Four-regular graphs with rigid vertices associated to DNA recombination

Genome rearrangement and homological recombination processes have been modeled by Angeleska et al. [A. Angeleska, N. Jonoska, M. Saito, DNA recombinations through assembly graphs, Discrete Appl. Math. 157 (2009) 3020–3037] as 4-regular spacial graphs with rigid vertices, called assembly graphs. These graphs can also be represented by double occurrence words called assembly words. The rearranged DNA segments are modeled by certain types of paths in the assembly graphs called polygonal paths. The minimum number of polygonal paths visiting all vertices in a graph is called an assembly number for the graph.In this paper, we give formulas for counting certain types of assembly graphs and assembly words. Some of these formulas produce sequences not previously reported at the Online Encyclopedia of Integer Sequences (http://oeis.org). We provide a sharp upper bound for the number of polygonal paths in Hamiltonian sets of polygonal paths, and present a family of graphs that achieves this bound. We investigate changes in the assembly numbers as a result of graph compositions. Finally, we introduce a polynomial invariant for assembly graphs and show properties of this invariant.     

On Narrow Hexagonal Graphs with a 3-Homogeneous Suborbit

A connected graph of girth m 3 is called a polygonal graph if it contains a set of m-gons such that every path of length two is contained in a unique element of the set. In this paper we investigate polygonal graphs of girth 6 or more having automorphism groups which are transitive on the vertices and such that the vertex stabilizers are 3-homogeneous on adjacent vertices. We previously showed that the study of such graphs divides naturally into a number of substantial subcases. Here we analyze one of these cases and characterize the k-valent polygonal graphs of girth 6 which have automorphism groups transitive on vertices, which preserve the set of special hexagons, and which have a suborbit of size k – 1 at distance three from a given vertex.     

Graph theoretic approach to parallel gene assembly

We study parallel complexity of signed graphs motivated by the highly complex genetic recombination processes in ciliates. The molecular gene assembly operations have been modeled by operations of signed graphs, i.e., graphs where the vertices have a sign + or −. In the optimization problem for signed graphs one wishes to find the parallel complexity by which the graphs can be reduced to the empty graph. We relate parallel complexity to matchings in graphs for some natural graph classes, especially bipartite graphs. It is shown, for instance, that a bipartite graph G has parallel complexity one if and only if G has a unique perfect matching. We also formulate some open problems of this research topic.     

More on betweenness-uniform graphs

We study graphs whose vertices possess the same value of betweenness centrality (which is defined as the sum of relative numbers of shortest paths passing through a given vertex). Extending previously known results of S. Gago, J. Hurajová, T. Madaras (2013), we show that, apart of cycles, such graphs cannot contain 2-valent vertices and, moreover, are 3-connected if their diameter is 2. In addition, we prove that the betweenness uniformity is satisfied in a wide graph family of semi-symmetric graphs, which enables us to construct a variety of nontrivial cubic betweenness-uniform graphs.     

On Kauffman invariants for 6-valent graphs

An explicit way for producing invariants for 6-valent graphs with rigid vertices within the framework of Kauffman's approach to graph invariants is presented. These invariants can be used to detect the chirality of a 6-valent graph with rigid vertices. A relevant example is considered. Bibliography: 19 titles. Translated fromZapiski Nauchnykh Seminarov POMI, Vol. 223, 1995, pp. 251–262. Translated by A. M. Nikitin     

Claw-free graphs. III. Circular interval graphs

Construct a graph as follows. Take a circle, and a collection of intervals from it, no three of which have union the entire circle; take a finite set of points V from the circle; and make a graph with vertex set V in which two vertices are adjacent if they both belong to one of the intervals. Such graphs are “long circular interval graphs,” and they form an important subclass of the class of all claw-free graphs. In this paper we characterize them by excluded induced subgraphs. This is a step towards the main goal of this series, to find a structural characterization of all claw-free graphs.This paper also gives an analysis of the connected claw-free graphs G with a clique the deletion of which disconnects G into two parts both with at least two vertices.     

Intervals in matroid basis graphs

An interval in a graph is a subgraph induced by all the vertices on shortest paths between two given vertices. Intervals in matroid basis graphs satisfy many nice properties. Key results are: (1) any two vertices of a basis graph are together in some longest interval; (2) every basis graph with the minimum number of vertices for its diameter is an interval, indeed a hypercube. (1) turns out to be a simple case of a theorem in Edmonds' theory of matroid partition.     

