The book consists of two parts: one corresponds to developing the necessary mathematics and the other discusses applications to physical problems. The section on mathematics is a qui...

Riemann, topology, and physics

CERN Document Server

Monastyrsky, Michael I

2008-01-01

This significantly expanded second edition of Riemann, Topology, and Physics combines a fascinating account of the life and work of Bernhard Riemann with a lucid discussion of current interaction between topology and physics. The author, a distinguished mathematical physicist, takes into account his own research at the Riemann archives of Göttingen University and developments over the last decade that connect Riemann with numerous significant ideas and methods reflected throughout contemporary mathematics and physics. Special attention is paid in part one to results on the Riemann–Hilbert problem and, in part two, to discoveries in field theory and condensed matter such as the quantum Hall effect, quasicrystals, membranes with nontrivial topology, "fake" differential structures on 4-dimensional Euclidean space, new invariants of knots and more. In his relatively short lifetime, this great mathematician made outstanding contributions to nearly all branches of mathematics; today Riemann’s name appears prom...

Independent Study Project, Topic: Topology.

Science.gov (United States)

Notre Dame High School, Easton, PA.

Using this guide and the four popular books noted in it, a student, working independently, will learn about some of the classical ideas and problems of topology: the Meobius strip and Klein bottle, the four color problem, genus of a surface, networks, Euler's formula, and the Jordan Curve Theorem. The unit culminates in a project of the students'…

Mathematical modeling and design parameters of crushing machines with variable-pitch helix of the screw

Directory of Open Access Journals (Sweden)

Pelenko V. V.

2017-11-01

Full Text Available From the point of view of the effectiveness of the top cutting unit, the helix angle in the end portion of the screw is the most important and characteristic parameter, as it determines the pressure of the meat material in the zone of interaction of a knife and grate. The importance of solving the problem of mathematical modeling of geometry is due to the need to address the problem of minimizing the reverse flow of the food material when injecting into the cutting zone, as the specified effect of "locking" significantly reduces the performance of the transfer process, increases energy consumption of the equipment and entails the deterioration of the quality of the raw materials output. The problem of determining the length of the helix variable pitch for screw chopper food materials has been formulated and solved by methods of differential geometry. The task of correct description of the law of changing the angle of helix inclination along its length has been defined in this case as a key to provide the required dependence of this angle tangent on the angle of the radius-vector of the circle. It has been taken into account that the reduction in the pitch of the screw in the direction of the product delivery should occur at a decreasing rate. The parametric equation of the helix has been written in the form of three functional dependencies of the corresponding cylindrical coordinates. Based on the wide range analysis and significant number of models of tops from different manufacturers the boundaries of possible changes in the angles of inclination of the helical line of the first and last turns of the screw have been identified. The auger screw length is determined mathematically in the form of an analytical relationship and both as a function of the variable angle of its rise, and as a function of the rotation angle of the radius-vector of the circle generatrix, which makes it possible to expand the design possibilities of this node. Along

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Multi-material topology design of laminates with strength criteria

DEFF Research Database (Denmark)

Lund, Erik

2012-01-01

The objective of this paper is to present a novel approach for multi-material topology optimization of laminated composite structures where strength constraints are taken into account together with other global structural performance measures. The topology design problem considered contains very...... many design variables, and when strength criteria are included in the problem, a very large number of criteria functions must be considered in the optimization problem to be solved. Thus, block aggregation methods are introduced, such that global strength measures are obtained. These formulations...... are illustrated for multi-material laminated design problems where the maximum failure index is minimized while compliance and mass constraints are taken into account....

Energy Management Dynamic Control Topology In MANET

Science.gov (United States)

Madhusudan, G.; Kumar, TNR

2017-08-01

Topology management via per-node transmission power adjustment has been shown effective in extending network lifetime. The existing algorithms constructs static topologies which fail to take the residual energy of network nodes, and cannot balance energy consumption efficiently. To address this problem, a Light Weighted Distributed Topology Control algorithm EMDCT(Energy Management Dynamic Control Topology ) is proposed in this paper. Based on the link metric of the network, both the energy consumption rate level and residual energy levels at the two end nodes are considered. EMDCT generates a Dynamic Topology that changes with the variation of node energy without the aid of location information, each node determines its transmission power according to local network information, which reduces the overhead complexity of EMDCT greatly. The experiment results show that EMDCT preserves network connectivity and manitains minimum-cost property of the network also it can extend network lifetime more remarkably.

Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

DEFF Research Database (Denmark)

Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

2017-01-01

linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

Regional Dimensions of the Triple Helix Model: Setting the Context

Science.gov (United States)

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

Basis for calculations in the topological expansion

International Nuclear Information System (INIS)

Levinson, M.A.

1982-12-01

Investigations aimed at putting the topological theory of particles on a more quantitative basis are described. First, the incorporation of spin into the topological structure is discussed and shown to successfully reproduce the observed lowest mass hadron spectrum. The absence of parity-doubled states represents a significant improvement over previous efforts in similar directions. This theory is applied to the lowest order calculation of elementary hadron coupling constant ratios. SU(6)/sub W/ symmetry is maintained and extended via the notions of topological supersymmetry and universality. Finally, efforts to discover a perturbative basis for the topological expansion are described. This has led to the formulation of off-shell Feynman-like rules which provide a calculational scheme for the strong interaction components of the topological expansion once the zero-entropy connected parts are known. These rules are shown to imply a topological asymptotic freedom. Even though the nonlinear zero-entropy problem cannot itself be treated perturbatively, plausible general assumptions about zero-entropy amplitudes allow immediate qualitative inferences concerning physical hadrons. In particular, scenarios for mass splittings beyond the supersymmetric level are described

FMRFamide receptors of Helix aspersa

International Nuclear Information System (INIS)

Payza, K.

1988-01-01

A receptor binding assay and an isolated heart bioassay were used to identify and characterize the FMRFamide receptors in Helix. In the heart bioassay, FMRFamide increased myocardial contraction force. A potent FMRFamide analog, desaminoTyr-Phe-norLeu-arg-Phe-amide (daYFnLRFamide), was used as a radioiodinated receptor ligand. The high affinity binding of 125 I-daYFnLRFamide at 0 degree C to Helix brain membranes was reversible, saturable, pH-dependent and specific, with a K D of 13-14 nM. A lower affinity (245 nM) site was also observed. Radioligand binding sites were also identified in the heart, male reproductive organs and digestive organs. The structure-activity relations (SAR) of cardiostimulation correlated with the specificity of 125 I-daYFnLRFamide binding to brain and heart receptors. The SAR were similar to those of other molluscan FMRFamide bioassays, except that they showed a marked preference for some analogs with blocked amino-terminals

Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

International Nuclear Information System (INIS)

Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine; Burimski, Irina; Kilgore, Nicole R.; Zoumplis, Dorian; Allaway, Graham P.; Wild, Carl T.; Salzwedel, Karl

2010-01-01

Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by the fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the mechanism of

Photoinduced Topological Phase Transitions in Topological Magnon Insulators.

Science.gov (United States)

Owerre, S A

2018-03-13

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

Guaranteed cost control of mobile sensor networks with Markov switching topologies.

Science.gov (United States)

Zhao, Yuan; Guo, Ge; Ding, Lei

2015-09-01

This paper investigates the consensus seeking problem of mobile sensor networks (MSNs) with random switching topologies. The network communication topologies are composed of a set of directed graphs (or digraph) with a spanning tree. The switching of topologies is governed by a Markov chain. The consensus seeking problem is addressed by introducing a global topology-aware linear quadratic (LQ) cost as the performance measure. By state transformation, the consensus problem is transformed to the stabilization of a Markovian jump system with guaranteed cost. A sufficient condition for global mean-square consensus is derived in the context of stochastic stability analysis of Markovian jump systems. A computational algorithm is given to synchronously calculate both the sub-optimal consensus controller gains and the sub-minimum upper bound of the cost. The effectiveness of the proposed design method is illustrated by three numerical examples. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

Science.gov (United States)

Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

2016-09-19

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Topology of tiling spaces

CERN Document Server

Sadun, Lorenzo

2008-01-01

Aperiodic tilings are interesting to mathematicians and scientists for both theoretical and practical reasons. The serious study of aperiodic tilings began as a solution to a problem in logic. Simpler aperiodic tilings eventually revealed hidden "symmetries" that were previously considered impossible, while the tilings themselves were quite striking. The discovery of quasicrystals showed that such aperiodicity actually occurs in nature and led to advances in materials science. Many properties of aperiodic tilings can be discerned by studying one tiling at a time. However, by studying families of tilings, further properties are revealed. This broader study naturally leads to the topology of tiling spaces. This book is an introduction to the topology of tiling spaces, with a target audience of graduate students who wish to learn about the interface of topology with aperiodic order. It isn't a comprehensive and cross-referenced tome about everything having to do with tilings, which would be too big, too hard to ...

On the helix equation

Directory of Open Access Journals (Sweden)

Taouil Hajer

2012-08-01

Full Text Available This paper is devoted to the helices processes, i.e. the solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω of the helix equation egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,oonumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω where Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω is a dynamical system on a measurable space (Ω, ℱ. More precisely, we investigate dominated solutions and non differentiable solutions of the helix equation. For the last case, the Wiener helix plays a fundamental role. Moreover, some relations with the cocycle equation defined by Φ, are investigated. Ce papier est consacré aux hélices, c’est-à-dire les solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω de l’équation fonctionnelle egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,o onumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω où Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω est un système dynamique défini sur un espace mesurable (Ω, ℱ. Plus présisément, nous déterminons d’abord les hélices dominées puis nous caractérisons les hélices non différentiables. Dans ce dernier cas, l’hélice de Wiener joue un rôle important. Nous précisons aussi quelques relations des hélices avec les cocycles définis par Φ.

Topology

CERN Document Server

Hocking, John G

1988-01-01

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

Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

Science.gov (United States)

Liu, Wu-Yi; Zhao, Chun-Jiang

2010-01-01

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Topological hierarchy matters — topological matters with superlattices of defects

International Nuclear Information System (INIS)

He Jing; Kou Su-Peng

2016-01-01

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

A genome-wide survey on basic helix-loop-helix transcription factors in giant panda.

Directory of Open Access Journals (Sweden)

Chunwang Dang

Full Text Available The giant panda (Ailuropoda melanoleuca is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6, EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.

Topology Optimization for Additive Manufacturing

DEFF Research Database (Denmark)

Clausen, Anders

This PhD thesis deals with the combination of topology optimization and additive man-ufacturing (AM, also known as 3D-printing). In addition to my own works, the thesis contains a broader review and assessment of the literature within the field. The thesis first presents a classification...... of the various AM technologies, a review of relevant manufacturing materials, the properties of these materials in the additively manufactured part, as well as manufacturing constraints with a potential for design optimization. Subsequently, specific topology optimization formulations relevant for the most im...... for scalable manufacturing. In relation to interface problems it is shown how a flexible void area may be included into a standard minimum compliance problem by employing an additional design variable field and a sensitivity filter. Furthermore, it is shown how the design of coated structures may be modeled...

On the usefulness of non-gradient approaches in topology optimization

DEFF Research Database (Denmark)

Sigmund, Ole

2011-01-01

Topology optimization is a highly developed tool for structural design and is by now being extensively used in mechanical, automotive and aerospace industries throughout the world. Gradient-based topology optimization algorithms may efficiently solve fine-resolution problems with thousands and up...

Canonical Duality Theory for Topology Optimization

OpenAIRE

Gao, David Yang

2016-01-01

This paper presents a canonical duality approach for solving a general topology optimization problem of nonlinear elastic structures. By using finite element method, this most challenging problem can be formulated as a mixed integer nonlinear programming problem (MINLP), i.e. for a given deformation, the first-level optimization is a typical linear constrained 0-1 programming problem, while for a given structure, the second-level optimization is a general nonlinear continuous minimization pro...

Organizing product innovation: hierarchy, market or triple-helix networks?

Science.gov (United States)

Fitjar, Rune Dahl; Gjelsvik, Martin; Rodríguez-Pose, Andrés

This paper assesses the extent to which the organization of the innovation effort in firms, as well as the geographical scale at which this effort is pursued, affects the capacity to benefit from product innovations. Three alternative modes of organization are studied: hierarchy, market and triple-helix-type networks. Furthermore, we consider triple-helix networks at three geographical scales: local, national and international. These relationships are tested on a random sample of 763 firms located in five urban regions of Norway which reported having introduced new products or services during the preceding 3 years. The analysis shows that firms exploiting internal hierarchy or triple-helix networks with a wide range of partners managed to derive a significantly higher share of their income from new products, compared to those that mainly relied on outsourcing within the market. In addition, the analysis shows that the geographical scale of cooperation in networks, as well as the type of partner used, matters for the capacity of firms to benefit from product innovation. In particular, firms that collaborate in international triple-helix-type networks involving suppliers, customers and R&D institutions extract a higher share of their income from product innovations, regardless of whether they organize the processes internally or through the network.

A series of three-dimensional lanthanide coordination polymers with rutile and unprecedented rutile-related topologies.

Science.gov (United States)

Qin, Chao; Wang, Xin-Long; Wang, En-Bo; Su, Zhong-Min

2005-10-03

The complexes of formulas Ln(pydc)(Hpydc) (Ln = Sm (1), Eu (2), Gd (3); H2pydc = pyridine-2,5-dicarboxylic acid) and Ln(pydc)(bc)(H2O) (Ln = Sm (4), Gd (5); Hbc = benzenecarboxylic acid) have been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG analysis, and single-crystal X-ray diffraction. Compounds 1-3 are isomorphous and crystallize in the orthorhombic system, space group Pbcn. Their final three-dimensional racemic frameworks can be considered as being constructed by helix-linked scalelike sheets. Compounds 4 and 5 are isostructural and crystallize in the monoclinic system, space group P2(1)/c. pydc ligands bridge dinuclear lanthanide centers to form the three-dimensional frameworks featuring hexagonal channels along the a-axis that are occupied by one-end-coordinated bc ligands. From the topological point of view, the five three-dimensional nets are binodal with six- and three-connected nodes, the former of which exhibit a rutile-related (4.6(2))(2)(4(2).6(9).8(4)) topology that is unprecedented within coordination frames, and the latter two species display a distorted rutile (4.6(2))(2)(4(2).6(10).8(3)) topology. Furthermore, the luminescent properties of 2 were studied.

An efficient second-order SQP method for structural topology optimization

DEFF Research Database (Denmark)

Rojas Labanda, Susana; Stolpe, Mathias

2016-01-01

This article presents a Sequential Quadratic Programming (SQP) solver for structural topology optimization problems named TopSQP. The implementation is based on the general SQP method proposed in Morales et al. J Numer Anal 32(2):553–579 (2010) called SQP+. The topology optimization problem...... nonlinear solvers IPOPT and SNOPT. Numerical experiments on a large set of benchmark problems show good performance of TopSQP in terms of number of function evaluations. In addition, the use of second-order information helps to decrease the objective function value....

Orbifolds, quantum cosmology, and nontrivial topology

International Nuclear Information System (INIS)

Fagundes, Helio V.; Vargas, Teofilo

2006-01-01

In order to include nontrivial topologies in the problem of quantum creation of a universe, it seems to be necessary to generalize the sum over compact, smooth 4-manifolds to a sum over finite-volume, compact 4-orbifolds. We consider in detail the case of a 4-spherical orbifold with a cone-point singularity. This allows for the inclusion of a nontrivial topology into the semiclassical path integral approach to quantum cosmology, in the context of a Robertson-Walker minisuperspace. (author)

The nature of the topological intuition

OpenAIRE

Sultanova L. B.

2016-01-01

The article is devoted to the nature of the topological intuition and disclosure of the specifics of topological heuristics in the framework of philosophical theory of knowledge. As we know, intuition is a one of the support categories of the theory of knowledge, the driving force of scientific research. Great importance is mathematical intuition for the solution of non-standard problems, for which there is no algorithm for such a solution. In such cases, the mathematician addresses the so-ca...

Modern methods in topological vector spaces

CERN Document Server

Wilansky, Albert

2013-01-01

Designed for a one-year course in topological vector spaces, this text is geared toward advanced undergraduates and beginning graduate students of mathematics. The subjects involve properties employed by researchers in classical analysis, differential and integral equations, distributions, summability, and classical Banach and Frechét spaces. Optional problems with hints and references introduce non-locally convex spaces, Köthe-Toeplitz spaces, Banach algebra, sequentially barrelled spaces, and norming subspaces.Extensive introductory chapters cover metric ideas, Banach space, topological vect

Optimal Coordination of Distance and Directional Overcurrent Relays Considering Different Network Topologies

Directory of Open Access Journals (Sweden)

Y. Damchi

2015-09-01

Full Text Available Most studies in relay coordination have focused solely on coordination of overcurrent relays while distance relays are used as the main protection of transmission lines. Since, simultaneous coordination of these two types of relays can provide a better protection, in this paper, a new approach is proposed for simultaneous coordination of distance and directional overcurrent relays (D&DOCRs. Also, pursued by most of the previously published studies, the settings of D&DOCRs are usually determined based on a main network topology which may result in mis-coordination of relays when changes occur in the network topology. In the proposed method, in order to have a robust coordination, network topology changes are taken into account in the coordination problem. In the new formulation, coordination constraints for different network topologies are added to those of the main topology. A complex nonlinear optimization problem is derived to find the desirable relay settings. Then, the problem is solved using hybridized genetic algorithm (GA with linear programming (LP method (HGA. The proposed method is evaluated using the IEEE 14-bus test system. According to the results, a feasible and robust solution is obtained for D&DOCRs coordination while all constraints, which are due to different network topologies, are satisfied.

Topology Design for Directional Range Extension Networks with Antenna Blockage

Science.gov (United States)

2017-03-19

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

Some geometry and topology

International Nuclear Information System (INIS)

Marmo, G.; Morandi, G.

1995-01-01

In this lecture some mathematical problems that arise when one deals with low-dimensional field theories, such as homotopy and topological invariants, differential calculus on Lie groups and coset spaces, fiber spaces and parallel transport, differential calculus on fiber bundles, sequences on principal bundles and Chern-Simons terms are discussed

Acoustic design by topology optimization

DEFF Research Database (Denmark)

Dühring, Maria Bayard; Jensen, Jakob Søndergaard; Sigmund, Ole

2008-01-01

To bring down noise levels in human surroundings is an important issue and a method to reduce noise by means of topology optimization is presented here. The acoustic field is modeled by Helmholtz equation and the topology optimization method is based on continuous material interpolation functions...... in the density and bulk modulus. The objective function is the squared sound pressure amplitude. First, room acoustic problems are considered and it is shown that the sound level can be reduced in a certain part of the room by an optimized distribution of reflecting material in a design domain along the ceiling...

Topology in Molecular Biology

CERN Document Server

Monastyrsky, Michail Ilych

2007-01-01

The book presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology. The text also provides a short course of modern topology intended for the broad audience of biologists and physicists. The authors are renowned specialists in their fields and some of the new results presented here are documented for the first time in monographic form.

Topological susceptibility in lattice QCD with unimproved Wilson fermions

International Nuclear Information System (INIS)

Chowdhury, Abhishek; De, Asit K.; De Sarkar, Sangita; Harindranath, A.; Mondal, Santanu; Sarkar, Anwesa; Maiti, Jyotirmoy

2012-01-01

We address a long standing problem regarding topology in lattice simulations of QCD with unimproved Wilson fermions. Earlier attempt with unimproved Wilson fermions at β=5.6 to verify the suppression of topological susceptibility with decreasing quark mass (m q ) was unable to unambiguously confirm the suppression. We carry out systematic calculations for two degenerate flavours at two different lattice spacings (β=5.6 and 5.8). The effects of quark mass, lattice volume and the lattice spacing on the spanning of different topological sectors are presented. We unambiguously demonstrate the suppression of the topological susceptibility with decreasing quark mass, expected from chiral Ward identity and chiral perturbation theory.

Topological Taxonomy of Water Distribution Networks

Directory of Open Access Journals (Sweden)

Carlo Giudicianni

2018-04-01

Full Text Available Water Distribution Networks (WDNs can be regarded as complex networks and modeled as graphs. In this paper, Complex Network Theory is applied to characterize the behavior of WDNs from a topological point of view, reviewing some basic metrics, exploring their fundamental properties and the relationship between them. The crucial aim is to understand and describe the topology of WDNs and their structural organization to provide a novel tool of analysis which could help to find new solutions to several arduous problems of WDNs. The aim is to understand the role of the topological structure in the WDNs functioning. The methodology is applied to 21 existing networks and 13 literature networks. The comparison highlights some topological peculiarities and the possibility to define a set of best design parameters for ex-novo WDNs that could also be used to build hypothetical benchmark networks retaining the typical structure of real WDNs. Two well-known types of network ((a square grid; and (b random graph are used for comparison, aiming at defining a possible mathematical model for WDNs. Finally, the interplay between topology and some performance requirements of WDNs is discussed.

