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16
Construction of planar triangulations with minimum degree 5
, 1969
"... In this article we describe a method of constructing all simple triangulations of the sphere with minimum degree 5; equivalently, 3connected planar cubic graphs with girth 5. We also present the results of a computer program based on this algorithm, including counts of convex polytopes of minimum d ..."
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In this article we describe a method of constructing all simple triangulations of the sphere with minimum degree 5; equivalently, 3connected planar cubic graphs with girth 5. We also present the results of a computer program based on this algorithm, including counts of convex polytopes of minimum degree 5. Key words: planar triangulation, cubic graph, generation, fullerene
Fullerenes and Coordination Polyhedra versus HalfCubes Embeddings
, 1997
"... A fullerene F n is a 3regular (or cubic) polyhedral carbon molecule for which the n vertices  the carbons atoms  are arranged in 12 pentagons and ( n 2 \Gamma 10) hexagons. Only a finite number of fullerenes are expected to be, up to scale, isometrically embeddable into a hypercube. Looking fo ..."
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A fullerene F n is a 3regular (or cubic) polyhedral carbon molecule for which the n vertices  the carbons atoms  are arranged in 12 pentagons and ( n 2 \Gamma 10) hexagons. Only a finite number of fullerenes are expected to be, up to scale, isometrically embeddable into a hypercube. Looking for the list of such fullerenes, we first check the embeddability of all fullerenes F n for n ! 60 and of all preferable fullerenes C n for n ! 86 and their duals. Then, we consider some infinite families, including fullerenes with icosahedral symmetry, which describe virus capsids, onionlike metallic clusters and geodesic domes. Quasiembeddings and fullerene analogues are considered. We also present some results on chemically relevant polyhedra such as coordination polyhedra and cluster polyhedra. Finally we conjecture that the list of known embeddable fullerenes is complete and present its relevance to the Katsura model for vesicles cells. Contents 1 Introduction and Basic Properties 2 1...
Generating Fullerenes at Random
, 1996
"... In the present paper a method for generating fullerenes at random is presented. It is based on the well known StoneWales (SW) transformation. The method could be further generalised so that other trivalent polyhedra with prescribed properties are generated. 1. INTRODUCTION Fullerenes and other pu ..."
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In the present paper a method for generating fullerenes at random is presented. It is based on the well known StoneWales (SW) transformation. The method could be further generalised so that other trivalent polyhedra with prescribed properties are generated. 1. INTRODUCTION Fullerenes and other pure carbon cages remain a subject of rigorous research. The mechanism of fullerenes growth is still not fully understood although much has been learned 1 . In the present paper a method for generating fullerenes at random is presented. It is based on the well known StoneWales (SW) transformation 2; 3 and it has been successfully implemented as a part of the VEGA: a system for manipulating discrete mathematical structures. 4; 5 The method could be further generalised so that it is able to narrow the population of carbon cages with special properties. From a mathematical standpoint a fullerene is planar trivalent graph whose faces are pentagons and hexagons. It turns out that the number...
Tree Orbits under Permutation Group Action: Algorithm, Enumeration and Application to Viral Assembly
, 2009
"... This paper uses combinatorics and group theory to answer questions about the assembly of icosahedral viral shells. Although the geometric structure of the capsid (shell) is fairly well understood in terms of its constituent subunits, the assembly process is not. For the purpose of this paper, the ca ..."
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This paper uses combinatorics and group theory to answer questions about the assembly of icosahedral viral shells. Although the geometric structure of the capsid (shell) is fairly well understood in terms of its constituent subunits, the assembly process is not. For the purpose of this paper, the capsid is modeled by a polyhedron whose facets represent the monomers. The assembly process is modeled by a rooted tree, the leaves representing the facets of the polyhedron, the root representing the assembled polyhedron, and the internal vertices representing intermediate stages of assembly (subsets of facets). Besides its virological motivation, the enumeration of orbits of trees under the action of a finite group is of independent mathematical interest. If G is a finite group acting on a finite set X, then there is a natural induced action of G on the set TX of trees whose leaves are bijectively labeled by the elements of X. If G acts simply on X, then X : = Xn  = n · G, where n is the number of Gorbits in X. The basic combinatorial results in this paper are (1) a formula for the number of orbits of each size in the action of G on TXn, for every n, and (2) a simple algorithm to find the stabilizer of a tree τ ∈ TX in G that runs in linear time and does not need memory in addition to its input tree.
Computers and Discovery in Algebraic Graph Theory
 Edinburgh, 2001), Linear Algebra Appl
, 2001
"... We survey computers systems which help to obtain and sometimes provide automatically conjectures and refutations in algebraic graph theory. ..."
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We survey computers systems which help to obtain and sometimes provide automatically conjectures and refutations in algebraic graph theory.
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"... Recursive generation of simple planar quadrangulations with vertices of degree 3 and 4 ..."
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Recursive generation of simple planar quadrangulations with vertices of degree 3 and 4
COUNTING AND ENUMERATION OF SELFASSEMBLY PATHWAYS FOR SYMMETRIC MACROMOLECULAR STRUCTURES
"... We consider the problem of explicitly enumerating and counting the assembly pathways by which an icosahedral viral shell forms from identical constituent protein monomers. This poorly understood assembly process is a remarkable example of symmetric macromolecular selfassembly occuring in nature and ..."
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We consider the problem of explicitly enumerating and counting the assembly pathways by which an icosahedral viral shell forms from identical constituent protein monomers. This poorly understood assembly process is a remarkable example of symmetric macromolecular selfassembly occuring in nature and possesses many features that are desirable while engineering selfassembly at the nanoscale. We use the new model of���that employs a static geometric constraint graph to represent the driving (weak) forces that cause a viral shell to assemble and hold it together. The model was developed to answer focused questions about the structural properties of the most probable types of successful assembly pathways. Specifically, the model reduces the study of pathway types and their probabilities to the study of the orbits of the automorphism group of the underlying geometric constraint graph, acting on the set of pathways. Since these are highly symmetric polyhedral graphs, it seems a viable approach to explicitly enumerate these orbits and count their sizes. The contribution of this paper is to isolate and simplify the core combinatorial questions, list related work and indicate the advantages of an explicit enumerative approach. 1.
THE INFLUENCE OF SYMMETRY ON THE PROBABILITY OF ASSEMBLY PATHWAYS FOR ICOSAHEDRAL VIRAL SHELLS
"... This paper motivates and sets up the mathematical framework for a new program of investigation: to isolate and clarify the precise influence of symmetry on the probability space of assembly pathways that successfully lead to icosahedral viral shells. Several tractable open questions are posed. Besid ..."
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This paper motivates and sets up the mathematical framework for a new program of investigation: to isolate and clarify the precise influence of symmetry on the probability space of assembly pathways that successfully lead to icosahedral viral shells. Several tractable open questions are posed. Besides its virology motivation, the topic is of independent mathematical interest for studying constructions of symmetric polyhedra. Preliminary results are presented: a natural, structural classification of subsets of facets of T = 1 polyhedra, based on their stabilizing subgroups of the icosahedral group; and a theorem that uses symmetry to formalize why increasing depth increases the numeracy (and hence probability) of an assembly pathway type (or symmetry class) for a T = 1 viral shell. 1.