Rigid and Generic Structures
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Algorithms in Rigidity Theory with Applications to Protein Flexibility and Mechanical Linkages
ALGORITHMS IN RIGIDITY THEORY WITH APPLICATIONS TO PROTEIN FLEXIBILITY AND MECHANICAL LINKAGES ADNAN SLJOKA A DISSERTATION SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN MATHEMATICS AND STATISTICS YORK UNIVERSITY, TORONTO, ONTARIO August 2012 ALGORITHMS IN RIGIDITY THEORY WITH APPLICATIONS TO PROTEIN FLEXIBILITY AND MECHANICAL LINKAGES by Adnan Sljoka a dissertation submitted to the Faculty of Graduate Studies of York University in partial fulfillment of the requirements for the degree of Doctor of Philosophy c 2012 Permission has been granted to: a) YORK UNIVERSITY LIBRARIES to lend or sell copies of this thesis in paper, microform or electronic formats, and b) LIBRARY AND ARCHIVES CANADA to reproduce, lend, distribute, or sell copies of this thesis any- where in the world in microform, paper or electronic formats and to authorize or pro- cure the reproduction, loan, distribution or sale of copies of this thesis anywhere in the world in microform, paper or electronic formats. The author reserves other publication rights, and neither the thesis nor extensive extracts from it may be printed or otherwise reproduced without the authors written permission. ii .......... iii Abstract A natural question was asked by James Clark Maxwell: Can we count vertices and edges in a framework in order to make predictions about its rigidity and flexibility? The first complete combinatorial generalization for (generic) bar and joint frameworks in dimension 2 was confirmed by Laman in 1970. The 6jV j − 6 counting condition for 3-dimensional molecular structures, and a fast `pebble game' algorithm which tracks this count in the multigraph have led to the development of the program FIRST for rapid predictions of the rigidity and flexibility of proteins. -
On Rigidity of Graphs
On Rigidity of Graphs Bachelor Thesis of Oliver Suchan at the Department of Informatics Institute of Theoretical Informatics Reviewers: Prof. Dr. Dorothea Wagner Prof. Dr. Peter Sanders Advisors: Dr. Torsten Ueckerdt Marcel Radermacher, M. Sc. Time Period: 05.11.2018 – 04.03.2019 KIT – The Research University in the Helmholtz Association www.kit.edu Acknowledgement I would like to thank my advisors Dr. Torsten Ueckerdt and Marcel Radermacher for many hours of sharing and discussing ideas. Statement of Authorship I hereby declare that this thesis has been composed by myself and describes my own work, unless otherwise acknowledged in the text. Karlsruhe, March 4, 2019 iii Abstract A rigid framework refers to an embedding of a graph, in which each edge is represented by a straight line. Additionally, the only continuous displacements of the vertices, that maintain the lengths of all edges, are isometries. If the edge lengths are allowed to only be perturbed in first order, the framework is called infinitesimally rigid. In this thesis the degrees of freedom of a certain, new type of rigidity, called edge-x- rigidity, for a given framework in the 2-dimensional Euclidean space are examined. It does not operate on the length of an edge, but on the intersection of an edge’s support line and the x-axis. This may then help to determine the class of graphs where every edge intersection with the x-axis can be repositioned along the x-axis, such that there still exists a framework that satisfies these position constraints. Deutsche Zusammenfassung Ein starres Fachwerk bezeichnet eine Einbettung eines Graphen - bei der jede Kante durch ein gerade Linie repräsentiert wird - und es keine stetige nicht-triviale Verschiebung der Knoten gibt, welche die Längen aller Kanten gleich lässt. -
Avis, David; Katoh, Naoki; Ohsaki, Makoto; Streinu, Ileana; Author(S) Tanigawa, Shin-Ichi