Stiffness design of geometrically nonlinear structures using topology optimization

DEFF Research Database (Denmark)

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

2000-01-01

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

DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain.

Science.gov (United States)

Northall, Sarah J; Buckley, Ryan; Jones, Nathan; Penedo, J Carlos; Soultanas, Panos; Bolt, Edward L

2017-09-01

Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by "reeling" ssDNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Brain network analysis: separating cost from topology using cost-integration.

Directory of Open Access Journals (Sweden)

Cedric E Ginestet

Full Text Available A statistically principled way of conducting brain network analysis is still lacking. Comparison of different populations of brain networks is hard because topology is inherently dependent on wiring cost, where cost is defined as the number of edges in an unweighted graph. In this paper, we evaluate the benefits and limitations associated with using cost-integrated topological metrics. Our focus is on comparing populations of weighted undirected graphs that differ in mean association weight, using global efficiency. Our key result shows that integrating over cost is equivalent to controlling for any monotonic transformation of the weight set of a weighted graph. That is, when integrating over cost, we eliminate the differences in topology that may be due to a monotonic transformation of the weight set. Our result holds for any unweighted topological measure, and for any choice of distribution over cost levels. Cost-integration is therefore helpful in disentangling differences in cost from differences in topology. By contrast, we show that the use of the weighted version of a topological metric is generally not a valid approach to this problem. Indeed, we prove that, under weak conditions, the use of the weighted version of global efficiency is equivalent to simply comparing weighted costs. Thus, we recommend the reporting of (i differences in weighted costs and (ii differences in cost-integrated topological measures with respect to different distributions over the cost domain. We demonstrate the application of these techniques in a re-analysis of an fMRI working memory task. We also provide a Monte Carlo method for approximating cost-integrated topological measures. Finally, we discuss the limitations of integrating topology over cost, which may pose problems when some weights are zero, when multiplicities exist in the ranks of the weights, and when one expects subtle cost-dependent topological differences, which could be masked by cost-integration.

Brain Network Analysis: Separating Cost from Topology Using Cost-Integration

Science.gov (United States)

Ginestet, Cedric E.; Nichols, Thomas E.; Bullmore, Ed T.; Simmons, Andrew

2011-01-01

A statistically principled way of conducting brain network analysis is still lacking. Comparison of different populations of brain networks is hard because topology is inherently dependent on wiring cost, where cost is defined as the number of edges in an unweighted graph. In this paper, we evaluate the benefits and limitations associated with using cost-integrated topological metrics. Our focus is on comparing populations of weighted undirected graphs that differ in mean association weight, using global efficiency. Our key result shows that integrating over cost is equivalent to controlling for any monotonic transformation of the weight set of a weighted graph. That is, when integrating over cost, we eliminate the differences in topology that may be due to a monotonic transformation of the weight set. Our result holds for any unweighted topological measure, and for any choice of distribution over cost levels. Cost-integration is therefore helpful in disentangling differences in cost from differences in topology. By contrast, we show that the use of the weighted version of a topological metric is generally not a valid approach to this problem. Indeed, we prove that, under weak conditions, the use of the weighted version of global efficiency is equivalent to simply comparing weighted costs. Thus, we recommend the reporting of (i) differences in weighted costs and (ii) differences in cost-integrated topological measures with respect to different distributions over the cost domain. We demonstrate the application of these techniques in a re-analysis of an fMRI working memory task. We also provide a Monte Carlo method for approximating cost-integrated topological measures. Finally, we discuss the limitations of integrating topology over cost, which may pose problems when some weights are zero, when multiplicities exist in the ranks of the weights, and when one expects subtle cost-dependent topological differences, which could be masked by cost-integration. PMID:21829437

Sensitivity Filters In Topology Optimisation As A Solution To Helmholtz Type Differential Equation

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov; Sigmund, Ole

2009-01-01

The focus of the study in this article is on the use of a Helmholtz type differential equation as a filter for topology optimisation problems. Until now various filtering schemes have been utilised in order to impose mesh independence in this type of problems. The usual techniques require topology...... information about the neighbour sub-domains is an expensive operation. The proposed filtering technique requires only mesh information necessary for the finite element discretisation of the problem. The main idea is to define the filtered variable implicitly as a solution of a Helmholtz type differential...... equation with homogeneous Neumann boundary conditions. The properties of the filter are demonstrated for various 2D and 3D topology optimisation problems in linear elasticity, solved on sequential and parallel computers....

Double helix vortex breakdown in a turbulent swirling annular jet flow

NARCIS (Netherlands)

Vanierschot, M.; Perçin, M.; van Oudheusden, B.W.

2018-01-01

In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is

The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

International Nuclear Information System (INIS)

Arakaki, Tracy; Neely, Helen; Boni, Erica; Mueller, Natasha; Buckner, Frederick S.; Van Voorhis, Wesley C.; Lauricella, Angela; DeTitta, George; Luft, Joseph; Hol, Wim G. J.; Merritt, Ethan A.

2007-01-01

The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix. The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family

Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein*

Science.gov (United States)

Padilla-Meier, G. Pauline; Gilcrease, Eddie B.; Weigele, Peter R.; Cortines, Juliana R.; Siegel, Molly; Leavitt, Justin C.; Teschke, Carolyn M.; Casjens, Sherwood R.

2012-01-01

Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction. PMID:22879595

Multiscale topology optimization of solid and fluid structures

DEFF Research Database (Denmark)

Andreasen, Casper Schousboe

This thesis considers the application of the topology optimization method to multiscale problems, specifically the fluid-structure interaction problem. By multiple-scale methods the governing equations, the Navier-Cauchy and the incompressible Navier-Stokes equations are expanded and separated...

Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

Directory of Open Access Journals (Sweden)

Wu-yi Liu

2010-01-01

Full Text Available Members of the basic helix-loop-helix (bHLH family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Topology of real algebraic varieties and related topics

CERN Document Server

Kharlamov, V M; Polotovskiĭ, G M; Viro, Oleg Ya

1996-01-01

This volume is dedicated to the memory of the Russian mathematician D. A. Gudkov. It contains papers written by his friends, students, and collaborators and is devoted mainly to the areas where D. A. Gudkov made important contributions. The main topic is the topology of real algebraic varieties. Several papers include new results on the topology of real plane algebraic curves (the Hilbert 16th problem).

Simultaneous topology optimization of structures and supports

DEFF Research Database (Denmark)

Buhl, Thomas

2002-01-01

supported areas. The method is applied to compliance minimization and mechanism design. In the case of mechanism design, the large displacements of the mechanism are modelled using geometrically nonlinear FE-analysis. Examples with minimization of the compliance demonstrate the effects of using variable......The purpose of this paper is to demonstrate a method for and the benefits of simultaneously designing structure and support distribution using topology optimization. The support conditions are included in the topology optimization by introducing, a new set of design variables that represents...... cost of supports in a design domain. Other examples show that more efficient mechanisms are obtained by introducing the support conditions in the topology optimization problem....

Induced topological pressure for topological dynamical systems

International Nuclear Information System (INIS)

Xing, Zhitao; Chen, Ercai

2015-01-01

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

Stone's representation theorem in fuzzy topology

Institute of Scientific and Technical Information of China (English)

刘应明; 张德学

2003-01-01

In this paper, a complete solution to the problem of Stone's repesentation theorem in fuzzy topology is given for a class of completely distributive lattices. Precisely, it is proved that if L is a frame such that 0 ∈ L is a prime or 1 ∈ L is a coprime, then the category of distributive lattices is dually equivalent to the category of coherent L-locales and that if L is moreover completely distributive, then the category of distributive lattices is dually equivalent to the category of coherent stratified L-topological spaces.

Definition of the topological structure of the automatic control system of spacecrafts

International Nuclear Information System (INIS)

KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" data-affiliation=" (Siberian State Aerospace University named after Academician M.F.Reshetnev 31 KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" >Zelenkov, P V; KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" data-affiliation=" (Siberian State Aerospace University named after Academician M.F.Reshetnev 31 KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" >Karaseva, M V; KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" data-affiliation=" (Siberian State Aerospace University named after Academician M.F.Reshetnev 31 KrasnoyarskiyRabochiy prospect, Krasnoyarsk, 660014 (Russian Federation))" >Tsareva, E A; Tsarev, R Y

2015-01-01

The paper considers the problem of selection the topological structure of the automated control system of spacecrafts. The integer linear model of mathematical programming designed to define the optimal topological structure for spacecraft control is proposed. To solve the determination problem of topological structure of the control system of spacecrafts developed the procedure of the directed search of some structure variants according to the scheme 'Branch and bound'. The example of the automated control system of spacecraft development included the combination of ground control stations, managing the spacecraft of three classes with a geosynchronous orbit with constant orbital periods is presented

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

International Nuclear Information System (INIS)

Diamantini, M. Cristina; Trugenberger, Carlo A.

2011-01-01

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

The Discovery of the Double Helix

CERN Multimedia

CERN. Geneva

2011-01-01

Professor James D. Watson has kindly agreed to make a presentation on the 1953 finding of the Double Helix at the Cavendish Laboratory by Francis Crick and himself. Being one of the greatest scientific discoveries in human history, little else needs to be added.

A first course in topology continuity and dimension

CERN Document Server

McCleary, John

2006-01-01

How many dimensions does our universe require for a comprehensive physical description? In 1905, Poincar� argued philosophically about the necessity of the three familiar dimensions, while recent research is based on 11 dimensions or even 23 dimensions. The notion of dimension itself presented a basic problem to the pioneers of topology. Cantor asked if dimension was a topological feature of Euclidean space. To answer this question, some important topological ideas were introduced by Brouwer, giving shape to a subject whose development dominated the twentieth century. The basic notions in topology are varied and a comprehensive grounding in point-set topology, the definition and use of the fundamental group, and the beginnings of homology theory requires considerable time. The goal of this book is a focused introduction through these classical topics, aiming throughout at the classical result of the Invariance of Dimension. This text is based on the author's course given at Vassar College and is intended fo...

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

Science.gov (United States)

Ng, Derek P; Deber, Charles M

2016-08-09

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

Discovering the Network Topology: An Efficient Approach for SDN

Directory of Open Access Journals (Sweden)

Leonardo OCHOA-ADAY

2016-11-01

Full Text Available Network topology is a physical description of the overall resources in the network. Collecting this information using efficient mechanisms becomes a critical task for important network functions such as routing, network management, quality of service (QoS, among many others. Recent technologies like Software-Defined Networks (SDN have emerged as promising approaches for managing the next generation networks. In order to ensure a proficient topology discovery service in SDN, we propose a simple agents-based mechanism. This mechanism improves the overall efficiency of the topology discovery process. In this paper, an algorithm for a novel Topology Discovery Protocol (SD-TDP is described. This protocol will be implemented in each switch through a software agent. Thus, this approach will provide a distributed solution to solve the problem of network topology discovery in a more simple and efficient way.

Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

Energy Technology Data Exchange (ETDEWEB)

Gao, Kai [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yong [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Lou, Jizhong, E-mail: jlou@ibp.ac.cn [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2016-05-13

Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.

Topology optimization and lattice Boltzmann methods

DEFF Research Database (Denmark)

Nørgaard, Sebastian Arlund

This thesis demonstrates the application of the lattice Boltzmann method for topology optimization problems. Specifically, the focus is on problems in which time-dependent flow dynamics have significant impact on the performance of the devices to be optimized. The thesis introduces new topology...... a discrete adjoint approach. To handle the complexity of the discrete adjoint approach more easily, a method for computing it based on automatic differentiation is introduced, which can be adapted to any lattice Boltzmann type method. For example, while it is derived in the context of an isothermal lattice...... Boltzmann model, it is shown that the method can be easily extended to a thermal model as well. Finally, the predicted behavior of an optimized design is compared to the equiva-lent prediction from a commercial finite element solver. It is found that the weakly compressible nature of the lattice Boltzmann...

FPGA helix tracking algorithm for PANDA

Energy Technology Data Exchange (ETDEWEB)

Liang, Yutie; Galuska, Martin; Gessler, Thomas; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches Institut, Giessen University (Germany); Ye, Hua [Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

2015-07-01

The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking algorithm for helix tracking reconstruction in the solenoidal field is shown. The tracking algorithm is composed by two parts, a road finding module followed by an iterative helix parameter calculation module. A performance study using C++ and the status of the VHDL implementation are presented.

Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach

Science.gov (United States)

Badasyan, A. V.; Hayrapetyan, G. N.; Tonoyan, Sh. A.; Mamasakhlisov, Y. Sh.; Benight, A. S.; Morozov, V. F.

2009-09-01

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy Ihh+Icc of (h-h, c-c) interactions overwhelms the energy Ihc+Ich of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when Ihh+Icchelix formation and disfavored intersegment interactions from the same theoretical perspective.

Comparing topological charge definitions using topology fixing actions

International Nuclear Information System (INIS)

Bruckmann, Falk; Gruber, Florian; Jansen, Karl; Marinkovic, Marina; Urbach, Carsten; Wagner, Marc

2009-05-01

We investigate both the hyperbolic action and the determinant ratio action designed to fix the topological charge on the lattice. We show to what extent topology is fixed depending on the parameters of these actions, keeping the physical situation fixed. At the same time the agreement between different definitions of topological charge - the field theoretic and the index definition - is directly correlated to the degree topology is fixed. Moreover, it turns out that the two definitions agree very well. We also study finite volume effects arising in the static potential and related quantities due to topology fixing. (orig.)

Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

Science.gov (United States)

Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

2003-08-15

DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

Filters in topology optimization based on Helmholtz‐type differential equations

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov; Sigmund, Ole

2011-01-01

The aim of this paper is to apply a Helmholtz‐type partial differential equation as an alternative to standard density filtering in topology optimization problems. Previously, this approach has been successfully applied as a sensitivity filter. The usual filtering techniques in topology...... from the neighbor subdomains is an expensive operation. The proposed filter technique requires only mesh information necessary for the finite element discretization of the problem. The main idea is to define the filtered variable implicitly as a solution of a Helmholtz‐type differential equation...

Selective intercalation of six ligands molecules in a self-assembled triple helix

NARCIS (Netherlands)

Mateos timoneda, Miguel; Kerckhoffs, J.M.C.A.; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

The addition of a ligand molecule to an artificial self-assembled triple helix leads to the selective intercalation of two hydrogen-bonded trimers in specific binding pockets. Furthermore, the triple helix suffers large conformational rearrangements in order to accommodate the ligand molecules in a

Thermal helix-coil transition in UV irradiated collagen from rat tail tendon.

Science.gov (United States)

Sionkowska, A; Kamińska, A

1999-05-01

The thermal helix-coil transition in UV irradiated collagen solution, collagen film and pieces of rat tail tendon (RTT) were compared. Their thermal stability's were determined by differential scanning calorimeter (DSC) and by viscometric measurements. The denaturation temperatures of collagen solution, film and pieces of RTT were different. The helix-coil transition occur near 40 degrees C in collagen solution, near 112 degrees C in collagen film, and near 101 degrees C in pieces of RTT. After UV irradiation the thermal helix-coil transition of collagen samples were changed. These changes depend on the degree of hydratation.

Triple helix interactions for eco-innovation

DEFF Research Database (Denmark)

Hermann, Roberto Rivas; Riisgaard, Henrik; Remmen, Arne

the role of science parks in promoting eco-innovation. This study uses qualitative data gathered in two units of analysis: Panama Canal Authority and City of Knowledge Science Park. The study examines how Triple Helix interactions have built the regional system of eco-innovation at the Panama Canal...

Solitons in an isolated helix chain

DEFF Research Database (Denmark)

Christiansen, Peter Leth; Zolotaryuk, Alexander; Savin, A.V.

1997-01-01

as a generalization of the well-known one-dimensional Fermi-Pasta-Ulam model to include transverse degrees of freedom of the chain molecules. In the particular case of the alpha-helix molecular chain, the intermolecular interactions involved into the model are the point-point bonds connecting the first-, second...

Topological Modeling and Stochastic Analysis of Images

National Research Council Canada - National Science Library

Krim, Hamid

2004-01-01

.... Concepts in classification and recognition problems. 1. We have explored the potential of combining geometrical as well as topological information in capturing the essence of an object for classification and recognition purposes...

Design of acoustic devices by topology optimization

DEFF Research Database (Denmark)

Sigmund, Ole; Jensen, Jakob Søndergaard

2003-01-01

The goal of this study is to design and optimize structures and devices that are subjected to acoustic waves. Examples are acoustic lenses, sound walls, waveguides and loud speakers. We formulate the design problem as a topology optimization problem, i.e. distribute material in a design domain...... such that the acoustic response is optimized....

Models and Methods for Structural Topology Optimization with Discrete Design Variables

DEFF Research Database (Denmark)

Stolpe, Mathias

in the conceptual design phase to find innovative designs. The strength of topology optimization is the capability of determining both the optimal shape and the topology of the structure. In some cases also the optimal material properties can be determined. Optimal structural design problems are modeled...... such as bridges, airplanes, wind turbines, cars, etc. Topology optimization is a collection of theory, mathematical models, and numerical methods and is often used in the conceptual design phase to find innovative designs. The strength of topology optimization is the capability of determining both the optimal......Structural topology optimization is a multi-disciplinary research field covering optimal design of load carrying mechanical structures such as bridges, airplanes, wind turbines, cars, etc. Topology optimization is a collection of theory, mathematical models, and numerical methods and is often used...

Democracy and environment as references for quadruple and quintuple helix innovation systems

Science.gov (United States)

Carayannis, Elias G.; Campbell, David F. J.; Orr, Barron J.

2015-04-01

The perspective of democracy and the ecological context define key references for knowledge production and innovation in innovation systems. Particularly under conditions of environmental change where enhancing the potential for adaptation is critical, this requires a closer look at ecological responsibility and sensitivity in the different innovation models and governance regimes. The "Quintuple Helix" innovation model is an approach that stresses the necessary socio-ecological transition of society and economy by adding an environment helix to an innovation system already made up of three (university-industry-government) or four (civil society relations) helices in a way that supports adaptation by incorporating global warming as both a challenge to and a driver of innovation. There is the proposition that knowledge production and innovation co-evolve with democracy (Carayannis and Campbell, 2014). In the Triple Helix model (Etzkowitz and Leydesdorff, 2000) the existence of a democracy does not appear to be necessary for knowledge production and innovation. However, the Quadruple Helix (Carayannis and Campbell, 2009, 2010 and 2014) is defined and represented by additional key attributes and components: "media-based and culture-based public", "civil society" and "arts, artistic research and arts-based innovation" (Bast, Carayannis and Campbell, 2015). Implications of this are that the fourth helix in the Quadruple Helix innovation systems brings in and represents the perspective of "dimension of democracy" or the "context of democracy" for knowledge in general and knowledge production and innovation in more particular. Within theories of democracy there is a competition between narrow and broader concepts of democracy (Campbell, 2013). This is particularly true when democracy is to be understood to transcend more substantially the narrow understanding of being primarily based on or being primarily rooted in government institutions (within a Triple Helix

Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

Energy Technology Data Exchange (ETDEWEB)

Xiang, Ye; Rossmann, Michael G. (Purdue)

2011-12-22

The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

Topology optimization of metallic devices for microwave applications

DEFF Research Database (Denmark)

Aage, Niels; Mortensen, Asger; Sigmund, Ole

2010-01-01

is the skin depth, which calls for highly refined meshing in order to capture the physics. The skin depth problem has therefore prohibited the application of topology optimization to this class of problem. We present a design parameterization that remedies these numerical issues, by the interpolation...

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

Science.gov (United States)

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

2017-07-01

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

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

Directory of Open Access Journals (Sweden)

Daniel Litinski

2017-09-01

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

Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

Science.gov (United States)

Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

2012-01-01

The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

Systematic design of microstructures by topology optimization

DEFF Research Database (Denmark)

Sigmund, Ole

2003-01-01

The topology optimization method can be used to determine the material distribution in a design domain such that an objective function is maximized and constraints are fulfilled. The method which is based on Finite Element Analysis may be applied to all kinds of material distribution problems like...... extremal material design, sensor and actuator design and MEMS synthesis. The state-of-the-art in topology optimization will be reviewed and older as well as new applications in phononic and photonic crystals design will be presented....

Wide baseline stereo matching based on double topological relationship consistency

Science.gov (United States)

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.

Topology Optimisation for Coupled Convection Problems

DEFF Research Database (Denmark)

Alexandersen, Joe; Andreasen, Casper Schousboe; Aage, Niels

stabilised finite elements implemented in a parallel multiphysics analysis and optimisation framework DFEM [1], developed and maintained in house. Focus is put on control of the temperature field within the solid structure and the problems can therefore be seen as conjugate heat transfer problems, where heat...... conduction governs in the solid parts of the design domain and couples to convection-dominated heat transfer to a surrounding fluid. Both loosely coupled and tightly coupled problems are considered. The loosely coupled problems are convection-diffusion problems, based on an advective velocity field from...

