Folding equilateral plane graphs

22nd International Symposium, ISAAC 2011, Yokohama, Japan, December 5-8, 2011. ProceedingsWe consider two types of folding applied to equilateral plane graph linkages. First, under continuous folding motions, we show how to reconfigure any linear equilateral tree (lying on a line) into a canonical configuration. By contrast, such reconfiguration is known to be impossible for linear (nonequilateral) trees and for (nonlinear) equilateral trees. Second, under instantaneous folding motions, we show that an equilateral plane graph has a noncrossing linear folded state if and only if it is bipartite. Not only is the equilateral constraint necessary for this result, but we show that it is strongly NP-complete to decide whether a (nonequilateral) plane graph has a linear folded state. Equivalently, we show strong NP-completeness of deciding whether an abstract metric polyhedral complex with one central vertex has a noncrossing flat folded state with a specified “outside region”. By contrast, the analogous problem for a polyhedral manifold with one central vertex (single-vertex origami) is only weakly NP-complete

Well-Posedness and Symmetries of Strongly Coupled Network Equations

We consider a diffusion process on the edges of a finite network and allow for feedback effects between different, possibly non-adjacent edges. This generalizes the setting that is common in the literature, where the only considered interactions take place at the boundary, i. e., in the nodes of the network. We discuss well-posedness of the associated initial value problem as well as contractivity and positivity properties of its solutions. Finally, we discuss qualitative properties that can be formulated in terms of invariance of linear subspaces of the state space, i. e., of symmetries of the associated physical system. Applications to a neurobiological model as well as to a system of linear Schroedinger equations on a quantum graph are discussed.Comment: 25 pages. Corrected typos and minor change

Band Connectivity for Topological Quantum Chemistry: Band Structures As A Graph Theory Problem

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 547, 298 (2017)], we have introduced the way to overcome this difficulty by formulating the problem of sewing together many disconnected local "k-dot-p" band structures across the Brillouin zone in terms of graph theory. In the current manuscript 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.Comment: 19 pages. Companion paper to arXiv:1703.02050 and arXiv:1706.08529 v2: Accepted version, minor typos corrected and references added. Now 19+epsilon page

Drawings of Complete Multipartite Graphs up to Triangle Flips

For a drawing of a labeled graph, the rotation of a vertex or crossing is the cyclic order of its incident edges, represented by the labels of their other endpoints. The extended rotation system (ERS) of the drawing is the collection of the rotations of all vertices and crossings. A drawing is simple if each pair of edges has at most one common point. Gioan's Theorem states that for any two simple drawings of the complete graph Kn with the same crossing edge pairs, one drawing can be transformed into the other by a sequence of triangle flips (a.k.a. Reidemeister moves of Type 3). This operation refers to the act of moving one edge of a triangular cell formed by three pairwise crossing edges over the opposite crossing of the cell, via a local transformation. We investigate to what extent Gioan-type theorems can be obtained for wider classes of graphs. A necessary (but in general not sufficient) condition for two drawings of a graph to be transformable into each other by a sequence of triangle flips is that they have the same ERS. As our main result, we show that for the large class of complete multipartite graphs, this necessary condition is in fact also sufficient. We present two different proofs of this result, one of which is shorter, while the other one yields a polynomial time algorithm for which the number of needed triangle flips for graphs on n vertices is bounded by O(n16). The latter proof uses a Carathéodory-type theorem for simple drawings of complete multipartite graphs, which we believe to be of independent interest. Moreover, we show that our Gioan-type theorem for complete multipartite graphs is essentially tight in the following sense: For the complete bipartite graph Km, n minus two edges and Km, n plus one edge for any m, n ≥ 4, as well as Kn minus a 4-cycle for any n ≥ 5, there exist two simple drawings with the same ERS that cannot be transformed into each other using triangle flips. So having the same ERS does not remain sufficient when removing or adding very few edges

Operations research: from computational biology to sensor network

In this dissertation we discuss the deployment of combinatorial optimization methods for modeling and solve real life problemS, with a particular emphasis to two biological problems arising from a common scenario: the reconstruction of the three-dimensional shape of a biological molecule from Nuclear Magnetic Resonance (NMR) data. The fi rst topic is the 3D assignment pathway problem (APP) for a RNA molecule. We prove that APP is NP-hard, and show a formulation of it based on edge-colored graphs. Taking into account that interactions between consecutive nuclei in the NMR spectrum are diff erent according to the type of residue along the RNA chain, each color in the graph represents a type of interaction. Thus, we can represent the sequence of interactions as the problem of fi nding a longest (hamiltonian) path whose edges follow a given order of colors (i.e., the orderly colored longest path). We introduce three alternative IP formulations of APP obtained with a max flow problem on a directed graph with packing constraints over the partitions, which have been compared among themselves. Since the last two models work on cyclic graphs, for them we proposed an algorithm based on the solution of their relaxation combined with the separation of cycle inequalities in a Branch & Cut scheme. The second topic is the discretizable distance geometry problem (DDGP), which is a formulation on discrete search space of the well-known distance geometry problem (DGP). The DGP consists in seeking the embedding in the space of a undirected graph, given a set of Euclidean distances between certain pairs of vertices. DGP has two important applications: (i) fi nding the three dimensional conformation of a molecule from a subset of interatomic distances, called Molecular Distance Geometry Problem, and (ii) the Sensor Network Localization Problem. We describe a Branch & Prune (BP) algorithm tailored for this problem, and two versions of it solving the DDGP both in protein modeling and in sensor networks localization frameworks. BP is an exact and exhaustive combinatorial algorithm that examines all the valid embeddings of a given weighted graph G=(V,E,d), under the hypothesis of existence of a given order on V. By comparing the two version of BP to well-known algorithms we are able to prove the e fficiency of BP in both contexts, provided that the order imposed on V is maintained

