Some characterizations of the exceptional planar embedding of W(2)

AbstractIn this paper, we study the representation of W(2) in PG(2,4) related to a hyperoval. We provide a group-theoretic characterization and some geometric ones

Steinitz Theorems for Orthogonal Polyhedra

We define a simple orthogonal polyhedron to be a three-dimensional polyhedron with the topology of a sphere in which three mutually-perpendicular edges meet at each vertex. By analogy to Steinitz's theorem characterizing the graphs of convex polyhedra, we find graph-theoretic characterizations of three classes of simple orthogonal polyhedra: corner polyhedra, which can be drawn by isometric projection in the plane with only one hidden vertex, xyz polyhedra, in which each axis-parallel line through a vertex contains exactly one other vertex, and arbitrary simple orthogonal polyhedra. In particular, the graphs of xyz polyhedra are exactly the bipartite cubic polyhedral graphs, and every bipartite cubic polyhedral graph with a 4-connected dual graph is the graph of a corner polyhedron. Based on our characterizations we find efficient algorithms for constructing orthogonal polyhedra from their graphs.Comment: 48 pages, 31 figure

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

On the cone of effective 2-cycles on M‾0,7\overline{M}_{0,7}

Fulton's question about effective $k$-cycles on $\overline{M}_{0,n}$ for $1<k<n-4$ can be answered negatively by appropriately lifting to $\overline{M}_{0,n}$ the Keel-Vermeire divisors on $\overline{M}_{0,k+1}$. In this paper we focus on the case of $2$-cycles on $\overline{M}_{0,7}$, and we prove that the $2$-dimensional boundary strata together with the lifts of the Keel-Vermeire divisors are not enough to generate the cone of effective $2$-cycles. We do this by providing examples of effective $2$-cycles on $\overline{M}_{0,7}$ that cannot be written as an effective combination of the aforementioned $2$-cycles. These examples are inspired by a blow up construction of Castravet and Tevelev.Comment: 22 pages, 4 figures. Final version. Minor corrections. To appear in the European Journal of Mathematic

Cohen-Macaulay Du Bois singularities with a torus action of complexity one

Using Altmann-Hausen-S\"u\ss\ description of T-varieties via divisorial fans and K\'ovacs-Schwede-Smith characterization of Du Bois singularities we prove that any rational T-variety of complexity one which is Cohen-Macaulay and Du Bois has rational singularities. In higher complexity, we prove an analogous result in the case where the Chow quotient of the T-variety has Picard rank one and trivial geometric genus.Comment: 16 page

Combinatorial RNA Design Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models

We consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure. We consider two free-energy models where the contributions of base pairs are additive and independent: the purely combinatorial Watson-Crick model, which only allows equally-contributing A -- U and C -- G base pairs, and the real-valued Nussinov-Jacobson model, which associates arbitrary energies to A -- U, C -- G and G -- U base pairs. We first provide a complete characterization of designable structures using restricted alphabets and, in the four-letter alphabet, provide a complete characterization for designable structures without unpaired bases. When unpaired bases are allowed, we characterize extensive classes of (non-)designable structures, and prove the closure of the set of designable structures under the stutter operation. Membership of a given structure to any of the classes can be tested in $\Theta$(n) time, including the generation of a solution sequence for positive instances. Finally, we consider a structure-approximating relaxation of the design, and provide a $\Theta$(n) algorithm which, given a structure S that avoids two trivially non-designable motifs, transforms S into a designable structure constructively by adding at most one base-pair to each of its stems.Comment: To appea

Three-coloring triangle-free graphs on surfaces II. 4-critical graphs in a disk

Let G be a plane graph of girth at least five. We show that if there exists a 3-coloring phi of a cycle C of G that does not extend to a 3-coloring of G, then G has a subgraph H on O(|C|) vertices that also has no 3-coloring extending phi. This is asymptotically best possible and improves a previous bound of Thomassen. In the next paper of the series we will use this result and the attendant theory to prove a generalization to graphs on surfaces with several precolored cycles.Comment: 48 pages, 4 figures This version: Revised according to reviewer comment

An extensive English language bibliography on graph theory and its applications, supplement 1

Graph theory and its applications - bibliography, supplement