Inactivation of colicin Y by intramembrane helix–helix interaction with its immunity protein

Czech Academy of Sciences Publication Activity Database

Šmajs, D.; Doležalová, M.; Macek, Pavel; Žídek, L.

2008-01-01

Roč. 275, č. 21 (2008), s. 5325-5331 ISSN 1742-464X Institutional research plan: CEZ:AV0Z50200510 Keywords : colicin immunity * colicin y * helix-helix interaction Subject RIV: CE - Biochemistry Impact factor: 3.139, year: 2008

Countable Fuzzy Topological Space and Countable Fuzzy Topological Vector Space

Directory of Open Access Journals (Sweden)

Apu Kumar Saha

2015-06-01

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

Accessing the topological susceptibility via the Gribov horizon

Science.gov (United States)

Dudal, D.; Felix, C. P.; Guimaraes, M. S.; Sorella, S. P.

2017-10-01

The topological susceptibility, χ4 , following the work of Witten and Veneziano, plays a key role in identifying the relative magnitude of the η' mass, the so-called U (1 )A problem. A nonzero χ4 is caused by the Veneziano ghost, the occurrence of an unphysical massless pole in the correlation function of the topological current Kμ. In this paper, we investigate the topological susceptibility, χ4, in S U (3 ) and S U (2 ) Euclidean Yang-Mills theory using an appropriate Padé approximation tool and a nonperturbative gluon propagator, within a Becchi-Rouet-Stora-Tyutin invariant framework and by taking into account Gribov copies in a general linear covariant gauge.

PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop-Helix transcription factors of the anthocyanin pathway.

NARCIS (Netherlands)

Quattrocchio, F.M.; Verweij, C.W.; Spelt, C.E.; Mol, J.N.M.; Koes, R.E.

2007-01-01

The Petunia hybrids genes ANTHOCYANIN1 (AN1) and AN2 encode transcription factors with a basic-helix-loop-helix (BHLH) and a MYB domain, respectively, that are required for anthocyanin synthesis and acidification of the vacuole in petal cells. Mutation of PH4 results in a bluer flower color,

A new configuration for multilevel converters with diode clamped topology

DEFF Research Database (Denmark)

Nami, A.; Zare, F.; Ledwich, G.

2008-01-01

Due to the increased use of renewable energy and power elctronic applications, more multilevel converters (MLC) are developed. A Neutral Point Clamped (NPC) inverter is one of the most used multilevel topologies for wind turbine (WT) and photovoltaic (PV) applications. One of the most crucial...... of load changes which can avoid neutral point balancing problem in such converters. In addition, the presented topology is suitable for renewable energy systems to boost the low rectified output-voltage. In order to verify the proposed topology, steady state analysis, modelling and simulations are carried...

A-Soft Separation Axioms in Soft Topological Space

Directory of Open Access Journals (Sweden)

Luay Abd –Al-Hani Al-Sweedi

2018-01-01

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

Topology Synthesis of Structures Using Parameter Relaxation and Geometric Refinement

Science.gov (United States)

Hull, P. V.; Tinker, M. L.

2007-01-01

Typically, structural topology optimization problems undergo relaxation of certain design parameters to allow the existence of intermediate variable optimum topologies. Relaxation permits the use of a variety of gradient-based search techniques and has been shown to guarantee the existence of optimal solutions and eliminate mesh dependencies. This Technical Publication (TP) will demonstrate the application of relaxation to a control point discretization of the design workspace for the structural topology optimization process. The control point parameterization with subdivision has been offered as an alternative to the traditional method of discretized finite element design domain. The principle of relaxation demonstrates the increased utility of the control point parameterization. One of the significant results of the relaxation process offered in this TP is that direct manufacturability of the optimized design will be maintained without the need for designer intervention or translation. In addition, it will be shown that relaxation of certain parameters may extend the range of problems that can be addressed; e.g., in permitting limited out-of-plane motion to be included in a path generation problem.

Topological Coherent Modes in Trapped Bose Gas

International Nuclear Information System (INIS)

Yukalov, V.I.; Marzlin, K.-P.; Yukalova, E.P.; Bagnato, V.S.

2005-01-01

The report reviews the problem of topological coherent modes, which are nonlinear collective states of Bose-condensed atoms. Such modes can be generated by means of alternating external fields, whose frequencies are in resonance with the transition frequencies between the related modes. The Bose gas with generated topological coherent modes is a collective nonlinear analog of a resonant atom. Such systems exhibit a variety of nontrivial effects, e.g. interference fringes, interference current, mode locking, dynamic transitions, critical phenomena, chaotic motion, harmonic generation, parametric conversion, atomic squeezing, and entanglement production

On topology optimization of plates with prestress

DEFF Research Database (Denmark)

Pedersen, Niels Leergaard

2001-01-01

of the sensitivities is complicated because of the initial stress stiffness matrix, but the computational cost can be kept low by using the adjoint method. The topology optimization problem is solved using the solid isotropic material with penalization (SIMP) method in combination with method of moving asymptotes (MMA......In this work, topology optimization is used to optimize the compliance or eigenvalues of prestressed plates. The prestress is accounted for by including the force equivalent to the prestressing and adding the initial stress stiffness matrix to the original stiffness matrix. The calculation...

Average-case analysis of incremental topological ordering

DEFF Research Database (Denmark)

Ajwani, Deepak; Friedrich, Tobias

2010-01-01

Many applications like pointer analysis and incremental compilation require maintaining a topological ordering of the nodes of a directed acyclic graph (DAG) under dynamic updates. All known algorithms for this problem are either only analyzed for worst-case insertion sequences or only evaluated...... experimentally on random DAGs. We present the first average-case analysis of incremental topological ordering algorithms. We prove an expected runtime of under insertion of the edges of a complete DAG in a random order for the algorithms of Alpern et al. (1990) [4], Katriel and Bodlaender (2006) [18], and Pearce...

Lysine as helix C-capping residue in a synthetic peptide.

Science.gov (United States)

Esposito, G; Dhanapal, B; Dumy, P; Varma, V; Mutter, M; Bodenhausen, G

1997-01-01

The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

Thermodynamic Effects of Replacements of Pro Residues in Helix Interiors of Maltose-Binding Protein

OpenAIRE

Prajapati, RS; Lingaraju, GM; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

2003-01-01

Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by...

Topological methods in Euclidean spaces

CERN Document Server

Naber, Gregory L

2000-01-01

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

Algebraic topology a first course

CERN Document Server

Fulton, William

1995-01-01

To the Teacher. This book is designed to introduce a student to some of the important ideas of algebraic topology by emphasizing the re­ lations of these ideas with other areas of mathematics. Rather than choosing one point of view of modem topology (homotopy theory, simplicial complexes, singular theory, axiomatic homology, differ­ ential topology, etc.), we concentrate our attention on concrete prob­ lems in low dimensions, introducing only as much algebraic machin­ ery as necessary for the problems we meet. This makes it possible to see a wider variety of important features of the subject than is usual in a beginning text. The book is designed for students of mathematics or science who are not aiming to become practicing algebraic topol­ ogists-without, we hope, discouraging budding topologists. We also feel that this approach is in better harmony with the historical devel­ opment of the subject. What would we like a student to know after a first course in to­ pology (assuming we reject the answer: ...

A Topology Visualization Early Warning Distribution Algorithm for Large-Scale Network Security Incidents

Directory of Open Access Journals (Sweden)

Hui He

2013-01-01

Full Text Available It is of great significance to research the early warning system for large-scale network security incidents. It can improve the network system’s emergency response capabilities, alleviate the cyber attacks’ damage, and strengthen the system’s counterattack ability. A comprehensive early warning system is presented in this paper, which combines active measurement and anomaly detection. The key visualization algorithm and technology of the system are mainly discussed. The large-scale network system’s plane visualization is realized based on the divide and conquer thought. First, the topology of the large-scale network is divided into some small-scale networks by the MLkP/CR algorithm. Second, the sub graph plane visualization algorithm is applied to each small-scale network. Finally, the small-scale networks’ topologies are combined into a topology based on the automatic distribution algorithm of force analysis. As the algorithm transforms the large-scale network topology plane visualization problem into a series of small-scale network topology plane visualization and distribution problems, it has higher parallelism and is able to handle the display of ultra-large-scale network topology.

One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

Science.gov (United States)

Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

2018-04-12

The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

Conformational Diffusion and Helix Formation Kinetics

International Nuclear Information System (INIS)

Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

2000-01-01

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

Conformational Diffusion and Helix Formation Kinetics

Energy Technology Data Exchange (ETDEWEB)

Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

2000-09-18

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

Once more about the topologically massive gauge theory

International Nuclear Information System (INIS)

Kogan, Ya.I.

1989-01-01

The general properties of the three-dimensional gauge theory with the topological mass is discussed namely the long-range interaction of the Aharonov-Bohm type. It is argued that Chern-Simons gauge theories must be considered as the infrared limit of the topologically massive theories. The analogy between the Landau problem of a charged particle in a magnetic field and quantization of this gauge theory is considered, as well as the quantization condition for the Abelian Chern-Simons term. 38 refs.; 5 figs

Analytic solutions of topologically disjoint systems

DEFF Research Database (Denmark)

Armstrong, J. R.; Volosniev, A. G.; Fedorov, D. V.

2015-01-01

We describe a procedure to solve an up to $2N$ problem where the particles are separated topologically in $N$ groups with at most two particles in each. Arbitrary interactions are allowed between the (two) particles within one group. All other interactions are approximated by harmonic oscillator...

Maximization of eigenvalues using topology optimization

DEFF Research Database (Denmark)

Pedersen, Niels Leergaard

2000-01-01

to localized modes in low density areas. The topology optimization problem is formulated using the SIMP method. Special attention is paid to a numerical method for removing localized eigenmodes in low density areas. The method is applied to numerical examples of maximizing the first eigenfrequency, One example...

An Overview of the Topological Gradient Approach in Image Processing: Advantages and Inconveniences

OpenAIRE

Jaafar Belaid, Lamia

2010-01-01

Image analysis by topological gradient approach is a technique based upon the historic application of the topological asymptotic expansion to crack localization problem from boundary measurements. This paper aims at reviewing this methodology through various applications in image processing; in particular image restoration with edge detection, classification and segmentation problems for both grey level and color images is presented in this work. The numerical experiments show the efficiency ...

Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

Science.gov (United States)

Harper, Shannon M; Christie, John M; Gardner, Kevin H

2004-12-28

Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

Topological Methods for Visualization

Energy Technology Data Exchange (ETDEWEB)

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

2016-04-07

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

Introduction to topology

CERN Document Server

Gamelin, Theodore W

1999-01-01

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

Topological variation in single-gene phylogenetic trees

OpenAIRE

Castresana, Jose

2007-01-01

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.

Topology Optimization Using Multiscale Finite Element Method for High-Contrast Media

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov

2014-01-01

The focus of this paper is on the applicability of multiscale finite element coarse spaces for reducing the computational burden in topology optimization. The coarse spaces are obtained by solving a set of local eigenvalue problems on overlapping patches covering the computational domain. The app......The focus of this paper is on the applicability of multiscale finite element coarse spaces for reducing the computational burden in topology optimization. The coarse spaces are obtained by solving a set of local eigenvalue problems on overlapping patches covering the computational domain...

Tight Network Topology Dependent Bounds on Rounds of Communication

OpenAIRE

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

2016-01-01

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

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

Directory of Open Access Journals (Sweden)

Jolene Read

2015-06-01

Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

p-topological Cauchy completions

Directory of Open Access Journals (Sweden)

J. Wig

1999-01-01

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

Emerging Trends in Topological Insulators and Topological ...

Indian Academy of Sciences (India)

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

Torus actions, combinatorial topology, and homological algebra

International Nuclear Information System (INIS)

Bukhshtaber, V M; Panov, T E

2000-01-01

This paper is a survey of new results and open problems connected with fundamental combinatorial concepts, including polytopes, simplicial complexes, cubical complexes, and arrangements of subspaces. Attention is concentrated on simplicial and cubical subdivisions of manifolds, and especially on spheres. Important constructions are described that enable one to study these combinatorial objects by using commutative and homological algebra. The proposed approach to combinatorial problems is based on the theory of moment-angle complexes recently developed by the authors. The crucial construction assigns to each simplicial complex K with m vertices a T m -space Z K with special bigraded cellular decomposition. In the framework of this theory, well-known non-singular toric varieties arise as orbit spaces of maximally free actions of subtori on moment-angle complexes corresponding to simplicial spheres. It is shown that diverse invariants of simplicial complexes and related combinatorial-geometric objects can be expressed in terms of bigraded cohomology rings of the corresponding moment-angle complexes. Finally, it is shown that the new relationships between combinatorics, geometry, and topology lead to solutions of some well-known topological problems

Stress-constrained topology optimization for compliant mechanism design

DEFF Research Database (Denmark)

de Leon, Daniel M.; Alexandersen, Joe; Jun, Jun S.

2015-01-01

This article presents an application of stress-constrained topology optimization to compliant mechanism design. An output displacement maximization formulation is used, together with the SIMP approach and a projection method to ensure convergence to nearly discrete designs. The maximum stress...... is approximated using a normalized version of the commonly-used p-norm of the effective von Mises stresses. The usual problems associated with topology optimization for compliant mechanism design: one-node and/or intermediate density hinges are alleviated by the stress constraint. However, it is also shown...

Electromagnetic topology: Characterization of internal electromagnetic coupling

Science.gov (United States)

Parmantier, J. P.; Aparicio, J. P.; Faure, F.

1991-01-01

The main principles are presented of a method dealing with the resolution of electromagnetic internal problems: Electromagnetic Topology. A very interesting way is to generalize the multiconductor transmission line network theory to the basic equation of the Electromagnetic Topology: the BLT equation. This generalization is illustrated by the treatment of an aperture as a four port junction. Analytical and experimental derivations of the scattering parameters are presented. These concepts are used to study the electromagnetic coupling in a scale model of an aircraft, and can be seen as a convenient means to test internal electromagnetic interference.

Geometry of the toroidal N-helix: optimal-packing and zero-twist

DEFF Research Database (Denmark)

Olsen, Kasper; Bohr, Jakob

2012-01-01

Two important geometrical properties of N-helix structures are influenced by bending. One is maximizing the volume fraction, which is called optimal-packing, and the other is having a vanishing strain-twist coupling, which is called zero-twist. Zero-twist helices rotate neither in one nor...... helix. General N-helices are discussed, as well as zero-twist helices for N > 1. The derived geometrical restrictions are gradually modified by changing the aspect ratio of the torus....

Topology

CERN Document Server

Manetti, Marco

2015-01-01

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

Beginning topology

CERN Document Server

Goodman, Sue E

2009-01-01

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

The Penta Helix Model of Innovation in Oman: An HEI Perspective

Directory of Open Access Journals (Sweden)

Alrence S Halibas

2017-05-01

government in Oman. HEI engagement is perceivably still weak. HEIs have yet to come out as a strong leading force in promoting systems of innovation. There is clear awareness of the need to adopt leading-edge practices in innovation strategy and management, curriculum and assessment, staff support and reward systems, funding and ICT infrastructure, research commercialization and IP management, and community engagement. Recommendations for Practitioners: There is need to conduct more in-depth analyses about the synergy and partnerships between key players of the Penta Helix model. A large-scale survey will help completely reveal the status and impact of innovation practices in the region and among HEIs. Recommendation for Researchers: There is need to conduct more in-depth analyses about the synergy and partnerships between key players of the Penta Helix model. A large-scale survey will help completely reveal the status and impact of innovation practices in the region and among HEIs. Impact on Society: The paper hopes to influence policy. It fully intends to convince policymakers increase the adoption of strategic interventions. The paper is not a theoretical description of the problem. It suggests several concrete courses of action. Future Research: The paper has seen the need to measure the effectiveness of the current innovation practices among key players in the innovation network and how these practices advance Oman’s knowledge economy. We propose a Likert-based bottom-up engagement metric.

Finite-life fatigue constraints in 2D topology optimization of continua

DEFF Research Database (Denmark)

Oest, Jacob; Lund, Erik

2017-01-01

of fatigue damage are estimated using the stress-based Sines fatigue criterion and S − N curves, while the accumulated damage is estimated using Palmgren-Miner’s rule. The method is a natural extension of classical density-based topology optimization with static stress constraints, and thus utilizes many......Topology optimization of 2D continua with the objective of minimizing the mass while considering finite-life fatigue constraint is considered. The structure is subjected to proportional variable-amplitude loading. The topology optimization problem is solved using the density approach. The fractions...

Topological Gyroscopic Metamaterials

Science.gov (United States)

Nash, Lisa Michelle

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

Parallel framework for topology optimization using the method of moving asymptotes

DEFF Research Database (Denmark)

Aage, Niels; Lazarov, Boyan Stefanov

2013-01-01

and simple to implement linear solvers and optimization algorithms. However, to ensure generality, the code is developed to be easily extendable in terms of physical models as well as in terms of solution methods, without compromising the parallel scalability. The widely used Method of Moving Asymptotes......The complexity of problems attacked in topology optimization has increased dramatically during the past decade. Examples include fully coupled multiphysics problems in thermo-elasticity, fluid-structure interaction, Micro-Electro Mechanical System (MEMS) design and large-scale three dimensional...... optimization algorithm is parallelized and included as a fundamental part of the code. The capabilities of the presented approaches are demonstrated on topology optimization of a Stokes flow problem with target outflow constraints as well as the minimum compliance problem with a volume constraint from linear...

Momentum dependence of the topological susceptibility with overlap fermions

Energy Technology Data Exchange (ETDEWEB)

Koma, Yoshiaki; Koma, Miho [Numazu College of Technology, Shizuoka (Japan); Ilgenfritz, Ernst-Michael [Humboldt Univ., Berlin (Germany). Inst. fuer Physik; Koller, Karl [Muenchen Univ. (Germany). Fakultaet fuer Physik; Schierholz, Gerrit [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Streuer, Thomas [Regensburg Univ. (Germany). Inst. fuer Theoretische Physik; Weinberg, Volker [Bayerische Akademie der Wissenschaften, Garching (Germany). Leibniz-Rechenzentrum

2010-12-15

Knowledge of the derivative of the topological susceptibility at zero momentum is important for assessing the validity of the Witten-Veneziano formula for the {eta}{sup '} mass, and likewise for the resolution of the EMC proton spin problem. We investigate the momentum dependence of the topological susceptibility and its derivative at zero momentum using overlap fermions in quenched lattice QCD simulations. We expose the role of the low-lying Dirac eigenmodes for the topological charge density, and find a negative value for the derivative. While the sign of the derivative is consistent with the QCD sum rule for pure Yang-Mills theory, the absolute value is overestimated if the contribution from higher eigenmodes is ignored. (orig.)

Momentum dependence of the topological susceptibility with overlap fermions

International Nuclear Information System (INIS)

Koma, Yoshiaki; Koma, Miho; Ilgenfritz, Ernst-Michael; Streuer, Thomas; Weinberg, Volker

2010-12-01

Knowledge of the derivative of the topological susceptibility at zero momentum is important for assessing the validity of the Witten-Veneziano formula for the η ' mass, and likewise for the resolution of the EMC proton spin problem. We investigate the momentum dependence of the topological susceptibility and its derivative at zero momentum using overlap fermions in quenched lattice QCD simulations. We expose the role of the low-lying Dirac eigenmodes for the topological charge density, and find a negative value for the derivative. While the sign of the derivative is consistent with the QCD sum rule for pure Yang-Mills theory, the absolute value is overestimated if the contribution from higher eigenmodes is ignored. (orig.)

Applications of automatic differentiation in topology optimization

DEFF Research Database (Denmark)

Nørgaard, Sebastian A.; Sagebaum, Max; Gauger, Nicolas R.

2017-01-01

The goal of this article is to demonstrate the applicability and to discuss the advantages and disadvantages of automatic differentiation in topology optimization. The technique makes it possible to wholly or partially automate the evaluation of derivatives for optimization problems and is demons...

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

Science.gov (United States)

Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

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

Locating the fourth helix: Rethinking the role of civil society in developing smart learning cities

Science.gov (United States)

Borkowska, Katarzyna; Osborne, Michael

2018-06-01

In the Global North and increasingly in the Global South, smart city technologies are enthusiastically seen as a solution to urban problems and as an alternative to austerity. However, to move beyond a narrow technological focus, it is necessary to explore the degree to which smart initiatives are committed to building socially inclusive innovation with learning at its core. Using the particular case of the Future City Demonstrator Initiative in Glasgow, United Kingdom, the most high-profile initiative of its kind funded by government, the authors of this article assess the extent to which this smart city adopts such an inclusive approach. They use the quadruple helix model (government - academia - industry - civil society) as a starting point and develop an analytic framework composed of four strands: (1) supporting participation of citizens in decision-making; (2) implementing technological innovation which positions citizens as active users; (3) implementing technological innovation to benefit the community; and (4) evaluating technological innovation in the light of the experiences and needs of citizens. Unlike most analyses, the principal focus of this article is on the fourth element of the helix, civil society. The authors argue that Glasgow's rhetoric of smart urbanism, while aspiring to problem-solving, devalues certain principles of human agency. They emphasise that urban change, including the city's desire to become technologically innovative, would more fully facilitate active citizenship, social inclusion and learning opportunities for all if it were underpinned by the broader conceptions and frameworks of learning cities.

