Finite Dimension: A Mathematical Tool to Analise Glycans

There is a need to develop widely applicable tools to understand glycan organization, diversity and structure. We present a graph-theoretical study of a large sample of glycans in terms of finite dimension, a new metric which is an adaptation to finite sets of the classical Hausdorff "fractal" dimension. Every glycan in the sample is encoded, via finite dimension, as a point of Glycan Space, a new notion introduced in this paper. Two major outcomes were found: (a) the existence of universal bounds that restrict the universe of possible glycans and show, for instance, that the graphs of glycans are a very special type of chemical graph, and (b) how Glycan Space is related to biological domains associated to the analysed glycans. In addition, we discuss briefly how this encoding may help to improve search in glycan databases.Fil: Alonso, Juan Manuel. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Arroyuelo, Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Garay, Pablo Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Martín, Osvaldo Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentin

Rainbow domination and related problems on some classes of perfect graphs

Let $k \in \mathbb{N}$ and let $G$ be a graph. A function $f: V(G) \rightarrow 2^{[k]}$ is a rainbow function if, for every vertex $x$ with $f(x)=\emptyset$, $f(N(x)) =[k]$. The rainbow domination number $\gamma_{kr}(G)$ is the minimum of $\sum_{x \in V(G)} |f(x)|$ over all rainbow functions. We investigate the rainbow domination problem for some classes of perfect graphs

A characterization of intersection graphs of the maximal rectangles of a polyomino

AbstractThe interior of an orthogonal polygon drawn on a regular grid of the plane defines a set of cells (or squares) called a polyomino. We prove that the intersection graph of the maximal rectangles contained in a polyomino is slightly triangulated or has a star cutset

On the linear extension complexity of stable set polytopes for perfect graphs

We study the linear extension complexity of stable set polytopes of perfect graphs. We make use of known structural results permitting to decompose perfect graphs into basic perfect graphs by means of two graph operations: 2-joins and skew partitions. Exploiting the link between extension complexity and the nonnegative rank of an associated slack matrix, we investigate the behavior of the extension complexity under these graph operations. We show bounds for the extension complexity of the stable set polytope of a perfect graph G depending linearly on the size of G and involving the depth of a decomposition tree of G in terms of basic perfect graphs

Covering orthogonal polygons with star polygons: The perfect graph approach

AbstractThis paper studies the combinatorial structure of visibility in orthogonal polygons. We show that the visibility graph for the problem of minimally covering simple orthogonal polygons with star polygons is perfect. A star polygon contains a point p, such that for every point q in the star polygon, there is an orthogonally convex polygon containing p and q. This perfectness property implies a polynomial algorithm for the above polygon covering problem. It further provides us with an interesting duality relationship. We first establish that a minimum clique cover of the visibility graph of a simple orthogonal polygon corresponds exactly to a minimum star cover of the polygon. In general, simple orthogonal polygons can have concavities (dents) with four possible orientations. In this case, we show that the visibility graph is weakly triangulated. We thus obtain an O(n8) algorithm. Since weakly triangulated graphs are perfect, we also obtain an interesting duality relationship. In the case where the polygon has at most three dent orientations, we show that the visibility graph is triangulated or chordal. This gives us an O(n3) algorithm

Independent sets in asteroidal triple-free graphs

An asteroidal triple is a set of three vertices such that there is a path between any pair of them avoiding the closed neighborhood of the third. A graph is called AT-free if it does not have an asteroidal triple. We show that there is an O(n 2 · (¯m+1)) time algorithm to compute the maximum cardinality of an independent set for AT-free graphs, where n is the number of vertices and ¯m is the number of non edges of the input graph. Furthermore we obtain O(n 2 · (¯m+1)) time algorithms to solve the INDEPENDENT DOMINATING SET and the INDEPENDENT PERFECT DOMINATING SET problem on AT-free graphs. We also show how to adapt these algorithms such that they solve the corresponding problem for graphs with bounded asteroidal number in polynomial time. Finally we observe that the problems CLIQUE and PARTITION INTO CLIQUES remain NP-complete when restricted to AT-free graphs