Scales in RNA, based on geometrical considerations, can be exploited for the analysis and prediction of RNA structures. By using spectral decomposition, geometric information that relates to a given RNA fold can be reduced to a single positive scalar number, the second eigenvalue of the Laplacian matrix corresponding to the tree-graph representation of the RNA secondary structure. Along with th...

Docking-i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)-represents the ground of drug action mechanism of the vast majority of bioactive chemicals. Ligand and receptor accommodate their geometry and energy, within this interaction, in the benefit of receptor-ligand complex. In an induced fit docking, the structure of ligand is most susceptible to changes in to...

A permutation graph is an intersection graph of segments lying between two parallel lines. A Seidel complementation of a finite graph at one of it vertex v consists to complement the edges between the neighborhood and the non-neighborhood of v. Two graphs are Seidel complement equivalent if one can be obtained from the other by a successive application of Seidel complementation. In this paper w...

Gauss-Seidel method is often the smoother of choice within multigrid applications. In the context of unstructured meshes, however, maintaining good parallel efficiency is difficult with multiplicative iterative methods such as Gauss-Seidel. This leads us to consider alternative smoothers. We discuss the computational advantages of polynomial smoothers within parallel multigrid algorithms for po...

For a simple digraph G of order n with vertex set {v1, v2, . . . , vn}, let d+i and d − i denote the out-degree and in-degree of a vertex vi in G, respectively. Let D (G) = diag(d+1 , d + 2 , . . . , d + n ) and D−(G) = diag(d1 , d − 2 , . . . , d − n ). In this paper we introduce S̃L(G) = D̃(G)−S(G) to be a new kind of skew Laplacian matrix of G, where D̃(G) = D+(G)−D−(G) and S(G) is the skew-adj...

By embedding images as surfaces in a high dimensional coordinate space defined by each pixel’s Cartesian coordinates and color values, we directly define and employ cotangent-based, discrete differentialgeometry operators. These operators define discrete energies useful for image segmentation and colorization.