Network topology analysis.

Energy Technology Data Exchange (ETDEWEB)

Kalb, Jeffrey L.; Lee, David S.

2008-01-01

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

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

Science.gov (United States)

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

2017-01-01

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

Research on connection structure of aluminumbody bus using multi-objective topology optimization

Science.gov (United States)

Peng, Q.; Ni, X.; Han, F.; Rhaman, K.; Ulianov, C.; Fang, X.

2018-01-01

For connecting Aluminum Alloy bus body aluminum components often occur the problem of failure, a new aluminum alloy connection structure is designed based on multi-objective topology optimization method. Determining the shape of the outer contour of the connection structure with topography optimization, establishing a topology optimization model of connections based on SIMP density interpolation method, going on multi-objective topology optimization, and improving the design of the connecting piece according to the optimization results. The results show that the quality of the aluminum alloy connector after topology optimization is reduced by 18%, and the first six natural frequencies are improved and the strength performance and stiffness performance are obviously improved.

The Topology Optimization of Three-dimensional Cooling Fins by the Internal Element Connectivity Parameterization Method

International Nuclear Information System (INIS)

Yoo, Sung Min; Kim, Yoon Young

2007-01-01

This work is concerned with the topology optimization of three-dimensional cooling fins or heat sinks. Motivated by earlier success of the Internal Element Connectivity Method (I-ECP) method in two dimensional problems, the extension of I-ECP to three-dimensional problems is carried out. The main efforts were made to maintain the numerical trouble-free characteristics of I-ECP for full three-dimensional problems; a serious numerical problem appearing in thermal topology optimization is erroneous temperature undershooting. The effectiveness of the present implementation was checked through the design optimization of three-dimensional fins

Truss topology optimization with simultaneous analysis and design

Science.gov (United States)

Sankaranarayanan, S.; Haftka, Raphael T.; Kapania, Rakesh K.

1992-01-01

Strategies for topology optimization of trusses for minimum weight subject to stress and displacement constraints by Simultaneous Analysis and Design (SAND) are considered. The ground structure approach is used. A penalty function formulation of SAND is compared with an augmented Lagrangian formulation. The efficiency of SAND in handling combinations of general constraints is tested. A strategy for obtaining an optimal topology by minimizing the compliance of the truss is compared with a direct weight minimization solution to satisfy stress and displacement constraints. It is shown that for some problems, starting from the ground structure and using SAND is better than starting from a minimum compliance topology design and optimizing only the cross sections for minimum weight under stress and displacement constraints. A member elimination strategy to save CPU time is discussed.

Topology optimization using the finite volume method

DEFF Research Database (Denmark)

Gersborg-Hansen, Allan; Bendsøe, Martin P.; Sigmund, Ole

2005-01-01

in this presentation is focused on a prototype model for topology optimization of steady heat diffusion. This allows for a study of the basic ingredients in working with FVM methods when dealing with topology optimization problems. The FVM and FEM based formulations differ both in how one computes the design...... derivative of the system matrix $\\mathbf K$ and in how one computes the discretized version of certain objective functions. Thus for a cost function for minimum dissipated energy (like minimum compliance for an elastic structure) one obtains an expression $ c = \\mathbf u^\\T \\tilde{\\mathbf K} \\mathbf u...... the arithmetic and harmonic average with the latter being the well known Reuss lower bound. [1] Bendsøe, MP and Sigmund, O 2004: Topology Optimization - Theory, Methods, and Applications. Berlin Heidelberg: Springer Verlag [2] Versteeg, HK and Malalasekera, W 1995: An introduction to Computational Fluid Dynamics...

Topology optimization using the finite volume method

DEFF Research Database (Denmark)

in this presentation is focused on a prototype model for topology optimization of steady heat diffusion. This allows for a study of the basic ingredients in working with FVM methods when dealing with topology optimization problems. The FVM and FEM based formulations differ both in how one computes the design...... derivative of the system matrix K and in how one computes the discretized version of certain objective functions. Thus for a cost function for minimum dissipated energy (like minimum compliance for an elastic structure) one obtains an expression c = u^\\T \\tilde{K}u $, where \\tilde{K} is different from K...... the well known Reuss lower bound. [1] Bendsøe, M.P.; Sigmund, O. 2004: Topology Optimization - Theory, Methods, and Applications. Berlin Heidelberg: Springer Verlag [2] Versteeg, H. K.; W. Malalasekera 1995: An introduction to Computational Fluid Dynamics: the Finite Volume Method. London: Longman...

Topological geons with self-gravitating phantom scalar field

Science.gov (United States)

Kratovitch, P. V.; Potashov, I. M.; Tchemarina, Ju V.; Tsirulev, A. N.

2017-12-01

A topological geon is the quotient manifold M/Z 2 where M is a static spherically symmetric wormhole having the reflection symmetry with respect to its throat. We distinguish such asymptotically at solutions of the Einstein equations according to the form of the time-time metric function by using the quadrature formulas of the so-called inverse problem for self-gravitating spherically symmetric scalar fields. We distinguish three types of geon spacetimes and illustrate them by simple examples. We also study possible observational effects associated with bounded geodesic motion near topological geons.

On the topology of real algebraic plane curves

DEFF Research Database (Denmark)

Cheng, Jinsan; Lazard, Sylvain; Peñaranda, Luis

2010-01-01

We revisit the problem of computing the topology and geometry of a real algebraic plane curve. The topology is of prime interest but geometric information, such as the position of singular and critical points, is also relevant. A challenge is to compute efficiently this information for the given...... and isolation with rational univariate representations. This has the advantage of avoiding computations with polynomials with algebraic coefficients, even in non-generic positions. Our algorithm isolates critical points in boxes and computes a decomposition of the plane by rectangular boxes. This decomposition...

Progesterone modulation of transmembrane helix-helix interactions between the α-subunit of Na/K-ATPase and phospholipid N-methyltransferase in the oocyte plasma membrane

Directory of Open Access Journals (Sweden)

Askari Amir

2010-05-01

Full Text Available Abstract Background Progesterone binding to the surface of the amphibian oocyte initiates the meiotic divisions. Our previous studies with Rana pipiens oocytes indicate that progesterone binds to a plasma membrane site within the external loop between the M1 and M2 helices of the α-subunit of Na/K-ATPase, triggering a cascade of lipid second messengers and the release of the block at meiotic prophase. We have characterized this site, using a low affinity ouabain binding isoform of the α1-subunit. Results Preparations of isolated plasma membranes from Rana oocytes demonstrate that physiological levels of progesterone (or the non-metabolizable progestin R5020 successively activate phosphatidylethanolamine-N-methyltransferase (PE-NMT and sphingomyelin synthase within seconds. Inhibition of PE-NMT blocks the progesterone induction of meiosis in intact oocytes, whereas its initial product, phosphatidylmonomethylethanolamine (PME, can itself initiate meiosis in the presence of the inhibitor. Published X-ray crystallographic data on Na/K-ATPase, computer-generated 3D projections, heptad repeat analysis and hydrophobic cluster analysis of the transmembrane helices predict that hydrophobic residues L, V, V, I, F and Y of helix M2 of the α1-subunit interact with F, L, G, L, L and F, respectively, of helix M3 of PE-NMT. Conclusion We propose that progesterone binding to the first external loop of the α1-subunit facilitates specific helix-helix interactions between integral membrane proteins to up-regulate PE-NMT, and, that successive interactions between two or more integral plasma membrane proteins induce the signaling cascades which result in completion of the meiotic divisions.

Routing in Networks with Random Topologies

Science.gov (United States)

Bambos, Nicholas

1997-01-01

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

Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.

Science.gov (United States)

Wang, Xu-Hua; Wang, Yong; Liu, A-Ke; Liu, Xiao-Ting; Zhou, Yang; Yao, Qin; Chen, Ke-Ping

2015-04-01

The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

State space Newton's method for topology optimization

DEFF Research Database (Denmark)

Evgrafov, Anton

2014-01-01

/10/1-type constraints on the design field through penalties in many topology optimization approaches. We test the algorithm on the benchmark problems of dissipated power minimization for Stokes flows, and in all cases the algorithm outperforms the traditional first order reduced space/nested approaches...

Efficient reanalysis techniques for robust topology optimization

DEFF Research Database (Denmark)

Amir, Oded; Sigmund, Ole; Lazarov, Boyan Stefanov

2012-01-01

efficient robust topology optimization procedures based on reanalysis techniques. The approach is demonstrated on two compliant mechanism design problems where robust design is achieved by employing either a worst case formulation or a stochastic formulation. It is shown that the time spent on finite...

Applications of automatic differentiation in topology optimization

DEFF Research Database (Denmark)

Nørgaard, Sebastian A.; Sagebaum, Max; Gauger, Nicolas R.

2017-01-01

and is demonstrated on two separate, previously published types of problems in topology optimization. Two separate software packages for automatic differentiation, CoDiPack and Tapenade are considered, and their performance and usability trade-offs are discussed and compared to a hand coded adjoint gradient...

Effect of the topology of the universe on the cosmic microwave background radiation

International Nuclear Information System (INIS)

Caillerie, Samuel

2005-01-01

Whereas geometrical problems of cosmology related to the local shape of the Universe are well described, this research thesis, after some recalls on cosmology, addresses the issue of Universe topology. The author explains how topology can be described by using the conventional image of 'ghost objects', and then shows that topology intervenes at the level of Eigenmodes of different physical values which describe the content of the Universe by discretizing them. Thus, the author proposes a reinterpretation of the behaviour of the power spectrum, and notably the weak quadrupole, in a topological effect related to the lack of modes for this scale. However, the problem of the shape of the Universe remains open as few estimators are actually reliable with respect to present observations. But the author states that some models can be discarded (like non simply connected non Euclidean models), and that some strong constraints can be obtained on the remaining models [fr

DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

Science.gov (United States)

Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

1995-09-05

Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

Research on social communication network evolution based on topology potential distribution

Science.gov (United States)

Zhao, Dongjie; Jiang, Jian; Li, Deyi; Zhang, Haisu; Chen, Guisheng

2011-12-01

Aiming at the problem of social communication network evolution, first, topology potential is introduced to measure the local influence among nodes in networks. Second, from the perspective of topology potential distribution the method of network evolution description based on topology potential distribution is presented, which takes the artificial intelligence with uncertainty as basic theory and local influence among nodes as essentiality. Then, a social communication network is constructed by enron email dataset, the method presented is used to analyze the characteristic of the social communication network evolution and some useful conclusions are got, implying that the method is effective, which shows that topology potential distribution can effectively describe the characteristic of sociology and detect the local changes in social communication network.

Topology with applications topological spaces via near and far

CERN Document Server

Naimpally, Somashekhar A

2013-01-01

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

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

International Nuclear Information System (INIS)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

2015-01-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90) 2 –Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

Energy Technology Data Exchange (ETDEWEB)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

2015-05-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

Topological derivatives of eigenvalues and neural networks in identification of imperfections

International Nuclear Information System (INIS)

Grzanek, M; Nowakowski, A; Sokolowski, J

2008-01-01

Numerical method for identification of imperfections is devised for elliptic spectral problems. The neural networks are employed for numerical solution. The topological derivatives of eigenvalues are used in the learning procedure of the neural networks. The topological derivatives of eigenvalues are determined by the methods of asymptotic analysis in singularly perturbed geometrical domains. The convergence of the numerical method in a probabilistic setting is analysed. The method is presented for the identification of small singular perturbations of the boundary of geometrical domain, however the framework is general and can be used for numerical solutions of inverse problems in the presence of small imperfections in the interior of the domain. Some numerical results are given for elliptic spectral problem in two spatial dimensions.

Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

Science.gov (United States)

Khadria, Ambalika S; Senes, Alessandro

2015-07-01

Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

Complexity of generic biochemical circuits: topology versus strength of interactions

Science.gov (United States)

Tikhonov, Mikhail; Bialek, William

2016-12-01

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

Topology for efficient information dissemination in ad-hoc networking

Science.gov (United States)

Jennings, E.; Okino, C. M.

2002-01-01

In this paper, we explore the information dissemination problem in ad-hoc wirless networks. First, we analyze the probability of successful broadcast, assuming: the nodes are uniformly distributed, the available area has a lower bould relative to the total number of nodes, and there is zero knowledge of the overall topology of the network. By showing that the probability of such events is small, we are motivated to extract good graph topologies to minimize the overall transmissions. Three algorithms are used to generate topologies of the network with guaranteed connectivity. These are the minimum radius graph, the relative neighborhood graph and the minimum spanning tree. Our simulation shows that the relative neighborhood graph has certain good graph properties, which makes it suitable for efficient information dissemination.

The topology of fullerenes

DEFF Research Database (Denmark)

Schwerdtfeger, Peter; Wirz, Lukas; Avery, James Emil

2014-01-01

Fullerenes are carbon molecules that form polyhedral cages. Their bond structures are exactly the planar cubic graphs that have only pentagon and hexagon faces. Strikingly, a number of chemical properties of a fullerene can be derived from its graph structure. A rich mathematics of cubic planar g....... In this paper, we present a general overview of recent topological and graph theoretical developments in fullerene research over the past two decades, describing both solved and open problems....

Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins.

Science.gov (United States)

Chou, K C; Némethy, G; Rumsey, S; Tuttle, R W; Scheraga, H A

1985-12-05

Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed alpha-helix on a right-twisted antiparallel or parallel beta-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the alpha-helix to the beta-sheet. The packing was investigated for a CH3CO-(L-Ala)16-NHCH3 alpha-helix interacting with five-stranded beta-sheets composed of CH3CO-(L-Val)6-NHCH3 chains. All internal and external variables for both the alpha-helix and the beta-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the alpha-helix interacting with both the parallel and the anti-parallel beta-sheet. The classes differ in the orientation of the axis of the alpha-helix relative to the direction of the strands of the right-twisted beta-sheet. In the class with the most favorable arrangement, the alpha-helix is oriented along the strands of the beta-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the alpha-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the beta-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted beta-sheet. In the other, it is oriented along the concave diagonal of the beta-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel beta-sheet are generally similar, although the antiparallel beta-sheet has been found to be more flexible. The major features of 163 observed alpha/beta packing arrangements in 37 proteins are accounted for in terms of the computed

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

CERN Document Server

Fujii, Keisuke

2015-01-01

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

Topological BF field theory description of topological insulators

International Nuclear Information System (INIS)

Cho, Gil Young; Moore, Joel E.

2011-01-01

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

Topological أ-algebras with Cأ-enveloping algebras II

Indian Academy of Sciences (India)

necessarily complete) pro-Cأ-topology which coincides with the relative uniform .... problems in Cأ-algebras, Phillips introduced more general weakly Cأ- .... Banach أ-algebra obtained by completing A=Np in the norm jjxpjjp ¼ pًxق where.

Density based topology optimization of turbulent flow heat transfer systems

DEFF Research Database (Denmark)

Dilgen, Sümer Bartug; Dilgen, Cetin Batur; Fuhrman, David R.

2018-01-01

The focus of this article is on topology optimization of heat sinks with turbulent forced convection. The goal is to demonstrate the extendibility, and the scalability of a previously developed fluid solver to coupled multi-physics and large 3D problems. The gradients of the objective and the con...... in the optimization process, while also demonstrating extension of the methodology to include coupling of heat transfer with turbulent flows.......The focus of this article is on topology optimization of heat sinks with turbulent forced convection. The goal is to demonstrate the extendibility, and the scalability of a previously developed fluid solver to coupled multi-physics and large 3D problems. The gradients of the objective...

Gate-controlled switching between persistent and inverse persistent spin helix states

International Nuclear Information System (INIS)

Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J.

2016-01-01

We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

Gate-controlled switching between persistent and inverse persistent spin helix states

Energy Technology Data Exchange (ETDEWEB)

Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J. [Department of Materials Science, Tohoku University, Sendai 980-8579 (Japan)

2016-03-28

We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

The Quadruple Helix Model Enhancing Innovative Performance Of Indonesian Creative Industry

Directory of Open Access Journals (Sweden)

Sri Wahyu Lelly Hana Setyanti

2017-11-01

Full Text Available The creative industry in Indonesia has contributed positively to the national economic growth. Creative industry grows from the creativity and innovation performance of the business actors. The challenge of creative industry is how to completely understand the creative and innovative processes in business management. Therefore it requires an approach that combines the synergy between academicians entrepreneurs government and society in a quadruple helix model. The objective of this research is to develop a creativity model through a quadruple helix model in improving innovation performance of the creative industry.

Design and synthesis of DNA four-helix bundles

Energy Technology Data Exchange (ETDEWEB)

Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

2011-06-10

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

Design and synthesis of DNA four-helix bundles

International Nuclear Information System (INIS)

Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

2011-01-01

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

SATA Stochastic Algebraic Topology and Applications

Science.gov (United States)

2017-01-23

discretized loops with topological constraints [8]. (10) Applications of critical point theory to statistical inference problems...comparison, which provides background material. 1: Statistics of random functions From a mathematical standpoint, our basic setup here starts... applications , leads to a need for statistical analysis, the first step of which requires asymptotic distribution results for estimators. The first such

Topological Aspects of Information Retrieval.

Science.gov (United States)

Egghe, Leo; Rousseau, Ronald

1998-01-01

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

WATS'17: Workshop Applied Topological Structures, 11 July to 12 July, 2017, Valencia, Illes Baleares (Spain)

Energy Technology Data Exchange (ETDEWEB)

NONE

2017-07-01

General Topology has become one of the fundamental parts of mathematics. Nowadays, as a consequence of an intensive research activity, this mathematical branch has been shown to be very useful in modeling several problems which arise in some branches of applied sciences as Economics, Artificial Intelligence and Computer Science.Due to this increasing interaction between applied and topological problems,we have promoted the creation of an annual workshop to encourage the collaboration between different national and international research groups in the area of General Topology and its Applications.

Topology Optimization - broadening the areas of application

DEFF Research Database (Denmark)

Bendsøe, Martin P.; Lund, Erik; Olhoff, Niels

2005-01-01

This paper deals with recent developments of topology optimization techniques for application in some new types of design problems. The emphasis is on recent work of the Danish research groups at Aalborg University and at the Technical University of Denmark and focus is on the central role that t...

Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

Science.gov (United States)

Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

2009-04-22

The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.

Optimal Topology of Aircraft Rib and Spar Structures under Aeroelastic Loads

Science.gov (United States)

Stanford, Bret K.; Dunning, Peter D.

2014-01-01

Several topology optimization problems are conducted within the ribs and spars of a wing box. It is desired to locate the best position of lightening holes, truss/cross-bracing, etc. A variety of aeroelastic metrics are isolated for each of these problems: elastic wing compliance under trim loads and taxi loads, stress distribution, and crushing loads. Aileron effectiveness under a constant roll rate is considered, as are dynamic metrics: natural vibration frequency and flutter. This approach helps uncover the relationship between topology and aeroelasticity in subsonic transport wings, and can therefore aid in understanding the complex aircraft design process which must eventually consider all these metrics and load cases simultaneously.

Multigrid Implementation of Cellular Automata for Topology Optimisation of Continuum Structures with Design Dependent loads

NARCIS (Netherlands)

Zakhama, R.

2009-01-01

Topology optimisation of continuum structures has become mature enough to be often applied in industry and continues to attract the attention of researchers and software companies in various engineering fields. Traditionally, most available algorithms for solving topology optimisation problems are

Topological mirror superconductivity.

Science.gov (United States)

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

2013-08-02

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

Interactive Topology Optimization

DEFF Research Database (Denmark)

Nobel-Jørgensen, Morten

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

pH-jump induced α-helix folding of poly-L-glutamic acid

International Nuclear Information System (INIS)

Donten, Mateusz L.; Hamm, Peter

2013-01-01

Highlights: ► pH-jump as truly biomimetic tool to initiate non-equilibrium dynamics of biomolecules. ► Design criteria to widen the applicability of pH-jumps are developed. ► Folding of poly-L-Glu in dependence of starting pH, pH jump size and helix length. ► Length dependence provides strong evidence for a nucleation–propagation scenario. - Abstract: pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly-L-glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly-L-glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation–propagation mechanism

The topology of architecture

DEFF Research Database (Denmark)

Marcussen, Lars

2003-01-01

Rummets topologi, Historiens topologi: betragtninger om menneskets orientering til rum - fra hulen over beherskelse af flere akser til det flydende rum.......Rummets topologi, Historiens topologi: betragtninger om menneskets orientering til rum - fra hulen over beherskelse af flere akser til det flydende rum....