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kyoto University Research Information Repository Enumerating Constrained Non-crossing Minimally Rigid Title Frameworks Avis, David; Katoh, Naoki; Ohsaki, Makoto; Streinu, Ileana; Author(s) Tanigawa, Shin-ichi Citation Discrete and Computational Geometry (2008), 40(1): 31-46 Issue Date 2008-07 URL http://hdl.handle.net/2433/84862 Right The original publication is available at www.springerlink.com. Type Journal Article Textversion author Kyoto University Enumerating Constrained Non-crossing Minimally Rigid Frameworks David Avis 1 Naoki Katoh 2 Makoto Ohsaki 2 Ileana Streinu 3 Shin-ichi Tanigawa 2 April 25, 2007 Abstract In this paper we present an algorithm for enumerating without repetitions all the non-crossing generically minimally rigid bar-and-joint frameworks under edge constraints, which we call constrained non-crossing Laman frameworks, on a given set of n points in the plane. Our algorithm is based on the reverse search paradigm of Avis and Fukuda. It generates each output graph in O(n4) time and O(n) space, or, with a slightly different implementation, in O(n3) time and O(n2) space. In particular, we obtain that the set of all the constrained non-crossing Laman frameworks on a given point set is connected by flips which preserve the Laman property. Key words: geometric enumeration; rigidity; constrained non-crossing minimally rigid frameworks; constrained Delaunay triangulation. 1 Introduction Let G be a graph with vertices {1,...,n} and m edges. G is a Laman graph if m = 2n − 3 and every subset of n′ ≤ n vertices spans at most 2n′ − 3 edges. -
The Maximum Matroid for a Graph
The Maximum Matroid for a Graph Meera Sitharam and Andrew Vince University of Florida Gainesville, FL, USA [email protected] Abstract The ground set for all matroids in this paper is the set of all edges of a complete graph. The notion of a maximum matroid for a graph is introduced. The maximum matroid for K3 (or 3-cycle) is shown to be the cycle (or graphic) matroid. This result is persued in two directions - to determine the maximum matroid for the m-cycle and to determine the maximum matroid for the complete graph Km. While the maximum matroid for an m-cycle is determined for all m ≥ 4; the determination of the maximum matroids for the complete graphs is more complex. The maximum matroid for K4 is the matroid whose bases are the Laman graphs, related to structural rigidity of frameworks in the plane. The maximum matroid for K5 is related to a famous 153 year old open problem of J. C. Maxwell. An Algorithm A is provided, whose input is a given graph G and whose output is a matroid MA(G), defined in terms of its closure operator. The matroid MA(G) is proved to be the maximum matroid for G, implying that every graph has a unique maximum matroid. Keywords: graph, matroid, framework Mathematical subject codes: 05B35, 05C85, 52C25 1 Introduction Fix n and let Kn be the complete graph on n vertices. A graph in this paper is a subset E of the edge set E(Kn) of Kn. The number of edges of a graph E is denoted jEj and graph isomorphism by ≈. -
Dos Problemas De Combinatoria Geométrica: Triangulaciones
Dos problemas de combinatoria geometrica:´ Triangulaciones eficientes del hipercubo; Grafos planos y rigidez. (Two problems in geometric combinatorics: Efficient triangulations of the hypercube; Planar graphs and rigidity). David Orden Mart´ın Universidad de Cantabria Tesis doctoral dirigida por el Profesor Francisco Santos Leal. Santander, Marzo de 2003. 2 ´Indice Agradecimientos iii Pre´ambulo v Preamble vii 1 Introducci´on y Preliminares 1 1.1 Triangulaciones y subdivisiones de politopos . 1 1.1.1 Preliminares sobre Teor´ıa de Politopos . 2 1.1.2 Triangulaciones de cubos . 6 1.2 Teor´ıa de Grafos . 11 1.2.1 Preliminares y relaciones con politopos . 11 1.2.2 Inmersiones planas de grafos: Teorema de Tutte . 15 1.3 Teor´ıa de Rigidez . 20 1.3.1 La matriz de rigidez . 20 1.3.2 Tensiones y grafos rec´ıprocos . 23 1.3.3 Rigidez infinitesimal y grafos isost´aticos . 26 1.4 Pseudo-triangulaciones de cuerpos convexos y puntos . 29 1.4.1 Pseudo-triangulaciones de cuerpos convexos . 29 1.4.2 Pseudo-triangulaciones de puntos . 31 1.5Resultados y Problemas abiertos . 35 1.5.1 Triangulaciones eficientes de cubos . 35 1.5.2 Grafos sin cruces, rigidez y pseudo-triangulaciones . 36 1 Introduction and Preliminaries 41 1.1 Triangulations and subdivisions of polytopes . 41 1.1.1 Preliminaries about Polytope Theory . 42 1.1.2 Triangulations of cubes . 46 1.2 Graph Theory . 50 1.2.1 Preliminaries and relations with polytopes . 51 1.2.2 Plane embeddings of graphs: Tutte’s Theorem . 54 1.3 Rigidity Theory . 59 1.3.1 The rigidity matrix .