Induced disjoint paths problem in a planar digraph

As an extension of the disjoint paths problem, we introduce a new problem which we call the induced disjoint paths problem. In this problem we are given a graph G and a collection of vertex pairs {(s₁,t₁),…,(s_k,t_k)}. The objective is to find k paths P₁,…,P_k such that P_i is a path from s_i to t_i and P_i and P_j have neither common vertices nor adjacent vertices for any distinct i,j.The induced disjoint paths problem has several variants depending on whether k is a fixed constant or a part of the input, whether the graph is directed or undirected, and whether the graph is planar or not. We investigate the computational complexity of several variants of the induced disjoint paths problem. We show that the induced disjoint paths problem is (i) solvable in polynomial time when k is fixed and G is a directed (or undirected) planar graph, (ii) NP-hard when k=2 and G is an acyclic directed graph, (iii) NP-hard when k=2 and G is an undirected general graph.As an application of our first result, we show that we can find in polynomial time certain structures called a “hole” and a “theta” in a planar graph.     

Non rank 3 strongly regular graphs with the 5-vertex condition

Three new strongly regular graphs on 256, 120, and 135 vertices are described in this paper. They satisfy thet-vertex condition — in the sense of [1] — on the edges and on the nonedges fort=4 but they are not rank 3 graphs. The problem to search for any such graph was discussed on a folklore level several times and was fixed in [2]. Here the graph on 256 vertices satisfies even the 5-vertex condition, and has the graphs on 120 and 135 vertices as its subgraphs. The existence of these graphs was announced in [3] and [4]. [4] contains M. H. Klin's interpretation of the graph on 120 vertices. Further results concerning these graphs were obtained by A. E. Brouwer, cf. [5].     

A construction of 3-connected graphs

We show that the 3-connected graphs can be generated from the complete graph on four vertices and the complete 3,3 bipartite graph by adding vertices and adding edges with endpoints on two edges meeting at a 3-valent vertex.     

Cubic graphs without cut‐vertices having the same path layer matrix

The path layer matrix (or path degree sequence) of a graph G contains quantitative information about all possible paths in G. The entry (i,j) of this matrix is the number of paths in G having initial vertex i and length j. It is known that there are cubic graphs on 62 vertices having the same path layer matrix (A. A. Dobrynin. J Graph Theory 17 (1993) 1–4). A new upper bound of 36 vertices for the least order of such cubic graphs is established. This bound is realized by cubic graphs without cut‐vertices. © 2001 John Wiley & Sons, Inc. J Graph Theory 38: 177–182, 2001     

Bigeodetic graphs

Bigeodetic graphs, a generalization of geodetic and interval-regular graphs, are defined as graphs in which each pair of vertices has at most two paths of minimum length between them. The block cut-vertex incidence pattern of bigeodetic separable graphs are discussed. Two characterizations of bigeodetic graphs are given and some properties of these graphs are studied. Construction of planar bigeodetic blocks with given girth and diameter, and construction of hamiltonian and eulerian/nonhamiltonian and noneulerian, perfect bigeodetic blocks are discussed. The extremal bigeodetic graph of diameterd onp d + 1 vertices is constructed.On leave from A.M. Jain College, Madras University, Madras 600114, India     

A classification of tightly attached half-arc-transitive graphs of valency 4

A graph is said to be half-arc-transitive if its automorphism group acts transitively on the set of its vertices and edges but not on the set of its arcs. With each half-arc-transitive graph of valency 4 a collection of the so-called alternating cycles is associated, all of which have the same even length. Half of this length is called the radius of the graph in question. Moreover, any two adjacent alternating cycles have the same number of common vertices. If this number, the so-called attachment number, coincides with the radius, we say that the graph is tightly attached. In [D. Marušič, Half-transitive group actions on finite graphs of valency 4, J. Combin. Theory Ser. B 73 (1998) 41–76], Marušič gave a classification of tightly attached half-arc-transitive graphs of valency 4 with odd radius. In this paper the even radius tightly attached graphs of valency 4 are classified, thus completing the classification of all tightly attached half-arc-transitive graphs of valency 4.     