Triple Helix and European Union (EU Funding: The case of Latin America, especially Mexico and the Seventh European Framework Program

Directory of Open Access Journals (Sweden)

Jürgen Haberleithner

2010-05-01

Full Text Available The following analysis not only seeks to develop new potential intervention models; it also aims to create a detailed analysis of the existing problems with regards to communication among the active participants of Triple Helix (especially in Mexico. The special situation in Latin America with regards to existing corruption, the unequal distribution of power between the government and the private sector, dependence on other economies and other social issues will be analysed in accordance with the main focus of the investigation. The subsequent linking of potential partners to the development of an initiative for submitting a future Triple Helix/FP7 project represent an important contribution to a longer-term perspective on the preceding investigation. The potential partnerships between Europe and Latin America (in addition to other possible world regions, such as, for example, Pacific Asia will create an initial project draft within the scope of the conference.

Overdetermined elliptic problems in topological disks

Science.gov (United States)

Mira, Pablo

2018-06-01

We introduce a method, based on the Poincaré-Hopf index theorem, to classify solutions to overdetermined problems for fully nonlinear elliptic equations in domains diffeomorphic to a closed disk. Applications to some well-known nonlinear elliptic PDEs are provided. Our result can be seen as the analogue of Hopf's uniqueness theorem for constant mean curvature spheres, but for the general analytic context of overdetermined elliptic problems.

Cosmic Topology

Science.gov (United States)

Luminet, Jean-Pierre

2015-08-01

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

Topological Invariants and Ground-State Wave functions of Topological Insulators on a Torus

Directory of Open Access Journals (Sweden)

Zhong Wang

2014-01-01

Full Text Available We define topological invariants in terms of the ground-state wave functions on a torus. This approach leads to precisely defined formulas for the Hall conductance in four dimensions and the topological magnetoelectric θ term in three dimensions, and their generalizations in higher dimensions. They are valid in the presence of arbitrary many-body interactions and disorder. These topological invariants systematically generalize the two-dimensional Niu-Thouless-Wu formula and will be useful in numerical calculations of disordered topological insulators and strongly correlated topological insulators, especially fractional topological insulators.

Elements of topology

CERN Document Server

Singh, Tej Bahadur

2013-01-01

Topological SpacesMetric Spaces Topologies Derived Concepts Bases Subspaces Continuity and ProductsContinuityProduct TopologyConnectednessConnected Spaces Components Path-Connected Spaces Local ConnectivityConvergence Sequences Nets Filters Hausdorff SpacesCountability Axioms 1st and 2nd Countable Spaces Separable and Lindelöf SpacesCompactnessCompact Spaces Countably Compact Spaces Compact Metric Spaces Locally Compact Spaces Proper Maps Topological Constructions Quotient Spaces Identification Maps Cones, Suspensions and Joins Wedge Sums and Smash Products Adjunction Spaces Coherent Topologie

A topological derivative method for topology optimization

DEFF Research Database (Denmark)

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

2007-01-01

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

Mechanism of death at high temperatures in Helix and Patella

Energy Technology Data Exchange (ETDEWEB)

Grainger, J N.R.

1975-10-01

In Patella vulgata and Helix aspersa which had been killed by exposure to high temperatures, the rates of oxygen consumption of gill, foot muscle and hepatopancreas are remarkably steady when measured at lower temperatures, although the absolute levels are in some cases different from normal animals. These tissues are thus substantially metabolically intact in heat dead individuals. In Helix there is a fall in blood sodium and a rise in blood potassium during heat death. In Patella there is a marked rise in blood Na/sup +/ and a consequent disturbance of the Na/sup +//K/sup +/ ratio. These ionic disturbances are thought to be a prime cause of heat death. The significance of the results is discussed.

Graph topology and gap topology for unstable systems

NARCIS (Netherlands)

Zhu, S.Q.

1989-01-01

A reformation is provided of the graph topology and the gap topology for a general setting (including lumped linear time-invariant systems and distributed linear time-invariant systems) in the frequency domain. Some essential properties and their comparisons are clearly presented in the

Ab initio theory of helix <-> coil phase transition

DEFF Research Database (Denmark)

Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

2008-01-01

In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix <-> random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely ...

Design of photonic bandgap fibers by topology optimization

DEFF Research Database (Denmark)

Dühring, Maria Bayard; Sigmund, Ole; Feurer, Thomas

2010-01-01

A method based on topology optimization is presented to design the cross section of hollow-core photonic bandgap fibers for minimizing energy loss by material absorption. The optical problem is modeled by the timeharmonic wave equation and solved with the finite element program Comsol Multiphysics...

Fault-tolerant topology in the wireless sensor networks for energy depletion and random failure

International Nuclear Information System (INIS)

Liu Bin; Dong Ming-Ru; Yin Rong-Rong; Yin Wen-Xiao

2014-01-01

Nodes in the wireless sensor networks (WSNs) are prone to failure due to energy depletion and poor environment, which could have a negative impact on the normal operation of the network. In order to solve this problem, in this paper, we build a fault-tolerant topology which can effectively tolerate energy depletion and random failure. Firstly, a comprehensive failure model about energy depletion and random failure is established. Then an improved evolution model is presented to generate a fault-tolerant topology, and the degree distribution of the topology can be adjusted. Finally, the relation between the degree distribution and the topological fault tolerance is analyzed, and the optimal value of evolution model parameter is obtained. Then the target fault-tolerant topology which can effectively tolerate energy depletion and random failure is obtained. The performances of the new fault tolerant topology are verified by simulation experiments. The results show that the new fault tolerant topology effectively prolongs the network lifetime and has strong fault tolerance. (general)

Topological and non-topological soliton solutions to some time

Indian Academy of Sciences (India)

Topological and non-topological soliton solutions to some time-fractional differential equations ... These equations have been widely applied in many branches of nonlinear ... Department of Engineering Sciences, Faculty of Technology and ...

Scalar-tensor approach to the construction of theory of topological transformations

International Nuclear Information System (INIS)

Konstantinov, M.Yu.

1985-01-01

Problem of construction of the classical gravitational theory, which solutions in the explicit form contain description of topological transformations, is under study. With this object in view, the scalar-tensor formalism is considered based on a representation of some subclass of space-like hypersurfaces as surfaces of a smooth function level in four-dimensional manifolds. Solutions of the theory along with the Lorentz space-time structure and space-like surface topology define some reference system, but the type of topological transformations is not dependent on the reference system option. All these facts prove the above approach correctness. Two variants of the scalar-tensor theory of topological transformations are considered as an example; one of them is reduced to the Einstein gravitational theory in the regular space region and another represents a nontrivial modification of the Brans-Dikker theory

Epsilon topological accelerating algorithms for difference method for initial-value problems

International Nuclear Information System (INIS)

Hristea, V.; Posirca, M.

1992-01-01

Linear and nonlinear parabolic equations can be solved by discretization methods which lead to linear and nonlinear algebraic systems. The iterative methods (e.g. Gauss - Seidel) show a very slow convergence and instability in the case of nonlinear equations. This paper proposes an ε topological algorithm for accelerating slow iterative methods used in the thermohydraulic code COBRA and the dynamic code ADEP. The results show an executing time approximately ten times lower than original algorithms. (Author)

Knots, topology and quantum field theories

International Nuclear Information System (INIS)

Lusanna, L.

1989-01-01

The title of the workshop, Knots, Topology and Quantum Field Theory, accurate reflected the topics discussed. There have been important developments in mathematical and quantum field theory in the past few years, which had a large impact on physicist thinking. It is historically unusual and pleasing that these developments are taking place as a result of an intense interaction between mathematical physicists and mathematician. On the one hand, topological concepts and methods are playing an increasingly important lead to novel mathematical concepts: for instance, the study of quantum groups open a new chapter in the deformation theory of Lie algebras. These developments at present will lead to new insights into the theory of elementary particles and their interactions. In essence, the talks dealt with three, broadly defined areas of theoretical physics. One was topological quantum field theories, the other the problem of quantum groups and the third one certain aspects of more traditional field theories, such as, for instance, quantum gravity. These topics, however, are interrelated and the general theme of the workshop defies rigid classification; this was evident from the cross references to be found in almo all the talks

De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein.

Science.gov (United States)

Faiella, Marina; Maglio, Ornella; Nastri, Flavia; Lombardi, Angela; Lista, Liliana; Hagen, Wilfred R; Pavone, Vincenzo

2012-12-07

A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.

Directory of Open Access Journals (Sweden)

The Quyen Nguyen

Full Text Available Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC. Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.

Abe homotopy classification of topological excitations under the topological influence of vortices

International Nuclear Information System (INIS)

Kobayashi, Shingo; Kobayashi, Michikazu; Kawaguchi, Yuki; Nitta, Muneto; Ueda, Masahito

2012-01-01

Topological excitations are usually classified by the nth homotopy group π n . However, for topological excitations that coexist with vortices, there are cases in which an element of π n cannot properly describe the charge of a topological excitation due to the influence of the vortices. This is because an element of π n corresponding to the charge of a topological excitation may change when the topological excitation circumnavigates a vortex. This phenomenon is referred to as the action of π 1 on π n . In this paper, we show that topological excitations coexisting with vortices are classified by the Abe homotopy group κ n . The nth Abe homotopy group κ n is defined as a semi-direct product of π 1 and π n . In this framework, the action of π 1 on π n is understood as originating from noncommutativity between π 1 and π n . We show that a physical charge of a topological excitation can be described in terms of the conjugacy class of the Abe homotopy group. Moreover, the Abe homotopy group naturally describes vortex-pair creation and annihilation processes, which also influence topological excitations. We calculate the influence of vortices on topological excitations for the case in which the order parameter manifold is S n /K, where S n is an n-dimensional sphere and K is a discrete subgroup of SO(n+1). We show that the influence of vortices on a topological excitation exists only if n is even and K includes a nontrivial element of O(n)/SO(n).

$L$-Topological Spaces

Directory of Open Access Journals (Sweden)

Ali Bajravani

2018-04-01

Full Text Available ‎By substituting the usual notion of open sets in a topological space $X$ with a suitable collection of maps from $X$ to a frame $L$, we introduce the notion of L-topological spaces. Then, we proceed to study the classical notions and properties of usual topological spaces to the newly defined mathematical notion. Our emphasis would be concentrated on the well understood classical connectedness, quotient and compactness notions, where we prove the Thychonoff's theorem and connectedness property for ultra product of $L$-compact and $L$-connected topological spaces, respectively.

Phase-Field Relaxation of Topology Optimization with Local Stress Constraints

DEFF Research Database (Denmark)

Stainko, Roman; Burger, Martin

2006-01-01

inequality constraints. We discretize the problem by finite elements and solve the arising finite-dimensional programming problems by a primal-dual interior point method. Numerical experiments for problems with local stress constraints based on different criteria indicate the success and robustness......We introduce a new relaxation scheme for structural topology optimization problems with local stress constraints based on a phase-field method. In the basic formulation we have a PDE-constrained optimization problem, where the finite element and design analysis are solved simultaneously...

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

Science.gov (United States)

Sakaue, Takahiro; Nakajima, Chihiro H

2016-04-01

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

Topological superconductors: a review.

Science.gov (United States)

Sato, Masatoshi; Ando, Yoichi

2017-07-01

This review elaborates pedagogically on the fundamental concept, basic theory, expected properties, and materials realizations of topological superconductors. The relation between topological superconductivity and Majorana fermions are explained, and the difference between dispersive Majorana fermions and a localized Majorana zero mode is emphasized. A variety of routes to topological superconductivity are explained with an emphasis on the roles of spin-orbit coupling. Present experimental situations and possible signatures of topological superconductivity are summarized with an emphasis on intrinsic topological superconductors.

Topological entropy of continuous functions on topological spaces

International Nuclear Information System (INIS)

Liu Lei; Wang Yangeng; Wei Guo

2009-01-01

Adler, Konheim and McAndrew introduced the concept of topological entropy of a continuous mapping for compact dynamical systems. Bowen generalized the concept to non-compact metric spaces, but Walters indicated that Bowen's entropy is metric-dependent. We propose a new definition of topological entropy for continuous mappings on arbitrary topological spaces (compactness, metrizability, even axioms of separation not necessarily required), investigate fundamental properties of the new entropy, and compare the new entropy with the existing ones. The defined entropy generates that of Adler, Konheim and McAndrew and is metric-independent for metrizable spaces. Yet, it holds various basic properties of Adler, Konheim and McAndrew's entropy, e.g., the entropy of a subsystem is bounded by that of the original system, topologically conjugated systems have a same entropy, the entropy of the induced hyperspace system is larger than or equal to that of the original system, and in particular this new entropy coincides with Adler, Konheim and McAndrew's entropy for compact systems

Topology, the Wilson flow and the HMC algorithm

CERN Document Server

Luscher, Martin

2010-01-01

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

Controlling chirality with helix inversion in cholesteric liquid crystals

NARCIS (Netherlands)

Katsonis, Nathalie Hélène; Lacaze, E.; Ferrarini, A.

2012-01-01

The helical organization of cholesteric liquid crystals is omnipresent in living matter. Achieving control over the structure of the cholesteric helix consequently holds great potential for developing stimuli-responsive materials matching the level of sophistication of biological systems. In

Toric topology

CERN Document Server

Buchstaber, Victor M

2015-01-01

This book is about toric topology, a new area of mathematics that emerged at the end of the 1990s on the border of equivariant topology, algebraic and symplectic geometry, combinatorics, and commutative algebra. It has quickly grown into a very active area with many links to other areas of mathematics, and continues to attract experts from different fields. The key players in toric topology are moment-angle manifolds, a class of manifolds with torus actions defined in combinatorial terms. Construction of moment-angle manifolds relates to combinatorial geometry and algebraic geometry of toric v

Topological insulators

CERN Document Server

Franz, Marcel

2013-01-01

Topological Insulators, volume six in the Contemporary Concepts of Condensed Matter Series, describes the recent revolution in condensed matter physics that occurred in our understanding of crystalline solids. The book chronicles the work done worldwide that led to these discoveries and provides the reader with a comprehensive overview of the field. Starting in 2004, theorists began to explore the effect of topology on the physics of band insulators, a field previously considered well understood. However, the inclusion of topology brings key new elements into this old field. Whereas it was

Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

Science.gov (United States)

Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

2014-01-27

Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

Science.gov (United States)

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

Topology optimization in acoustics and elasto-acoustics via a level-set method

Science.gov (United States)

Desai, J.; Faure, A.; Michailidis, G.; Parry, G.; Estevez, R.

2018-04-01

Optimizing the shape and topology (S&T) of structures to improve their acoustic performance is quite challenging. The exact position of the structural boundary is usually of critical importance, which dictates the use of geometric methods for topology optimization instead of standard density approaches. The goal of the present work is to investigate different possibilities for handling topology optimization problems in acoustics and elasto-acoustics via a level-set method. From a theoretical point of view, we detail two equivalent ways to perform the derivation of surface-dependent terms and propose a smoothing technique for treating problems of boundary conditions optimization. In the numerical part, we examine the importance of the surface-dependent term in the shape derivative, neglected in previous studies found in the literature, on the optimal designs. Moreover, we test different mesh adaptation choices, as well as technical details related to the implicit surface definition in the level-set approach. We present results in two and three-space dimensions.

On projection methods, convergence and robust formulations in topology optimization

DEFF Research Database (Denmark)

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

2011-01-01

alleviated using various projection methods. In this paper we show that simple projection methods do not ensure local mesh-convergence and propose a modified robust topology optimization formulation based on erosion, intermediate and dilation projections that ensures both global and local mesh-convergence.......Mesh convergence and manufacturability of topology optimized designs have previously mainly been assured using density or sensitivity based filtering techniques. The drawback of these techniques has been gray transition regions between solid and void parts, but this problem has recently been...

Convex integration theory solutions to the h-principle in geometry and topology

CERN Document Server

Spring, David

1998-01-01

This book provides a comprehensive study of convex integration theory in immersion-theoretic topology. Convex integration theory, developed originally by M. Gromov, provides general topological methods for solving the h-principle for a wide variety of problems in differential geometry and topology, with applications also to PDE theory and to optimal control theory. Though topological in nature, the theory is based on a precise analytical approximation result for higher order derivatives of functions, proved by M. Gromov. This book is the first to present an exacting record and exposition of all of the basic concepts and technical results of convex integration theory in higher order jet spaces, including the theory of iterated convex hull extensions and the theory of relative h-principles. A second feature of the book is its detailed presentation of applications of the general theory to topics in symplectic topology, divergence free vector fields on 3-manifolds, isometric immersions, totally real embeddings, u...

Topological insulators, topological superconductors and Weyl fermion semimetals: discoveries, perspectives and outlooks

International Nuclear Information System (INIS)

Hasan, M Zahid; Xu, Su-Yang; Bian, Guang

2015-01-01

Unlike string theory, topological physics in lower dimensional condensed matter systems is an experimental reality since the bulk-boundary correspondence can be probed experimentally in lower dimensions. In addition, recent experimental discoveries of non-quantum-Hall-like topological insulators, topological superconductors, Weyl semimetals and other topological states of matter also signal a clear departure from the quantum-Hall-effect-like transport paradigm that has dominated the field since the 1980s. It is these new forms of matter that enabled realizations of topological-Dirac, Weyl cones, helical-Cooper-pairs, Fermi-arc-quasiparticles and other emergent phenomena in fine-tuned photoemission (ARPES) experiments since ARPES experiments directly allow the study of bulk-boundary (topological) correspondence. In this proceeding we provide a brief overview of the key experiments and discuss our perspectives regarding the new research frontiers enabled by these experiments. Taken collectively, we argue in favor of the emergence of ‘topological-condensed-matter-physics’ in laboratory experiments for which a variety of theoretical concepts over the last 80 years paved the way. (review)

Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

Directory of Open Access Journals (Sweden)

Wuyi Liu

2013-01-01

Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

Science.gov (United States)

Urano, Ryo; Okamoto, Yuko

2015-12-01

We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

From topology to geometry

International Nuclear Information System (INIS)

Eberhart, M.

1996-01-01

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

Three-dimensional fractional topological insulators in coupled Rashba layers

Science.gov (United States)

Volpez, Yanick; Loss, Daniel; Klinovaja, Jelena

2017-08-01

We propose a model of three-dimensional topological insulators consisting of weakly coupled electron- and hole-gas layers with Rashba spin-orbit interaction stacked along a given axis. We show that in the presence of strong electron-electron interactions the system realizes a fractional strong topological insulator, where the rotational symmetry and condensation energy arguments still allow us to treat the problem as quasi-one-dimensional with bosonization techniques. We also show that if Rashba and Dresselhaus spin-orbit interaction terms are equally strong, by doping the system with magnetic impurities, one can bring it into the Weyl semimetal phase.

Topological Acoustics

Science.gov (United States)

Yang, Zhaoju; Gao, Fei; Shi, Xihang; Lin, Xiao; Gao, Zhen; Chong, Yidong; Zhang, Baile

2015-03-01

The manipulation of acoustic wave propagation in fluids has numerous applications, including some in everyday life. Acoustic technologies frequently develop in tandem with optics, using shared concepts such as waveguiding and metamedia. It is thus noteworthy that an entirely novel class of electromagnetic waves, known as "topological edge states," has recently been demonstrated. These are inspired by the electronic edge states occurring in topological insulators, and possess a striking and technologically promising property: the ability to travel in a single direction along a surface without backscattering, regardless of the existence of defects or disorder. Here, we develop an analogous theory of topological fluid acoustics, and propose a scheme for realizing topological edge states in an acoustic structure containing circulating fluids. The phenomenon of disorder-free one-way sound propagation, which does not occur in ordinary acoustic devices, may have novel applications for acoustic isolators, modulators, and transducers.

General Topology of the Universe

OpenAIRE

Pandya, Aalok

2002-01-01

General topology of the universe is descibed. It is concluded that topology of the present universe is greater or stronger than the topology of the universe in the past and topology of the future universe will be stronger or greater than the present topology of the universe. Consequently, the universe remains unbounded.

