Switching Reconstruction of Digraphs

Switching about a vertex in a digraph means to reverse the direction of every edge incident with that vertex. Bondy and Mercier introduced the problem of whether a digraph can be reconstructed up to isomorphism from the multiset of isomorphism types of digraphs obtained by switching about each vertex. Since the largest known non-reconstructible oriented graphs have 8 vertices, it is natural to ask whether there are any larger non-reconstructible graphs. In this paper we continue the investigation of this question. We find that there are exactly 44 non-reconstructible oriented graphs whose underlying undirected graphs have maximum degree at most 2. We also determine the full set of switching-stable oriented graphs, which are those graphs for which all switchings return a digraph isomorphic to the original

Eulerian digraphs and toric Calabi-Yau varieties

We investigate the structure of a simple class of affine toric Calabi-Yau varieties that are defined from quiver representations based on finite eulerian directed graphs (digraphs). The vanishing first Chern class of these varieties just follows from the characterisation of eulerian digraphs as being connected with all vertices balanced. Some structure theory is used to show how any eulerian digraph can be generated by iterating combinations of just a few canonical graph-theoretic moves. We describe the effect of each of these moves on the lattice polytopes which encode the toric Calabi-Yau varieties and illustrate the construction in several examples. We comment on physical applications of the construction in the context of moduli spaces for superconformal gauged linear sigma models.Comment: 27 pages, 8 figure

On the structure of quadrilateral brane tilings

Brane tilings provide the most general framework in string and M-theory for matching toric Calabi-Yau singularities probed by branes with superconformal fixed points of quiver gauge theories. The brane tiling data consists of a bipartite tiling of the torus which encodes both the classical superpotential and gauge-matter couplings for the quiver gauge theory. We consider the class of tilings which contain only tiles bounded by exactly four edges and present a method for generating any tiling within this class by iterating combinations of certain graph-theoretic moves. In the context of D3-branes in IIB string theory, we consider the effect of these generating moves within the corresponding class of supersymmetric quiver gauge theories in four dimensions. Of particular interest are their effect on the superpotential, the vacuum moduli space and the conditions necessary for the theory to reach a superconformal fixed point in the infrared. We discuss the general structure of physically admissible quadrilateral brane tilings and Seiberg duality in terms of certain composite moves within this class.Comment: 57 pages, 22 figure

Reconstructing Gene Trees From Fitch's Xenology Relation

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains within the ancestral lineage. Hence xenology is more precisely thought of as a non-symmetric relation: $y$ is xenologous to $x$ if $y$ has been horizontally transferred at least once since it diverged from the least common ancestor of $x$ and $y$. We show that xenology relations are characterized by a small set of forbidden induced subgraphs on three vertices. Furthermore, each xenology relation can be derived from a unique least-resolved edge-labeled phylogenetic tree. We provide a linear-time algorithm for the recognition of xenology relations and for the construction of its least-resolved edge-labeled phylogenetic tree. The fact that being a xenology relation is a heritable graph property, finally has far-reaching consequences on approximation problems associated with xenology relations

Seurat games on Stockmeyer graphs

We define a family of vertex colouring games played over a pair of graphs or digraphs (G, H) by players ∀ and ∃. These games arise from work on a longstanding open problem in algebraic logic. It is conjectured that there is a natural number n such that ∀ always has a winning strategy in the game with n colours whenever G 6∼= H. This is related to the reconstruction conjecture for graphs and the degree-associated reconstruction conjecture for digraphs. We show that the reconstruction conjecture implies our game conjecture with n = 3 for graphs, and the same is true for the degree-associated reconstruction conjecture and our conjecture for digraphs. We show (for any k < ω) that the 2-colour game can distinguish certain non-isomorphic pairs of graphs that cannot be distinguished by the k-dimensional Weisfeiler-Leman algorithm. We also show that the 2-colour game can distinguish the non-isomorphic pairs of graphs in the families defined by Stockmeyer as counterexamples to the original digraph reconstruction conjecture

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations