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Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the…

Populations and Evolution · Quantitative Biology 2021-05-31 Andrew Francis , Daniel H. Huson , Mike Steel

Minimum braids are a complete invariant of knots and links. This paper defines minimum braids, describes how they can be generated, presents tables for knots up to ten crossings and oriented links up to nine crossings, and uses minimum…

Geometric Topology · Mathematics 2007-05-23 Thomas A. Gittings

Networks grow and evolve by local events, such as the addition of new nodes and links, or rewiring of links from one node to another. We show that depending on the frequency of these processes two topologically different networks can…

Disordered Systems and Neural Networks · Physics 2009-10-31 Reka Albert , Albert-Laszlo Barabasi

We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with…

Data Structures and Algorithms · Computer Science 2013-04-23 Ferdinando Cicalese , Travis Gagie , Emanuele Giaquinta , Eduardo Sany Laber , Zsuzsanna Lipták , Romeo Rizzi , Alexandru I. Tomescu

Linkages are mechanical devices constructed from rigid bars and freely rotating joints studied both for their utility in engineering and as mathematical idealizations in a number of physical systems. Recently, there has been a resurgence of…

Soft Condensed Matter · Physics 2022-11-23 M. Berry , David Limberg , M. E. Lee-Trimble , Ryan Hayward , C. D. Santangelo

Convergence is a fundamental topic in analysis that is most commonly modelled using topology. However, there are many natural convergences that are not given by any topology; e.g., convergence almost everywhere of a sequence of measurable…

Functional Analysis · Mathematics 2021-03-03 M. O'Brien , V. G. Troitsky , J. H. van der Walt

Complex networks are ubiquitous in nature and play a role of paramount importance in many contexts. Internet and the cyberworld, which permeate our everyday life, are self-organized hierarchical graphs. Urban traffic flows on intricate road…

Physics and Society · Physics 2014-08-08 Francesca Di Patti , Duccio Fanelli , Francesco Piazza

It is shown that every orthogonal terrain, i.e., an orthogonal (right-angled) polyhedron based on a rectangle that meets every vertical line in a segment, has a grid unfolding: its surface may be unfolded to a single non-overlapping piece…

Computational Geometry · Computer Science 2007-07-12 Joseph O'Rourke

A new methodological approach for the study of topology for shapes made of arrangements of lines, planes or solids is presented. Topologies for shapes are traditionally built on the classical theory of point-sets. In this paper, topologies…

General Topology · Mathematics 2022-01-28 Alexandros Haridis

Many natural, engineered, and social systems can be represented using the framework of a layered network, where each layer captures a different type of interaction between the same set of nodes. The study of such multiplex networks is a…

Physics and Society · Physics 2020-05-12 Haochen Wu , Ryan G. James , James P. Crutchfield , Raissa M. D'Souza

It is shown how different globally coupled map systems can be analyzed under a common framework by focusing on the dynamics of their respective global coupling functions. We investigate how the functional form of the coupling determines the…

Chaotic Dynamics · Physics 2009-11-07 M. G. Cosenza , A. Parravano

We prove that the cohomology algebra of elliptic arrangements depends only on the poset of layers. In the particular case of braid elliptic arrangements, we study the cohomology as representation and we compute some Hodge numbers. Finally,…

Algebraic Topology · Mathematics 2019-01-08 Roberto Pagaria

This paper introduces a new algebra, the crossing algebra, that is applied to count the number of components for arborescent knots, links, tangles or states (of a state polynomial expansion such as the Kauffman bracket). This algebra is…

Geometric Topology · Mathematics 2025-05-20 Louis H Kauffman

We prove the following "linkage" theorem: two p-regular graphs of the same genus can be obtained from one another by a finite alternating sequence of one-edge-contractions; moreover this preserves 3-edge-connectivity. We use the linkage…

Algebraic Geometry · Mathematics 2011-11-18 Lucia Caporaso

This paper is a study of the dynamics of a new family of maps from the complex plane to itself, which we call twisted tent maps. A twisted tent map is a complex generalization of a real tent map. The action of this map can be visualized as…

Dynamical Systems · Mathematics 2012-04-30 Stephen Joseph Chamblee

We study the topdrop map, a mapping on permutations in $S_n$ related to card shuffling. We show this map is bijective and study its orbit structure. We introduce the notion of the topdrop-necklace as a way of classifying the orbits of the…

Combinatorics · Mathematics 2025-10-21 Nathan R. Krause

We slightly extend the notion of a natural fibre bundle by requiring diffeomorphisms of the base to lift to automorphisms of the bundle only infinitesimally, i.e. at the level of the Lie algebra of vector fields. Spin structures are natural…

Differential Geometry · Mathematics 2009-11-19 Bas Janssens

Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…

Disordered Systems and Neural Networks · Physics 2024-10-22 Blai Vidiella , Salva Duran-Nebreda , Sergi Valverde

Population structure can be modelled by evolutionary graphs, which can have a substantial, but very subtle influence on the fate of the arising mutants. Individuals are located on the nodes of these graphs, competing with each other to…

Populations and Evolution · Quantitative Biology 2018-10-31 Marius Möller , Laura Hindersin , Arne Traulsen

In this paper we introduce the tied links, i.e. ordinary links provided with some ties between strands. The motivation for introducing such objects originates from a diagrammatical interpretation of the defining generators of the so-called…

Geometric Topology · Mathematics 2016-06-06 Francesca Aicardi , Jesus Juyumaya
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