Transportation Network Topologies

Science.gov (United States)

Holmes, Bruce J.; Scott, John

2004-01-01

A discomforting reality has materialized on the transportation scene: our existing air and ground infrastructures will not scale to meet our nation's 21st century demands and expectations for mobility, commerce, safety, and security. The consequence of inaction is diminished quality of life and economic opportunity in the 21st century. Clearly, new thinking is required for transportation that can scale to meet to the realities of a networked, knowledge-based economy in which the value of time is a new coin of the realm. This paper proposes a framework, or topology, for thinking about the problem of scalability of the system of networks that comprise the aviation system. This framework highlights the role of integrated communication-navigation-surveillance systems in enabling scalability of future air transportation networks. Scalability, in this vein, is a goal of the recently formed Joint Planning and Development Office for the Next Generation Air Transportation System. New foundations for 21st thinking about air transportation are underpinned by several technological developments in the traditional aircraft disciplines as well as in communication, navigation, surveillance and information systems. Complexity science and modern network theory give rise to one of the technological developments of importance. Scale-free (i.e., scalable) networks represent a promising concept space for modeling airspace system architectures, and for assessing network performance in terms of scalability, efficiency, robustness, resilience, and other metrics. The paper offers an air transportation system topology as framework for transportation system innovation. Successful outcomes of innovation in air transportation could lay the foundations for new paradigms for aircraft and their operating capabilities, air transportation system architectures, and airspace architectures and procedural concepts. The topology proposed considers air transportation as a system of networks, within which

Machine learning topological states

Science.gov (United States)

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

2017-11-01

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

Self-assembled RNA-triple-helix hydrogel scaffold for microRNA modulation in the tumour microenvironment

Science.gov (United States)

Conde, João; Oliva, Nuria; Atilano, Mariana; Song, Hyun Seok; Artzi, Natalie

2016-03-01

The therapeutic potential of miRNA (miR) in cancer is limited by the lack of efficient delivery vehicles. Here, we show that a self-assembled dual-colour RNA-triple-helix structure comprising two miRNAs--a miR mimic (tumour suppressor miRNA) and an antagomiR (oncomiR inhibitor)--provides outstanding capability to synergistically abrogate tumours. Conjugation of RNA triple helices to dendrimers allows the formation of stable triplex nanoparticles, which form an RNA-triple-helix adhesive scaffold upon interaction with dextran aldehyde, the latter able to chemically interact and adhere to natural tissue amines in the tumour. We also show that the self-assembled RNA-triple-helix conjugates remain functional in vitro and in vivo, and that they lead to nearly 90% levels of tumour shrinkage two weeks post-gel implantation in a triple-negative breast cancer mouse model. Our findings suggest that the RNA-triple-helix hydrogels can be used as an efficient anticancer platform to locally modulate the expression of endogenous miRs in cancer.

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

Science.gov (United States)

Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

2012-09-26

Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

Ordered groups and topology

CERN Document Server

Clay, Adam

2016-01-01

This book deals with the connections between topology and ordered groups. It begins with a self-contained introduction to orderable groups and from there explores the interactions between orderability and objects in low-dimensional topology, such as knot theory, braid groups, and 3-manifolds, as well as groups of homeomorphisms and other topological structures. The book also addresses recent applications of orderability in the studies of codimension-one foliations and Heegaard-Floer homology. The use of topological methods in proving algebraic results is another feature of the book. The book was written to serve both as a textbook for graduate students, containing many exercises, and as a reference for researchers in topology, algebra, and dynamical systems. A basic background in group theory and topology is the only prerequisite for the reader.

Topology optimization of 3D shell structures with porous infill

DEFF Research Database (Denmark)

Clausen, Anders; Andreassen, Erik; Sigmund, Ole

2017-01-01

This paper presents a 3D topology optimization approach for designing shell structures with a porous or void interior. It is shown that the resulting structures are significantly more robust towards load perturbations than completely solid structures optimized under the same conditions. The study...... indicates that the potential benefit of using porous structures is higher for lower total volume fractions. Compared to earlier work dealing with 2D topology optimization, we found several new effects in 3D problems. Most notably, the opportunity for designing closed shells significantly improves...

What can triple helix frameworks offer to the analysis of eco-innovation dynamics? Theoretical and methodological considerations

DEFF Research Database (Denmark)

Yang, Yan; Holgaard, Jette Egelund; Remmen, Arne

2012-01-01

stakeholder groups are interacting in this connection. Taking the triple helix as the theoretical departure point, this paper discusses the opportunities offered by these triple helix frameworks for analyzing eco-innovation dynamics from both theoretical and practical perspectives. It adds to the debate about......Bringing environmental concerns into focus of innovation processes will in several cases also expand the numbers of actors involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concerns are integrated in the innovation processes and how different...

Living Labs as boundary-spanners between Triple Helix actors

NARCIS (Netherlands)

van Geenhuizen, M.S.

2016-01-01

Living labs are an increasingly popular methodology to enhance innovation. Living labs aim to span boundaries between different organizations, among others Triple helix actors, by acting as a network organization typically in a real-life environment to foster co-creation by user-groups. This paper

The Triple Helix Model and the Knowledge-Based Economy

NARCIS (Netherlands)

Leydesdorff, L.; Meyer, M.

2010-01-01

The Triple Helix model of university-industry-government relations can be generalized from a neo-institutional model of networks of relations to a neo-evolutionary model of how three selection environments operate upon one another. Two selection mechanisms operating upon each other can mutually

Topological phases of topological-insulator thin films

Science.gov (United States)

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

2018-02-01

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

Role of amphipathic helix of a herpesviral protein in membrane deformation and T cell receptor downregulation.

Directory of Open Access Journals (Sweden)

Chan-Ki Min

2008-11-01

Full Text Available Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking. Tyrosine kinase interacting protein (Tip of T lymphotropic Herpesvirus saimiri (HVS is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression. Here, we report that the membrane-proximal amphipathic helix preceding Tip's transmembrane (TM domain mediates lipid raft localization and membrane deformation. In turn, this motif directs Tip's lysosomal trafficking and selective TCR downregulation. The amphipathic helix binds to the negatively charged lipids and induces liposome tubulation, the TM domain mediates oligomerization, and cooperation of the membrane-proximal helix with the TM domain is sufficient for localization to lipid rafts and lysosomal compartments, especially the mutivesicular bodies. These findings suggest that the membrane-proximal amphipathic helix and TM domain provide HVS Tip with the unique ability to deform the cellular membranes in lipid rafts and to downregulate TCRs potentially through MVB formation.

A rare polyglycine type II-like helix motif in naturally occurring proteins.

Science.gov (United States)

Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

2017-11-01

Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

Fine topology and locally Minkowskian manifolds

Science.gov (United States)

Agrawal, Gunjan; Sinha, Soami Pyari

2018-05-01

Fine topology is one of the several well-known topologies of physical and mathematical relevance. In the present paper, it is obtained that the nonempty open sets of different dimensional Minkowski spaces with the fine topology are not homeomorphic. This leads to the introduction of a new class of manifolds. It turns out that the technique developed here is also applicable to some other topologies, namely, the s-topology, space topology, f-topology, and A-topology.

Novel topological descriptors for analyzing biological networks

Directory of Open Access Journals (Sweden)

Varmuza Kurt K

2010-06-01

Full Text Available Abstract Background Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the developed descriptors and graph-theoretical methods does not have the ability to take vertex- and edge-labels into account, e.g., atom- and bond-types when considering molecular graphs. Indeed, this feature is important to characterize biological networks more meaningfully instead of only considering pure topological information. Results In this paper, we put the emphasis on analyzing a special type of biological networks, namely bio-chemical structures. First, we derive entropic measures to calculate the information content of vertex- and edge-labeled graphs and investigate some useful properties thereof. Second, we apply the mentioned measures combined with other well-known descriptors to supervised machine learning methods for predicting Ames mutagenicity. Moreover, we investigate the influence of our topological descriptors - measures for only unlabeled vs. measures for labeled graphs - on the prediction performance of the underlying graph classification problem. Conclusions Our study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully. For instance, we have found that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs are clearly underrepresented so far, the further development of such methods might be valuable and fruitful for solving problems within biological network analysis.

Helical magnetic structure and the anomalous and topological Hall effects in epitaxial B20 Fe1 -yCoyGe films

Science.gov (United States)

Spencer, Charles S.; Gayles, Jacob; Porter, Nicholas A.; Sugimoto, Satoshi; Aslam, Zabeada; Kinane, Christian J.; Charlton, Timothy R.; Freimuth, Frank; Chadov, Stanislav; Langridge, Sean; Sinova, Jairo; Felser, Claudia; Blügel, Stefan; Mokrousov, Yuriy; Marrows, Christopher H.

2018-06-01

Epitaxial films of the B20-structure compound Fe1 -yCoyGe were grown by molecular beam epitaxy on Si (111) substrates. The magnetization varied smoothly from the bulklike values of one Bohr magneton per Fe atom for FeGe to zero for nonmagnetic CoGe. The chiral lattice structure leads to a Dzyaloshinskii-Moriya interaction (DMI), and the films' helical magnetic ground state was confirmed using polarized neutron reflectometry measurements. The pitch of the spin helix, measured by this method, varies with Co content y and diverges at y ˜0.45 . This indicates a zero crossing of the DMI, which we reproduced in calculations using first-principles methods. We also measured the longitudinal and Hall resistivity of our films as a function of magnetic field, temperature, and Co content y . The Hall resistivity is expected to contain contributions from the ordinary, anomalous, and topological Hall effects. Both the anomalous and topological Hall resistivities show peaks around y ˜0.5 . Our first-principles calculations show a peak in the topological Hall constant at this value of y , related to the strong spin polarization predicted for intermediate values of y . Our calculations predict half-metallicity for y =0.6 , consistent with the experimentally observed linear magnetoresistance at this composition, and potentially related to the other unusual transport properties for intermediate value of y . While it is possible to reconcile theory with experiment for the various Hall effects for FeGe, the large topological Hall resistivities for y ˜0.5 are much larger than expected when the very small emergent fields associated with the divergence in the DMI are taken into account.

Topological and sizing optimization of reinforced ribs for a machining centre

Science.gov (United States)

Chen, T. Y.; Wang, C. B.

2008-01-01

The topology optimization technique is applied to improve rib designs of a machining centre. The ribs of the original design are eliminated and new ribs are generated by topology optimization in the same 3D design space containing the original ribs. Two-dimensional plate elements are used to replace the optimum rib topologies formed by 3D rectangular elements. After topology optimization, sizing optimization is used to determine the optimum thicknesses of the ribs. When forming the optimum design problem, multiple configurations of the structure are considered simultaneously. The objective is to minimize rib weight. Static constraints confine displacements of the cutting tool and the workpiece due to cutting forces and the heat generated by spindle bearings. The dynamic constraint requires the fundamental natural frequency of the structure to be greater than a given value in order to reduce dynamic deflection. Compared with the original design, the improvement resulting from this approach is significant.

Efficient Fatigue Analysis of Helix Elements in Umbilicals and Flexible Risers: Theory and Applications

Directory of Open Access Journals (Sweden)

Geir Skeie

2012-01-01

Full Text Available Fatigue analysis of structural components such as helix tensile armors and steel tubes is a critical design issue for dynamic umbilicals and flexible pipes. The basis for assessment of fatigue damage of such elements is the long-term stress cycle distribution at critical locations on the helix elements caused by long-term environmental loading on the system. The long-term stress cycle distribution will hence require global dynamic time domain analysis followed by a detailed cross-sectional analysis in a large number of irregular sea states. An overall computational consistent and efficient fatigue analysis scheme is outlined with due regard of the cross-sectional analysis technique required for fatigue stress calculation with particular attention to the helix elements. The global cross-section is exposed to pure bending, tensile, torsion, and pressure loading. The state of the different cross-section elements is based on the global response. Special emphasis is placed on assessment of friction stresses caused by the stick-slip behavior of helix elements in bending that are of special importance for fatigue life assessments. The described cross-sectional analysis techniques are based on an extensive literature survey and are hence considered to represent industry consensus. The performance of the described calculation scheme is illustrated by case studies.

Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

Science.gov (United States)

Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

2009-09-01

We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

Topology control

NARCIS (Netherlands)

Buchin, K.; Buchin, M.; Wagner, D.; Wattenhofer, R.

2007-01-01

Information between two nodes in a network is sent based on the network topology, the structure of links connecting pairs of nodes of a network. The task of topology control is to choose a connecting subset from all possible links such that the overall network performance is good. For instance, a

Nonlinear time-dependent simulation of helix traveling wave tubes

International Nuclear Information System (INIS)

Peng Wei-Feng; Yang Zhong-Hai; Hu Yu-Lu; Li Jian-Qing; Lu Qi-Ru; Li Bin

2011-01-01

A one-dimensional nonlinear time-dependent theory for helix traveling wave tubes is studied. A generalized electromagnetic field is applied to the expression of the radio frequency field. To simulate the variations of the high frequency structure, such as the pitch taper and the effect of harmonics, the spatial average over a wavelength is substituted by a time average over a wave period in the equation of the radio frequency field. Under this assumption, the space charge field of the electron beam can be treated by a space charge wave model along with the space charge coefficient. The effects of the radio frequency and the space charge fields on the electrons are presented by the equations of the electron energy and the electron phase. The time-dependent simulation is compared with the frequency-domain simulation for a helix TWT, which validates the availability of this theory. (interdisciplinary physics and related areas of science and technology)

Tunable single photonic defect-mode in cholesteric liquid crystals with laser-induced local modifications of helix

International Nuclear Information System (INIS)

Yoshida, Hiroyuki; Lee, Chee Heng; Fujii, Akihiko; Ozaki, Masanori

2006-01-01

The authors demonstrate a tunable single photonic defect-mode in a single cholesteric liquid crystal material based on a structural defect introduced by local modification of the helix. An unpolymerized region of cholesteric liquid crystal acting as the defect was left between two polymerized regions via a two-photon excitation laser-lithography process. Upon polymerization, the cholesteric liquid crystal helix elongated and became thermally stable, and a single photonic defect mode was exhibited due to the contrast in the helix pitch at the defect. The defect mode showed tunability upon heating, and a 36 nm redshift was seen over a temperature range of 30 deg. C

A new topology to mitigate the effect of shading for small photovoltaic installations in rural sub-Saharan Africa

International Nuclear Information System (INIS)

Ubisse, A.; Sebitosi, A.

2009-01-01

Many field researchers have in the past grappled with the problems of energy loss and panel damage as a result of shading and staining of PV panels after installation. A number of solutions have been proposed to try and minimize the effects of this problem in the field. The problem with all these solutions is that they address inter-panel connection topologies for very large installations. No particular attention has been paid to the topologies of individual panels. In sub-Saharan Africa most installations are single panel solar home systems and therefore small shading can result in an entire installation being disabled. This paper aims to study the effect of shading and staining on photovoltaic modules and propose a new topology that will reduce the effect of shading on the performance of individual photovoltaic modules.

Kevlar: Transitioning Helix for Research to Practice

Science.gov (United States)

2016-03-01

x86 binaries, although it can be targeted to any platform that is targeted by IDA Pro. Currently, IDA Pro targets more than 40 processors and...effects its own transformations. Helix/Kevlar then automatically generates SPRI rules for any program variants by essentially performing a “ smart diff...execute permission on the pages of memory it uses, leaving only execute (but not write) permission on the code cache. Strata also watches for attempts

Temperature-dependence of the QCD topological susceptibility

Science.gov (United States)

Kovacs, Tamas G.

2018-03-01

We recently obtained an estimate of the axion mass based on the hypothesis that axions make up most of the dark matter in the universe. A key ingredient for this calculation was the temperature-dependence of the topological susceptibility of full QCD. Here we summarize the calculation of the susceptibility in a range of temperatures from well below the finite temperature cross-over to around 2 GeV. The two main difficulties of the calculation are the unexpectedly slow convergence of the susceptibility to its continuum limit and the poor sampling of nonzero topological sectors at high temperature. We discuss how these problems can be solved by two new techniques, the first one with reweighting using the quark zero modes and the second one with the integration method.

Strain effects in topological insulators: Topological order and the emergence of switchable topological interface states in Sb2Te3/Bi2Te3 heterojunctions

Science.gov (United States)

Aramberri, H.; Muñoz, M. C.

2017-05-01

We investigate the effects of strain on the topological order of the Bi2Se3 family of topological insulators by ab initio first-principles methods. Strain can induce a topological phase transition and we present the phase diagram for the 3D topological insulators, Bi2Te3 , Sb2Te3 , Bi2Se3 , and Sb2Se3 , under combined uniaxial and biaxial strain. Their phase diagram is universal and shows metallic and insulating phases, both topologically trivial and nontrivial. In particular, uniaxial tension can drive the four compounds into a topologically trivial insulating phase. We propose a Sb2Te3/Bi2Te3 heterojunction in which a strain-induced topological interface state arises in the common gap of this normal insulator-topological insulator heterojunction. Unexpectedly, the interface state is confined in the topologically trivial subsystem and is physically protected from ambient impurities. It can be switched on or off by means of uniaxial strain and therefore Sb2Te3 /Bi2Te3 heterojunctions provide a topological system which hosts tunable robust helical interface states with promising spintronic applications.

Element stacking method for topology optimization with material-dependent boundary and loading conditions

DEFF Research Database (Denmark)

Yoon, Gil Ho; Park, Y.K.; Kim, Y.Y.

2007-01-01

A new topology optimization scheme, called the element stacking method, is developed to better handle design optimization involving material-dependent boundary conditions and selection of elements of different types. If these problems are solved by existing standard approaches, complicated finite...... element models or topology optimization reformulation may be necessary. The key idea of the proposed method is to stack multiple elements on the same discretization pixel and select a single or no element. In this method, stacked elements on the same pixel have the same coordinates but may have...... independent degrees of freedom. Some test problems are considered to check the effectiveness of the proposed stacking method....

Neural nets with varying topology for high energy particle recognition. Theory and applications

International Nuclear Information System (INIS)

Perrone, A.L.; Basti, G.; Messi, R.; Paoluzi, L.; Picozza, P.

1995-01-01

In this paper we propose a strategy to solve the problem of parallel compuation based on a dynamic definition of the net topology showing its effectiveness for problems of particle track recognition in high-energy physics. In this way, we can maintain the linear architecture like in the geometric perceptron, but with a partial and dynamic connectivity so to overcome the intrinsic limiations of the geometric perceptron. Namely, the computation is truly parallel because of the partial connectivity but the net topology is always the optimal one because of its dynamic redefinition on the single input pattern. For these properties, we call this new architecture dynamic perceptron

Hybrid Spatial Data Model for Indoor Space: Combined Topology and Grid

Directory of Open Access Journals (Sweden)

Zhiyong Lin

2017-11-01

Full Text Available The construction and application of an indoor spatial data model is an important prerequisite to meet the requirements of diversified indoor spatial location services. The traditional indoor spatial topology model focuses on the construction of topology information. It has high path analysis and query efficiency, but ignores the spatial location information. The grid model retains the plane position information by grid, but increases the data volume and complexity of the model and reduces the efficiency of the model analysis. This paper presents a hybrid model for interior space based on topology and grid. Based on the spatial meshing and spatial division of the interior space, the model retains the position information and topological connectivity information of the interior space by establishing the connection or affiliation between the grid subspace and the topological subspace. The model improves the speed of interior spatial analysis and solves the problem of the topology information and location information updates not being synchronized. In this study, the A* shortest path query efficiency of typical daily indoor activities under the grid model and the hybrid model were compared for the indoor plane of an apartment and a shopping mall. The results obtained show that the hybrid model is 43% higher than the A* algorithm of the grid model as a result of the existence of topology communication information. This paper provides a useful idea for the establishment of a highly efficient and highly available interior spatial data model.

Pure spinor formalism as an N = 2 topological string

International Nuclear Information System (INIS)

Berkovits, Nathan

2005-01-01

Following suggestions of Nekrasov and Siegel, a non-minimal set of fields are added to the pure spinor formalism for the superstring. Twisted c-circumflex = 3 N = 2 generators are then constructed where the pure spinor BRST operator is the fermionic spin-one generator, and the formalism is interpreted as a critical topological string. Three applications of this topological string theory include the super-Poincare covariant computation of multiloop superstring amplitudes without picture-changing operators, the construction of a cubic open superstring field theory without contact-term problems, and a new four-dimensional version of the pure spinor formalism which computes F-terms in the spacetime action

Homogenization and structural topology optimization theory, practice and software

CERN Document Server

Hassani, Behrooz

1999-01-01

Structural topology optimization is a fast growing field that is finding numerous applications in automotive, aerospace and mechanical design processes. Homogenization is a mathematical theory with applications in several engineering problems that are governed by partial differential equations with rapidly oscillating coefficients Homogenization and Structural Topology Optimization brings the two concepts together and successfully bridges the previously overlooked gap between the mathematical theory and the practical implementation of the homogenization method. The book is presented in a unique self-teaching style that includes numerous illustrative examples, figures and detailed explanations of concepts. The text is divided into three parts which maintains the book's reader-friendly appeal.

Algebraic K- and L-theory and applications to the topology of manifolds

Energy Technology Data Exchange (ETDEWEB)

Hambleton, I [Department of Mathematics and Statistics, McMaster University, Hamilton (Canada)

2002-08-15

The development of geometric topology has led to the identification of specific algebraic structures of great richness and usefulness. A common theme in this area is the study of algebraic invariants of discrete groups or rings by topological methods. The resulting subject is now called algebraic K-theory. The purpose of these lecture notes is to survey some of the main constructions and techniques in algebraic K-theory, together with an indication of the topological backnd and applications. More details about proofs can be found in the references. The material is organized into some introductory sections, concerning linear and unitary K-theory, followed by descriptions of four important geometric problems and their related algebraic methods.

New topological theories and conjugacy classes of the Weyl group

International Nuclear Information System (INIS)

Hollowood, T.J.; Miramontes, J.L.

