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...

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.

In geometry processing, smoothness energies are commonly used to model scattered data interpolation, dense data denoising, and regularization during shape optimization. The squared Laplacian energy is a popular choice of energy and has a corresponding standard implementation: squaring the discrete Laplacian matrix. For compact domains, when values along the boundary are not known in advance, th...

In this work, we study the stability of Hopf vector fields on Lorentzian Berger spheres as critical points of the energy, the volume and the generalized energy. In order to do so, we construct a family of vector fields using the simultaneous eigenfunctions of the Laplacian and of the vertical Laplacian of the sphere. The Hessians of the functionals are negative when they act on these particular...