A solitaire game played on 2-colored graphs

We introduce a solitaire game played on a graph. Initially one disk is placed at each vertex, one face green and the other red, oriented with either color facing up. Each move of the game consists of selecting a vertex whose disk shows green, flipping over the disks at neighboring vertices, and deleting the selected vertex. The game is won if all vertices are eliminated. We derive a simple parity-based necessary condition for winnability of a given game instance. By studying graph operations that construct new graphs from old ones, we obtain broad classes of graphs where this condition also suffices, thus characterizing the winnable games on such graphs. Concerning two familiar (but narrow) classes of graphs, we show that for trees a game is winnable if and only if the number of green vertices is odd, and for n-cubes a game is winnable if and only if the number of green vertices is even and not all vertices have the same color. We provide a linear-time algorithm for deciding winnability for games on maximal outerplanar graphs. We reduce the decision problem for winnability of a game on an arbitrary graph G to winnability of games on its blocks, and to winnability on homeomorphic images of G obtained by contracting edges at 2-valent vertices.     

On the harmonious coloring of collections of graphs

The hermonious coloring number of the graph G, HC(G), is the smallest number of colors needed to label the vertices of G such that adjacent vertices received different colors and no two edges are incident with the same color pair. In this paper, we investigate the HC-number of collections of disjoint paths, cycles, complete graphs, and complete bipartite graphs. We determine exact expressions for the HC-number of collections of paths and 4m-cycles. © 1995, John Wiley & Sons, Inc.     

A sufficient condition for a graph to be hamiltonian

Those non-hamiltonian graphsG withn vertices are characterized, which satisfy the Ore-type degree-conditiond(x)+d(y)n–2 for each pairx,yM of different nonadjacent vertices whereM consists of two vertices ofG. As an application a theorem on hamiltonian connectivity of graphs is given. Furthermore, a condition is presented which is sufficient for the existence of a covering of a graph by two disjoint paths with prescribed set of startpoints and prescribed set of endpoints. A class of graphs is described which have no covering of this kind.     

An exact algorithm for subgraph homeomorphism

The subgraph homeomorphism problem is to decide if there is an injective mapping of the vertices of a pattern graph into vertices of a host graph so that the edges of the pattern graph can be mapped into (internally) vertex-disjoint paths in the host graph. The restriction of subgraph homeomorphism where an injective mapping of the vertices of the pattern graph into vertices of the host graph is already given in the input instance is termed fixed-vertex subgraph homeomorphism.We show that fixed-vertex subgraph homeomorphism for a pattern graph on p vertices and a host graph on n vertices can be solved in time 2^n−pn^O(1) or in time 3^n−pn^O(1) and polynomial space. In effect, we obtain new non-trivial upper bounds on the time complexity of the problem of finding k vertex-disjoint paths and general subgraph homeomorphism.     

Finding Optimal Routings in Hamming Graphs

A routing R in a graph consists of a simple path p_uvfromu to v for each ordered pair of distinct vertices (u, v). We will call R optimal if all the paths p_uvare shortest paths and if edges of the graph occur equally often in the paths of R. In 1994, Solé gave a sufficient condition involving the automorphism group for a graph to have an optimal routing in this sense. Graphs which satisfy Solé’s condition are called orbital regular graphs. It is often difficult to determine whether or not a given graph is orbital regular. In this paper, we give a necessary and sufficient condition for a Hamming graph to be orbital regular with respect to a certain natural subgroup of automorphisms.     

On the Convexity Number of Graphs

A set of vertices S in a graph is convex if it contains all vertices which belong to shortest paths between vertices in S. The convexity number c(G) of a graph G is the maximum cardinality of a convex set of vertices which does not contain all vertices of G. We prove NP-completeness of the problem to decide for a given bipartite graph G and an integer k whether c(G) ≥ k. Furthermore, we identify natural necessary extension properties of graphs of small convexity number and study the interplay between these properties and upper bounds on the convexity number.     

Automorphism groups of graphs with forbidden subgraphs

For a graph Ф letF(Ф) be the class of finite graphs which do not contain an induced subgraph isomorphic to Ф. We show that whenever Ф is not isomorphic to a path on at most 4 vertices or to the complement of such a graph then for every finite groupG there exists a graph ГєF(Ф) such thatG is isomorphic to the automorphism group of Г. For all paths д on at most 4 vertices we determine the class of all automorphism groups of members ofF(д).