1993-01-01

The problem of interpreting a set of W-algebra constraints constructed in terms of an arbitrarily twisted scalar field as recursion relations of some topological theory is addressed. In this picture, the models of topological gravity coupled to A, D or E topological matter, correspond to taking the scalar field twisted by the Coxeter element of the Weyl group. It turns out that not all conjugacy classes of the Weyl group lead to models which allow for such an interpretation. For example, it is shown that for the A algebras there are two possible choices for the conjugacy class, giving a new set of theories in addition to the conventional ones. Furthermore, it is shown how the new series of theories contains the conventional series as a subsector. A tentative interpretation of this new series in terms of intersection theory is presented. (orig.)

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

Science.gov (United States)

Divan, Deepakraj M.

1990-01-01

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

A Cp-theory problem book special features of function spaces

CERN Document Server

Tkachuk, Vladimir V

2014-01-01

The books in Vladimir Tkachuk’s A Cp-Theory Problem Book series will be the ‘go to’ texts for basic reference to Cp-theory. This second volume, Special Features of Function Spaces, gives a reasonably complete coverage of Cp-theory, systematically introducing each of the major topics and providing  500 carefully selected problems and exercises with complete solutions. Bonus results and open problems are also given. The text is designed to bring a dedicated reader from basic topological principles to the frontiers of modern research covering a wide variety of topics in Cp-theory and general topology at the professional level. The first volume, Topological and Function Spaces © 2011, provided an introduction from scratch to Cp-theory and general topology, preparing the reader for a professional understanding of Cp-theory in the last section of its main text. This second volume continues from the first, and can be used as a textbook for courses in both Cp-theory and general topology as well as a referenc...

Robustness of Topological Superconductivity in Solid State Hybrid Structures

Science.gov (United States)

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

Topological massive sigma models

International Nuclear Information System (INIS)

Lambert, N.D.

1995-01-01

In this paper we construct topological sigma models which include a potential and are related to twisted massive supersymmetric sigma models. Contrary to a previous construction these models have no central charge and do not require the manifold to admit a Killing vector. We use the topological massive sigma model constructed here to simplify the calculation of the observables. Lastly it is noted that this model can be viewed as interpolating between topological massless sigma models and topological Landau-Ginzburg models. ((orig.))

Topics in general topology

CERN Document Server

Morita, K

1989-01-01

Being an advanced account of certain aspects of general topology, the primary purpose of this volume is to provide the reader with an overview of recent developments.The papers cover basic fields such as metrization and extension of maps, as well as newly-developed fields like categorical topology and topological dynamics. Each chapter may be read independently of the others, with a few exceptions. It is assumed that the reader has some knowledge of set theory, algebra, analysis and basic general topology.

Topological nearly entropy

Science.gov (United States)

Gulamsarwar, Syazwani; Salleh, Zabidin

2017-08-01

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

Architectural design for a topological cluster state quantum computer

International Nuclear Information System (INIS)

Devitt, Simon J; Munro, William J; Nemoto, Kae; Fowler, Austin G; Stephens, Ashley M; Greentree, Andrew D; Hollenberg, Lloyd C L

2009-01-01

The development of a large scale quantum computer is a highly sought after goal of fundamental research and consequently a highly non-trivial problem. Scalability in quantum information processing is not just a problem of qubit manufacturing and control but it crucially depends on the ability to adapt advanced techniques in quantum information theory, such as error correction, to the experimental restrictions of assembling qubit arrays into the millions. In this paper, we introduce a feasible architectural design for large scale quantum computation in optical systems. We combine the recent developments in topological cluster state computation with the photonic module, a simple chip-based device that can be used as a fundamental building block for a large-scale computer. The integration of the topological cluster model with this comparatively simple operational element addresses many significant issues in scalable computing and leads to a promising modular architecture with complete integration of active error correction, exhibiting high fault-tolerant thresholds.

Distributed cooperative guidance for multiple missiles with fixed and switching communication topologies

Directory of Open Access Journals (Sweden)

Qilun ZHAO

2017-08-01

Full Text Available This study investigates cooperative guidance problems for multiple missiles with fixed and switching directed communication topologies. A two-step guidance strategy is proposed to realize the simultaneous attack. In the first step, a distributed cooperative guidance law is designed using local neighboring information for multiple missiles to achieve consensus on range-to-go and leading angle. The second step begins when the consensus of multiple missiles is realized. During the second step, multiple missiles disconnect from each other and hit the target using the proportional navigation guidance law. First, based on the local neighboring communications, a sufficient condition for multiple missiles to realize simultaneous attack with a fixed communication topology is presented, where the topology is only required to have a directed spanning tree. Then, the results are extended to the case of switching communication topologies. Finally, numerical simulations are provided to validate the theoretical results.

Comparative study on gene set and pathway topology-based enrichment methods.

Science.gov (United States)

Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

2015-10-22

Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both

Enabling Controlling Complex Networks with Local Topological Information.

Science.gov (United States)

Li, Guoqi; Deng, Lei; Xiao, Gaoxi; Tang, Pei; Wen, Changyun; Hu, Wuhua; Pei, Jing; Shi, Luping; Stanley, H Eugene

2018-03-15

Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs. For large complex networks without global information of network topology, both problems remain essentially open. Here we combine graph theory and control theory for tackling the two problems in one go, using only local network topology information. For the structural controllability problem, a distributed local-game matching method is proposed, where every node plays a simple Bayesian game with local information and local interactions with adjacent nodes, ensuring a suboptimal solution at a linear complexity. Starring from any structural controllability solution, a minimizing longest control path method can efficiently reach a good solution for the optimal control in large networks. Our results provide solutions for distributed complex network control and demonstrate a way to link the structural controllability and optimal control together.

Some problems in differential geometry and topology

International Nuclear Information System (INIS)

Donaldson, S K

2008-01-01

This does not attempt to be a systematic overview or to present a comprehensive list of problems. We outline some questions in three different areas which seem interesting to the author. Experts will learn little that is new; our goal is to give some picture of the fields for non-specialists. (open problem)

Efficient use of iterative solvers in nested topology optimization

DEFF Research Database (Denmark)

Amir, Oded; Stolpe, Mathias; Sigmund, Ole

2009-01-01

In the nested approach to structural optimization, most of the computational effort is invested in the solution of the finite element analysis equations. In this study, it is suggested to reduce this computational cost by using an approximation to the solution of the nested problem, generated...... measures. The approximation is shown to be sufficiently accurate for the practical purpose of optimization even though the nested equation system is not solved accurately. The approach is tested on several medium-scale topology optimization problems, including three dimensional minimum compliance problems...

Efficient use of iterative solvers in nested topology optimization

DEFF Research Database (Denmark)

Amir, Oded; Stolpe, Mathias; Sigmund, Ole

2010-01-01

In the nested approach to structural optimization, most of the computational effort is invested in the solution of the analysis equations. In this study, it is suggested to reduce this computational cost by using an approximation to the solution of the analysis problem, generated by a Krylov....... The approximation is computationally shown to be sufficiently accurate for the purpose of optimization though the nested equation system is not necessarily solved accurately. The approach is tested on several large-scale topology optimization problems, including minimum compliance problems and compliant mechanism...

Rotational symmetry and the transformation of innovation systems in a Triple Helix of university-industry-government relations

NARCIS (Netherlands)

Ivanova, I.A.; Leydesdorff, L.

2014-01-01

Using a mathematical model, we show that a Triple Helix (TH) system contains self-interaction, and therefore self-organization of innovations can be expected in waves, whereas a Double Helix (DH) remains determined by its linear constituents. (The mathematical model is fully elaborated in the

Probing the topological properties of complex networks modeling short written texts.

Directory of Open Access Journals (Sweden)

Diego R Amancio

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

The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

Science.gov (United States)

Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

2018-04-09

The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

Signatures of topological superconductivity

Energy Technology Data Exchange (ETDEWEB)

Peng, Yang

2017-07-19

The prediction and experimental discovery of topological insulators brought the importance of topology in condensed matter physics into the limelight. Topology hence acts as a new dimension along which more and more new states of matter start to emerge. One of these topological states of matter, namely topological superconductors, comes into the focus because of their gapless excitations. These gapless excitations, especially in one dimensional topological superconductors, are Majorana zero modes localized at the ends of the superconductor and exhibit exotic nonabelian statistics, which can be potentially applied to fault-tolerant quantum computation. Given their highly interesting physical properties and potential applications to quantum computation, both theorists and experimentalists spend great efforts to realize topological supercondoctors and to detect Majoranas. In two projects within this thesis, we investigate the properties of Majorana zero modes in realistic materials which are absent in simple theoretical models. We find that the superconducting proximity effect, an essential ingredient in all existing platforms for topological superconductors, plays a significant role in determining the localization property of the Majoranas. Strong proximity coupling between the normal system and the superconducting substrate can lead to strongly localized Majoranas, which can explain the observation in a recent experiment. Motivated by experiments in Molenkamp's group, we also look at realistic quantum spin Hall Josephson junctions, in which charge puddles acting as magnetic impurities are coupled to the helical edge states. We find that with this setup, the junction generically realizes an exotic 8π periodic Josephson effect, which is absent in a pristine Josephson junction. In another two projects, we propose more pronounced signatures of Majoranas that are accessible with current experimental techniques. The first one is a transport measurement, which uses

Topology for Statistical Modeling of Petascale Data

Energy Technology Data Exchange (ETDEWEB)

Pascucci, Valerio [Univ. of Utah, Salt Lake City, UT (United States); Levine, Joshua [Univ. of Utah, Salt Lake City, UT (United States); Gyulassy, Attila [Univ. of Utah, Salt Lake City, UT (United States); Bremer, P. -T. [Univ. of Utah, Salt Lake City, UT (United States)

2013-10-31

Many commonly used algorithms for mathematical analysis do not scale well enough to accommodate the size or complexity of petascale data produced by computational simulations. The primary goal of this project is to develop new mathematical tools that address both the petascale size and uncertain nature of current data. At a high level, the approach of the entire team involving all three institutions is based on the complementary techniques of combinatorial topology and statistical modelling. In particular, we use combinatorial topology to filter out spurious data that would otherwise skew statistical modelling techniques, and we employ advanced algorithms from algebraic statistics to efficiently find globally optimal fits to statistical models. The overall technical contributions can be divided loosely into three categories: (1) advances in the field of combinatorial topology, (2) advances in statistical modelling, and (3) new integrated topological and statistical methods. Roughly speaking, the division of labor between our 3 groups (Sandia Labs in Livermore, Texas A&M in College Station, and U Utah in Salt Lake City) is as follows: the Sandia group focuses on statistical methods and their formulation in algebraic terms, and finds the application problems (and data sets) most relevant to this project, the Texas A&M Group develops new algebraic geometry algorithms, in particular with fewnomial theory, and the Utah group develops new algorithms in computational topology via Discrete Morse Theory. However, we hasten to point out that our three groups stay in tight contact via videconference every 2 weeks, so there is much synergy of ideas between the groups. The following of this document is focused on the contributions that had grater direct involvement from the team at the University of Utah in Salt Lake City.

Topology Optimization - Engineering Contribution to Architectural Design

Science.gov (United States)

Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2017-10-01

The idea of the topology optimization is to find within a considered design domain the distribution of material that is optimal in some sense. Material, during optimization process, is redistributed and parts that are not necessary from objective point of view are removed. The result is a solid/void structure, for which an objective function is minimized. This paper presents an application of topology optimization to multi-material structures. The design domain defined by shape of a structure is divided into sub-regions, for which different materials are assigned. During design process material is relocated, but only within selected region. The proposed idea has been inspired by architectural designs like multi-material facades of buildings. The effectiveness of topology optimization is determined by proper choice of numerical optimization algorithm. This paper utilises very efficient heuristic method called Cellular Automata. Cellular Automata are mathematical, discrete idealization of a physical systems. Engineering implementation of Cellular Automata requires decomposition of the design domain into a uniform lattice of cells. It is assumed, that the interaction between cells takes place only within the neighbouring cells. The interaction is governed by simple, local update rules, which are based on heuristics or physical laws. The numerical studies show, that this method can be attractive alternative to traditional gradient-based algorithms. The proposed approach is evaluated by selected numerical examples of multi-material bridge structures, for which various material configurations are examined. The numerical studies demonstrated a significant influence the material sub-regions location on the final topologies. The influence of assumed volume fraction on final topologies for multi-material structures is also observed and discussed. The results of numerical calculations show, that this approach produces different results as compared with classical one

Ultrafilters and topologies on groups

CERN Document Server

Zelenyuk, Yevhen

2011-01-01

This book presents the relationship between ultrafilters and topologies on groups. It shows how ultrafilters are used in constructing topologies on groups with extremal properties and how topologies on groups serve in deriving algebraic results aboutultrafilters. Topics covered include: topological and left topological groups, ultrafilter semigroups, local homomorphisms and automorphisms, subgroups and ideal structure of ßG, almost maximal spaces and projectives of finite semigroups, resolvability of groups. This is a self-contained book aimed at graduate students and researchers working in to

Fermionic Casimir effect with helix boundary condition

International Nuclear Information System (INIS)

Zhai, Xiang-hua; Li, Xin-zhou; Feng, Chao-Jun

2011-01-01

In this paper, we consider the fermionic Casimir effect under a new type of space-time topology using the concept of quotient topology. The relation between the new topology and that in Feng and Li (Phys. Lett. B 691:167, 2010), Zhai et al. (Mod. Phys. Lett. A 26:669, 2011) is something like that between a Moebius strip and a cylindric. We obtain the exact results of the Casimir energy and force for the massless and massive Dirac fields in the (D+1)-dimensional space-time. For both massless and massive cases, there is a Z 2 symmetry for the Casimir energy. To see the effect of the mass, we compare the result with that of the massless one and we found that the Casimir force approaches the result of the force in the massless case when the mass tends to zero and vanishes when the mass tends to infinity. (orig.)

Geometry and topology in hamiltonian dynamics and statistical mechanics

CERN Document Server

Pettini, Marco

2007-01-01

Explores the foundations of hamiltonian dynamical systems and statistical mechanics, in particular phase transitions, from the point of view of geometry and topology. This book provides an overview of the research in the area. Using geometrical thinking to solve fundamental problems in these areas could be highly productive

Polynomial invariants for torus knots and topological strings

International Nuclear Information System (INIS)

Labastida, J.M.F.

2001-01-01

We make a precision test of a recently proposed conjecture relating Chern-Simons gauge theory to topological string theory on the resolution of the conifold. First, we develop a systematic procedure to extract string amplitudes from vacuum expectation values (vevs) of Wilson loops in Chern-Simons gauge theory, and then we evaluate these vevs in arbitrary irreducible representations of SU(N) for torus knots. We find complete agreement with the predictions derived from the target space interpretation of the string amplitudes. We also show that the structure of the free energy of topological open string theory gives further constraints on the Chern-Simons vevs. Our work provides strong evidence towards an interpretation of knot polynomial invariants as generating functions associated to enumerative problems. (orig.)

Inverse design of dielectric materials by topology optimization

DEFF Research Database (Denmark)

Otomori, M.; Andkjær, Jacob Anders; Sigmund, Ole

2012-01-01

The capabilities and operation of electromagnetic devices can be dramatically enhanced if artificial materials that provide certain prescribed properties can be designed and fabricated. This paper presents a systematic methodology for the design of dielectric materials with prescribed electric...... permittivity. A gradient-based topology optimization method is used to find the distribution of dielectric material for the unit cell of a periodic microstructure composed of one or two dielectric materials. The optimization problem is formulated as a problem to minimize the square of the difference between...

Toward the topology design of mechanisms that exhibit snap-through behavior

DEFF Research Database (Denmark)

Burns, T. E.; Sigmund, Ole

2004-01-01

Topology optimization has proven to be a powerful method for the conceptual design of structures and mechanisms. In previously published work, we concentrated on the development of numerical methods that accommodate the finite deformation and incorporated these analyses into the topology...... optimization. We demonstrated by relatively straightforward transversely loaded clamped-clamped beam examples that topology optimization can be used to design structures that experience snap-through behavior. Here, we focus our attention on the design problem formulation where the goal is to develop a general...... approach for the design of mechanisms that experience more complex snap-through behavior. A multiphase design strategy is outlined, numerous significant challenges to this complex design process are discussed, and several examples are presented that demonstrate progress toward this goal. (C) 2004 Elsevier...

Broadcasting Topology and Routing Information in Computer Networks

Science.gov (United States)

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

Some topological properties of the Inverse Lens Mapping

Energy Technology Data Exchange (ETDEWEB)

Mediavilla, T; Ariza, O [Departamento de Estadistica e Investigacion Operativa, Universidad de Cadiz, Avda de Ramon Puyol, s/n 11202 Algeciras (Spain); Mediavilla, E; Oscoz, A [Instituto de Astrofisica de Canarias, Avda Via Lactea s/n, La Laguna (Spain); Munoz, J A, E-mail: teresa.mediavilla@ca.uca.es, E-mail: octavio.ariza@uca.es, E-mail: emg@iac.es, E-mail: jmunoz@uv.es, E-mail: aoscoz@iac.es [Departamento de Astronomia y Astrofisica, Universidad de Valencia, c/ Dr. Moliner, 50, 46100 Burjassot (Spain)

2011-09-22

Away from critical curves, lens mapping can be seen as a linear invertible transformation of the plane even for regions (cells) of relatively large size. However, close to critical curves the departures from linearity can be very strong. We discuss the topological problems induced by the mapping of regions of the image plane that include critical curves (critical cells).

UPGRADE FOR HARDWARE/SOFTWARE SERVER AND NETWORK TOPOLOGY IN INFORMATION SYSTEMS

Directory of Open Access Journals (Sweden)

Oleksii O. Kaplun

2011-02-01

Full Text Available The network modernization, educational information systems software and hardware updates problem is actual in modern term of information technologies prompt development. There are server applications and network topology of Institute of Information Technology and Learning Tools of National Academy of Pedagogical Sciences of Ukraine analysis and their improvement methods expound in the article. The article materials represent modernization results implemented to increase network efficiency and reliability, decrease response time in Institute’s network information systems. The article gives diagrams of network topology before upgrading and after finish of optimization and upgrading processes.

Hydrated and Dehydrated Tertiary Interactions–Opening and Closing–of a Four-Helix Bundle Peptide

Science.gov (United States)

Lignell, Martin; Tegler, Lotta T.; Becker, Hans-Christian

2009-01-01

Abstract The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9°C to 23°C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30°C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60°C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions. PMID:19619472

Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

Science.gov (United States)

Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

1999-03-12

In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

Undergraduate topology a working textbook

CERN Document Server

McCluskey, Aisling

2014-01-01

This textbook offers an accessible, modern introduction at undergraduate level to an area known variously as general topology, point-set topology or analytic topology with a particular focus on helping students to build theory for themselves. It is the result of several years of the authors' combined university teaching experience stimulated by sustained interest in advanced mathematical thinking and learning, alongside established research careers in analytic topology. Point-set topology is a discipline that needs relatively little background knowledge, but sufficient determination to grasp i

Equivariant topological quantum field theory and symmetry protected topological phases

Energy Technology Data Exchange (ETDEWEB)

Kapustin, Anton [Division of Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA, 91125 (United States); Turzillo, Alex [Simons Center for Geometry and Physics, State University of New York,Stony Brook, NY, 11794 (United States)

2017-03-01

Short-Range Entangled topological phases of matter are closely related to Topological Quantum Field Theory. We use this connection to classify Symmetry Protected Topological phases in low dimensions, including the case when the symmetry involves time-reversal. To accomplish this, we generalize Turaev’s description of equivariant TQFT to the unoriented case. We show that invertible unoriented equivariant TQFTs in one or fewer spatial dimensions are classified by twisted group cohomology, in agreement with the proposal of Chen, Gu, Liu and Wen. We also show that invertible oriented equivariant TQFTs in spatial dimension two or fewer are classified by ordinary group cohomology.

Helix Nebula Science Cloud pilot phase open session

CERN Multimedia

CERN. Geneva

2018-01-01

This Helix Nebula Science Cloud (HNSciCloud) public session is open to everyone and will be webcast. The session will provide the audience with an overview of the HNSciCloud pre-commercial procurement project and the innovative cloud platforms that have been developed. A number of practical use-cases from the physics community will be presented as well as the next steps to be undertaken.

An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

Directory of Open Access Journals (Sweden)

Ling Liu

2009-03-01

Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

Topologically massive supergravity

Directory of Open Access Journals (Sweden)

S. Deser

1983-01-01

Full Text Available The locally supersymmetric extension of three-dimensional topologically massive gravity is constructed. Its fermionic part is the sum of the (dynamically trivial Rarita-Schwinger action and a gauge-invariant topological term, of second derivative order, analogous to the gravitational one. It is ghost free and represents a single massive spin 3/2 excitation. The fermion-gravity coupling is minimal and the invariance is under the usual supergravity transformations. The system's energy, as well as that of the original topological gravity, is therefore positive.

Topological pregauge-pregeometry

International Nuclear Information System (INIS)

Akama, Keiichi; Oda, Ichiro.