Fine-Grained Complexity Analysis of Two Classic TSP Variants

We analyze two classic variants of the Traveling Salesman Problem using the toolkit of fine-grained complexity. Our first set of results is motivated by the Bitonic TSP problem: given a set of $n$ points in the plane, compute a shortest tour consisting of two monotone chains. It is a classic dynamic-programming exercise to solve this problem in $O(n^2)$ time. While the near-quadratic dependency of similar dynamic programs for Longest Common Subsequence and Discrete Frechet Distance has recently been proven to be essentially optimal under the Strong Exponential Time Hypothesis, we show that bitonic tours can be found in subquadratic time. More precisely, we present an algorithm that solves bitonic TSP in $O(n \log^2 n)$ time and its bottleneck version in $O(n \log^3 n)$ time. Our second set of results concerns the popular $k$-OPT heuristic for TSP in the graph setting. More precisely, we study the $k$-OPT decision problem, which asks whether a given tour can be improved by a $k$-OPT move that replaces $k$ edges in the tour by $k$ new edges. A simple algorithm solves $k$-OPT in $O(n^k)$ time for fixed $k$. For 2-OPT, this is easily seen to be optimal. For $k=3$ we prove that an algorithm with a runtime of the form $\tilde{O}(n^{3-\epsilon})$ exists if and only if All-Pairs Shortest Paths in weighted digraphs has such an algorithm. The results for $k=2,3$ may suggest that the actual time complexity of $k$-OPT is $\Theta(n^k)$. We show that this is not the case, by presenting an algorithm that finds the best $k$-move in $O(n^{\lfloor 2k/3 \rfloor + 1})$ time for fixed $k \geq 3$. This implies that 4-OPT can be solved in $O(n^3)$ time, matching the best-known algorithm for 3-OPT. Finally, we show how to beat the quadratic barrier for $k=2$ in two important settings, namely for points in the plane and when we want to solve 2-OPT repeatedly.Comment: Extended abstract appears in the Proceedings of the 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016

A Discrete Morse Approach for Computing Homotopy Types: An Exploration of the Morse, Generalized Morse, Matching, and Independence Complexes

In this thesis, we study possible homotopy types of four families of simplicial complexes–the Morse complex, the generalized Morse complex, the matching complex, and the independence complex–using discrete Morse theory. Given a simplicial complex, K, we can construct its Morse complex from all possible discrete gradient vector fields on K. A similar construction will allow us to build the generalized Morse complex while considering edges and vertices will allow us to construct the matching complex and independence complex. In Chapter 3, we use the Cluster Lemma and the notion of star clusters to apply matchings to families of Morse, generalized Morse, and matching complexes, computing their homotopy types. Notably, we show that the Morse complex of a subset of extended star graphs is homotopy equivalent to a wedge of spheres and the matching complex of a Dutch windmill graph is homotopy equivalent to a point, sphere, or wedge of spheres. In Chapter 4, we use a degenerate Hasse diagram and strong collapses to compute the homotopy type of many families of Morse complexes. Recognizably, we provide computations showing wedged complexes as suspensions and provide a sufficient condition for strongly collapsible Morse complexes. Lastly, in Chapter 5 we study chord diagrams–a largely unexplored topic–and provide insight into the possible homotopy types of the independence complex of intersection graphs of chord diagrams. We realize spheres and wedges of spheres as possible homotopy types and begin to explore what families of intersection graphs can be represented as a chord diagram. From here, most interesting, we show that ladder graphs can be represented as chord diagrams, and the independence complex of a ladder graph has the homotopy type of a sphere

Topological evolution of networks : case studies in the US airlines and language Wikipedias

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 195-198).This thesis examines the topology of engineering systems and how that topology changes over time. Topology refers to the relative arrangement and connectivity of the elements of a system. We review network theory relevant to topological evolution and use graph-theoretical methods to analyze real systems, represented as networks. Using existing graph generative models, we develop a profile of canonical graphs and tools to compare a real network to that profile. The developed metrics are used to track topology changes over the history of real networks. This theoretical work is applied to two case studies. The first discusses the US airline industry in terms of routes. We study various airlines and segments of the industry statistically and find commonly occurring patterns. We show that there are topology transitions in the history of airlines in the period 1990-2007. Most airline networks have similar topology and historical patterns, with the exception of Southwest Airlines. We show mathematically that Southwest's topology is different. We propose two heuristic growth models, one featuring hub-seeding derived from the underlying patterns of evolution of JetBlue Airways and one featuring local interconnectedness, derived from the patterns of growth of Southwest. The two models match the topologies of these airlines better than canonical models over time. Results suggest that Southwest is becoming more centralized, closer to the hub-spoke topologies of other airlines. Our second case study discusses the growth of language Wikipedia networks, where nodes are articles and hyperlinks are the connections between them. These knowledge networks are subject to different constraints than air transportation systems. The topology of these networks and their growth principles are completely different. Most Wikipedias studied grow by coalescence, with multiple disconnected thematic clusters of pages growing separately and over time, converging to a giant connected component via weak links. These topologies start out as simple trees, and coalesce into sparse hierarchical structures with random interlinking. One striking exception is the history of the Chinese Wikipedia, which grows fully connected from its inception. We discuss these patterns of growth comparatively across Wikipedias, and in general, compared to airline networks. Our work suggests that complex engineering systems are hybrids of pure canonical forms and that they undergo distinct phase transitions during their evolution. We find commonality among systems and uncover important differences by learning from the exceptions.by Gergana Assenova Bounova.Ph.D