1990-12-01

The pregauge-pregeometric action, i.e. the fundamental matter action whose quantum fluctuations give rise to the Einstein-Hilbert and the Yang-Mills actions is investigated from the viewpoint of the topological field theory. We show that the scalar pregauge-pregeometric action is a topological invariant for appropriate choices of the internal gauge group. This model realizes the picture that the gravitational and internal gauge theory at the low energy scale is induced as the quantum effects of the topological field theory at the Planck scale. (author)

Tunable Topological Phononic Crystals

KAUST Repository

Chen, Zeguo

2016-05-27

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

Tunable Topological Phononic Crystals

KAUST Repository

Chen, Zeguo; Wu, Ying

2016-01-01

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

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

Science.gov (United States)

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

A time-reversal invariant topological phase at the surface of a 3D topological insulator

International Nuclear Information System (INIS)

Bonderson, Parsa; Nayak, Chetan; Qi, Xiao-Liang

2013-01-01

A 3D fermionic topological insulator has a gapless Dirac surface state protected by time-reversal symmetry and charge conservation symmetry. The surface state can be gapped by introducing ferromagnetism to break time-reversal symmetry, introducing superconductivity to break charge conservation, or entering a topological phase. In this paper, we construct a minimal gapped topological phase that preserves both time-reversal and charge conservation symmetries and supports Ising-type non-Abelian anyons. This phase can be understood heuristically as emerging from a surface s-wave superconducting state via the condensation of eight-vortex composites. The topological phase inherits vortices supporting Majorana zero modes from the surface superconducting state. However, since it is time-reversal invariant, the surface topological phase is a distinct phase from the Ising topological phase, which can be viewed as a quantum-disordered spin-polarized p x + ip y superconductor. We discuss the anyon model of this topological phase and the manner in which time-reversal symmetry is realized in it. We also study the interfaces between the topological state and other surface gapped phases. (paper)

Topology optimized permanent magnet systems

DEFF Research Database (Denmark)

Bjørk, Rasmus; Bahl, Christian; Insinga, Andrea Roberto

2017-01-01

Topology optimization of permanent magnet systems consisting of permanent magnets, high permeability iron and air is presented. An implementation of topology optimization for magnetostatics is discussed and three examples are considered. The Halbach cylinder is topology optimized with iron...... and an increase of 15% in magnetic efficiency is shown. A topology optimized structure to concentrate a homogeneous field is shown to increase the magnitude of the field by 111%. Finally, a permanent magnet with alternating high and low field regions is topology optimized and a ΛcoolΛcool figure of merit of 0...

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

Science.gov (United States)

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

2014-11-07

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

Free Boolean Topological Groups

Directory of Open Access Journals (Sweden)

Ol’ga Sipacheva

2015-11-01

Full Text Available Known and new results on free Boolean topological groups are collected. An account of the properties that these groups share with free or free Abelian topological groups and properties specific to free Boolean groups is given. Special emphasis is placed on the application of set-theoretic methods to the study of Boolean topological groups.

RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via The Ribbon-Helix-Helix Motif in RelB

DEFF Research Database (Denmark)

Overgaard, Martin; Borch, Jonas; Gerdes, Kenn

2009-01-01

RelB, the Ribbon-Helix-Helix (RHH) repressor encoded by the relBE toxin-antitoxin locus of Escherichia coli, forms a tight complex with RelE and thereby counteracts the mRNA cleavage activity of RelE. In addition, RelB dimers repress the strong relBE promoter and this repression by RelB is enhanced...... by RelE - that is - RelE functions as a transcriptional co-repressor. RelB is a Lon protease substrate and Lon is required both for activation of relBE transcription and for activation of the mRNA cleavage activity of RelE. Here we characterize the molecular interactions important for transcriptional...... motif recognizes four 6 bp repeats within the bipartite binding site. The spacing between each half-site was found to be essential for cooperative interactions between adjacently bound RelB dimers stabilized by the co-repressor RelE. Kinetic and stoichiometric measurements of the interaction between Rel...

From Family Based to Industrial Based Production: Local Economic Development Initiatives and the HELIX Model

Directory of Open Access Journals (Sweden)

Bartjan W Pennink

2013-01-01

Full Text Available To build a strong local economy, good practice tells us that each community should undertake a collaborative, strategically planned process to understand and then act upon its own strengths, weaknesses, opportunities and threats. From this perspective we start with the local communities but how is this related to the perspective from the Helix model in which three actors are explicitly introduced: the Government, the Industry and the Universities? The purpose of local economic development (LED is to build up the economic capacity of a local area to improve its economic future and the quality of life for all. To support  the Local Economic Development in remote areas,   a program  has been developed based on the LED frame work of the world bank. This approach and  the experiences over  the past years with this program are  described in the first part.  In the second part of the paper, We analyse work done with that program with the help of the social capital concept and the triple helix model.  In all cases it is important to pay attention to who is taken the initiative after the first move (and it is not always the governance as actor and for the triple helix we suggest  that the concepts of (national Government, Industry and University need a translation to Local Governance Agency, Cooperation or other ways of cooperation of local communities and Local Universities. Although a push from outside might help  a local region in development the endogenous factors are  also needed. Keywords: Triple Helix model, Local Economic Development, Local Actors, Double Triangle within the Helix Model

Topology general & algebraic

CERN Document Server

Chatterjee, D

2007-01-01

About the Book: This book provides exposition of the subject both in its general and algebraic aspects. It deals with the notions of topological spaces, compactness, connectedness, completeness including metrizability and compactification, algebraic aspects of topological spaces through homotopy groups and homology groups. It begins with the basic notions of topological spaces but soon going beyond them reaches the domain of algebra through the notions of homotopy, homology and cohomology. How these approaches work in harmony is the subject matter of this book. The book finally arrives at the

Floquet topological insulators for sound

Science.gov (United States)

Fleury, Romain; Khanikaev, Alexander B.; Alù, Andrea

2016-06-01

The unique conduction properties of condensed matter systems with topological order have recently inspired a quest for the similar effects in classical wave phenomena. Acoustic topological insulators, in particular, hold the promise to revolutionize our ability to control sound, allowing for large isolation in the bulk and broadband one-way transport along their edges, with topological immunity against structural defects and disorder. So far, these fascinating properties have been obtained relying on moving media, which may introduce noise and absorption losses, hindering the practical potential of topological acoustics. Here we overcome these limitations by modulating in time the acoustic properties of a lattice of resonators, introducing the concept of acoustic Floquet topological insulators. We show that acoustic waves provide a fertile ground to apply the anomalous physics of Floquet topological insulators, and demonstrate their relevance for a wide range of acoustic applications, including broadband acoustic isolation and topologically protected, nonreciprocal acoustic emitters.

Topological Acoustic Delay Line

Science.gov (United States)

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

2018-03-01

Topological protected wave engineering in artificially structured media is at the frontier of ongoing metamaterials research that is inspired by quantum mechanics. Acoustic analogues of electronic topological insulators have recently led to a wealth of new opportunities in manipulating sound propagation with strikingly unconventional acoustic edge modes immune to backscattering. Earlier fabrications of topological insulators are characterized by an unreconfigurable geometry and a very narrow frequency response, which severely hinders the exploration and design of useful devices. Here we establish topologically protected sound in reconfigurable phononic crystals that can be switched on and off simply by rotating its three-legged "atoms" without altering the lattice structure. In particular, we engineer robust phase delay defects that take advantage of the ultrabroadband reflection-free sound propagation. Such topological delay lines serve as a paradigm in compact acoustic devices, interconnects, and electroacoustic integrated circuits.

Topological X-Rays Revisited

Science.gov (United States)

Lynch, Mark

2012-01-01

We continue our study of topological X-rays begun in Lynch ["Topological X-rays and MRI's," iJMEST 33(3) (2002), pp. 389-392]. We modify our definition of a topological magnetic resonance imaging and give an affirmative answer to the question posed there: Can we identify a closed set in a box by defining X-rays to probe the interior and without…

Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

Energy Technology Data Exchange (ETDEWEB)

Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

2016-04-01

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

Science.gov (United States)

Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

2014-10-07

Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

Foundations of topological racks and quandles

OpenAIRE

Mohamed Moutuou, El-Kaioum; Elhamdadi, Mohamed

2016-01-01

We give a foundational account on topological racks and quandles. Specifically, we define the notions of ideals, kernels, units, and inner automorphism group in the context of topological racks. Further, we investigate topological rack modules and principal rack bundles. Central extensions of topological racks are then introduced providing a first step towards a general continuous cohomology theory for topological racks and quandles

Selection of G-quadruplex folding topology with LNA-modified human telomeric sequences in K+ solution

DEFF Research Database (Denmark)

Pradhan, Devranjan; Hansen, Lykke H; Vester, Birte

2011-01-01

G-rich nucleic acid oligomers can form G-quadruplexes built by G-tetrads stacked upon each other. Depending on the nucleotide sequence, G-quadruplexes fold mainly with two topologies: parallel, in which all G-tracts are oriented parallel to each other, or antiparallel, in which one or more G......-tracts are oriented antiparallel to the other G-tracts. In the former topology, all glycosidic bond angles conform to anti conformations, while in the latter topology they adopt both syn and anti conformations. It is of interest to understand the molecular forces that govern G-quadruplex folding. Here, we approach...... this problem by examining the impact of LNA (locked nucleic acid) modifications on the folding topology of the dimeric model system of the human telomere sequence. In solution, this DNA G-quadruplex forms a mixture of G-quadruplexes with antiparallel and parallel topologies. Using CD and NMR spectroscopies, we...

Generation of structural topologies using efficient technique based on sorted compliances

Science.gov (United States)

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.

Topological fixed point theory for singlevalued and multivalued mappings and applications

CERN Document Server

Ben Amar, Afif

2016-01-01

This is a monograph covering topological fixed point theory for several classes of single and multivalued maps. The authors begin by presenting basic notions in locally convex topological vector spaces. Special attention is then devoted to weak compactness, in particular to the theorems of Eberlein–Šmulian, Grothendick and Dunford–Pettis. Leray–Schauder alternatives and eigenvalue problems for decomposable single-valued nonlinear weakly compact operators in Dunford–Pettis spaces are considered, in addition to some variants of Schauder, Krasnoselskii, Sadovskii, and Leray–Schauder type fixed point theorems for different classes of weakly sequentially continuous operators on general Banach spaces. The authors then proceed with an examination of Sadovskii, Furi–Pera, and Krasnoselskii fixed point theorems and nonlinear Leray–Schauder alternatives in the framework of weak topologies and involving multivalued mappings with weakly sequentially closed graph. These results are formulated in terms of ax...

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-07-18

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

Topological Magnonics: A Paradigm for Spin-Wave Manipulation and Device Design

Science.gov (United States)

Wang, X. S.; Zhang, H. W.; Wang, X. R.

2018-02-01

Conventional magnonic devices use magnetostatic waves whose properties are sensitive to device geometry and the details of magnetization structure, so the design and the scalability of the device or circuitry are difficult. We propose topological magnonics, in which topological exchange spin waves are used as information carriers, that do not suffer from conventional problems of magnonic devices with additional nice features of nanoscale wavelength and high frequency. We show that a perpendicularly magnetized ferromagnet on a honeycomb lattice is generically a topological magnetic material in the sense that topologically protected chiral edge spin waves exist in the band gap as long as a spin-orbit-induced nearest-neighbor pseudodipolar interaction (and/or a next-nearest-neighbor Dzyaloshinskii-Moriya interaction) is present. The edge spin waves propagate unidirectionally along sample edges and domain walls regardless of the system geometry and defects. As a proof of concept, spin-wave diodes, spin-wave beam splitters, and spin-wave interferometers are designed by using sample edges and domain walls to manipulate the propagation of topologically protected chiral spin waves. Since magnetic domain walls can be controlled by magnetic fields or electric current or fields, one can essentially draw, erase, and redraw different spin-wave devices and circuitry on the same magnetic plate so that the proposed devices are reconfigurable and tunable. The topological magnonics opens up an alternative direction towards a robust, reconfigurable and scalable spin-wave circuitry.

Topological Structures on DMC Spaces †

Directory of Open Access Journals (Sweden)

Rajai Nasser

2018-05-01

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

Topological surface states in nodal superconductors.

Science.gov (United States)

Schnyder, Andreas P; Brydon, Philip M R

2015-06-24

Topological superconductors have become a subject of intense research due to their potential use for technical applications in device fabrication and quantum information. Besides fully gapped superconductors, unconventional superconductors with point or line nodes in their order parameter can also exhibit nontrivial topological characteristics. This article reviews recent progress in the theoretical understanding of nodal topological superconductors, with a focus on Weyl and noncentrosymmetric superconductors and their protected surface states. Using selected examples, we review the bulk topological properties of these systems, study different types of topological surface states, and examine their unusual properties. Furthermore, we survey some candidate materials for topological superconductivity and discuss different experimental signatures of topological surface states.

Topological surface states in nodal superconductors

International Nuclear Information System (INIS)

Schnyder, Andreas P; Brydon, Philip M R

2015-01-01

Topological superconductors have become a subject of intense research due to their potential use for technical applications in device fabrication and quantum information. Besides fully gapped superconductors, unconventional superconductors with point or line nodes in their order parameter can also exhibit nontrivial topological characteristics. This article reviews recent progress in the theoretical understanding of nodal topological superconductors, with a focus on Weyl and noncentrosymmetric superconductors and their protected surface states. Using selected examples, we review the bulk topological properties of these systems, study different types of topological surface states, and examine their unusual properties. Furthermore, we survey some candidate materials for topological superconductivity and discuss different experimental signatures of topological surface states. (topical review)

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

Energy Technology Data Exchange (ETDEWEB)

Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by ³¹P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

Energy Technology Data Exchange (ETDEWEB)

Storrs, R.W.

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

Extreme bendability of DNA double helix due to bending asymmetry

NARCIS (Netherlands)

Salari, H.; Eslami-Mossallam, B.; Nederi, S.; Ejtehadi, M.R.

2015-01-01

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for

An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

Science.gov (United States)

Herlo, Rasmus; Lund, Viktor K; Lycas, Matthew D; Jansen, Anna M; Khelashvili, George; Andersen, Rita C; Bhatia, Vikram; Pedersen, Thomas S; Albornoz, Pedro B C; Johner, Niklaus; Ammendrup-Johnsen, Ina; Christensen, Nikolaj R; Erlendsson, Simon; Stoklund, Mikkel; Larsen, Jannik B; Weinstein, Harel; Kjærulff, Ole; Stamou, Dimitrios; Gether, Ulrik; Madsen, Kenneth L

2018-05-15

BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS. Mutational disruption of the helix in PICK1 impaired MCS without affecting membrane binding per se. In insulin-producing INS-1E cells, super-resolution microscopy revealed that disruption of the helix selectively compromised PICK1 density on insulin granules of high curvature during their maturation. This was accompanied by reduced hormone storage in the INS-1E cells. In Drosophila, disruption of the helix compromised growth regulation. By demonstrating size-dependent binding on insulin granules, our finding highlights the function of MCS for BAR domain proteins in a biological context distinct from their function, e.g., at the plasma membrane during endocytosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

One-dimensional nonlinear theory for rectangular helix traveling-wave tube

Energy Technology Data Exchange (ETDEWEB)

Fu, Chengfang, E-mail: fchffchf@126.com; Zhao, Bo; Yang, Yudong; Ju, Yongfeng [Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai' an 223003 (China); Wei, Yanyu [School of Physical Electronics, University of Electronic and Technology of China, Chengdu 610054 (China)

2016-08-15

A 1-D nonlinear theory of a rectangular helix traveling-wave tube (TWT) interacting with a ribbon beam is presented in this paper. The RF field is modeled by a transmission line equivalent circuit, the ribbon beam is divided into a sequence of thin rectangular electron discs with the same cross section as the beam, and the charges are assumed to be uniformly distributed over these discs. Then a method of computing the space-charge field by solving Green's Function in the Cartesian Coordinate-system is fully described. Nonlinear partial differential equations for field amplitudes and Lorentz force equations for particles are solved numerically using the fourth-order Runge-Kutta technique. The tube's gain, output power, and efficiency of the above TWT are computed. The results show that increasing the cross section of the ribbon beam will improve a rectangular helix TWT's efficiency and reduce the saturated length.

Graph topologies on closed multifunctions

Directory of Open Access Journals (Sweden)

Giuseppe Di Maio

2003-10-01

Full Text Available In this paper we study function space topologies on closed multifunctions, i.e. closed relations on X x Y using various hypertopologies. The hypertopologies are in essence, graph topologies i.e topologies on functions considered as graphs which are subsets of X x Y . We also study several topologies, including one that is derived from the Attouch-Wets filter on the range. We state embedding theorems which enable us to generalize and prove some recent results in the literature with the use of known results in the hyperspace of the range space and in the function space topologies of ordinary functions.

Nobel Lecture: Topological quantum matter*

Science.gov (United States)

Haldane, F. Duncan M.

2017-10-01

Nobel Lecture, presented December 8, 2016, Aula Magna, Stockholm University. I will describe the history and background of three discoveries cited in this Nobel Prize: The "TKNN" topological formula for the integer quantum Hall effect found by David Thouless and collaborators, the Chern insulator or quantum anomalous Hall effect, and its role in the later discovery of time-reversal-invariant topological insulators, and the unexpected topological spin-liquid state of the spin-1 quantum antiferromagnetic chain, which provided an initial example of topological quantum matter. I will summarize how these early beginnings have led to the exciting, and currently extremely active, field of "topological matter."

Topology optimized permanent magnet systems

Science.gov (United States)

Bjørk, R.; Bahl, C. R. H.; Insinga, A. R.

2017-09-01

Topology optimization of permanent magnet systems consisting of permanent magnets, high permeability iron and air is presented. An implementation of topology optimization for magnetostatics is discussed and three examples are considered. The Halbach cylinder is topology optimized with iron and an increase of 15% in magnetic efficiency is shown. A topology optimized structure to concentrate a homogeneous field is shown to increase the magnitude of the field by 111%. Finally, a permanent magnet with alternating high and low field regions is topology optimized and a Λcool figure of merit of 0.472 is reached, which is an increase of 100% compared to a previous optimized design.

QCD in a nonsimply connected spacetime: The topological origin of flavours and topological gluon mass generation

International Nuclear Information System (INIS)

Goncharov, Yu.P.

1982-01-01

In a spacetime having a nontrivial topology QCD may have properties which are absent for QCD in Minkowski spacetime. Two new possibilities for QCD are discussed by the example of spacetime with topology R x (S 1 ) 3 and flat metric: the topological origin of flavours and topological gluon mass generation. (orig.)

Adjoint entropy vs topological entropy

OpenAIRE

Giordano Bruno, Anna

2012-01-01

Recently the adjoint algebraic entropy of endomorphisms of abelian groups was introduced and studied. We generalize the notion of adjoint entropy to continuous endomorphisms of topological abelian groups. Indeed, the adjoint algebraic entropy is defined using the family of all finite-index subgroups, while we take only the subfamily of all open finite-index subgroups to define the topological adjoint entropy. This allows us to compare the (topological) adjoint entropy with the known topologic...

Topological mapping and navigation in indoor environment with invisible barcode

International Nuclear Information System (INIS)

Huh, Jin Wook; Chung, Woong Sik; Chung, Wan Kyun

2006-01-01

This paper addresses the localization and navigation problem using invisible two dimensional barcodes on the floor. Compared with other methods using natural/artificial landmark, the proposed localization method has great advantages in cost and appearance, since the location of the robot is perfectly known using the barcode information after the mapping is finished. We also propose a navigation algorithm which uses the topological structure. For the topological information, we define nodes and edges which are suitable for indoor navigation, especially for large area having multiple rooms, many walls and many static obstacles. The proposed algorithm also has an advantage that errors occurred in each node are mutually independent and can be compensated exactly after some navigation using barcode. Simulation and experimental results were performed to verify the algorithm in the barcode environment, and the result showed an excellent performance. After mapping, it is also possible to solve the kidnapped case and generate paths using topological information

Kink dynamics in a topological φ4 lattice

Science.gov (United States)

Adib, A. B.; Almeida, C. A. S.

2001-09-01

Recently proposed was a discretization for nonlinear Klein-Gordon field theories in which the resulting lattice preserves the topological (Bogomol'nyi) lower bound on the kink energy and, as a consequence, has no Peierls-Nabarro barrier even for large spatial discretizations (h~1.0). It was then suggested that these ``topological discrete systems'' are a natural choice for the numerical study of continuum kink dynamics. Giving particular emphasis to the φ4 theory, we numerically investigate kink-antikink scattering and breather formation in these topological lattices. Our results indicate that, even though these systems are quite accurate for studying free kinks in coarse lattices, for legitimate dynamical kink problems the accuracy is rather restricted to fine lattices (h~0.1). We suggest that this fact is related to the breaking of the Bogomol'nyi bound during the kink-antikink interaction, where the field profile loses its static property as required by the Bogomol'nyi argument. We conclude, therefore, that these lattices are not suitable for the study of more general kink dynamics, since a standard discretization is simpler and has effectively the same accuracy for such resolutions.