The tetrahedral Cys2His2 Zn(II)-binding site in the de novo designed protein Z alpha 4 [Regan, L., & Clarke, N. D. (1990) Biochemistry 29, 10878] has been studied by independently mutating each of the metal-binding ligands to alanine. The contribution of each ligand to the geometry and affinity of metal binding has been characterized using Co(II), Zn(II), and Cd(II). The results indicate that a...

Topological drawings are natural representations of graphs in the plane, where vertices are represented by points, and edges by curves connecting the points. Topological drawings of complete graphs and of complete bipartite graphs have been studied extensively in the context of crossing number problems. We consider a natural class of simple topological drawings of complete bipartite graphs, in ...

The refinement of tetrahedral meshes is a significant task in many numerical and discretizations methods. The computational aspects for implementing refinement of meshes with complex geometry need to be carefully considered in order to have real-time and optimal results. In this paper we study some computational aspects of a class of tetrahedral refinement algorithms. For local adaptive refinem...

In this paper, we examine the numerical dispersion properties of the tetrahedral edge element in comparison to other edge and nodal elements. For all nodal elements as well as hexahedral edge elements, the phase error is always either positive or negative for waves propagating at any incidence angle, which means that the error accumulates as the wave propagates from element to element. This eff...

We address the problem of performing spatial queries on tetrahedral meshes. These latter arise in several application domains including 3D GIS, scientific visualization, finite element analysis. We have defined and implemented a family of spatial indexes, that we call tetrahedral trees. Tetrahedral trees are based on a subdivision of a cubic domain containing the mesh defined either by an octre...

We study the simplification of triangular and tetrahedral meshes using techniques based on successive edge collapses, as well as the exploitation of the generated multiple levels of detail for the effective processing of the models. Regarding triangular meshes, we present a method for the construction of progressive hulls, by suitable edge collapses; we use the generated hulls for the accelerat...

A new hybrid mesh generation method is proposed and applied to generate mesh for three-dimensional solids with open-ended tubular holes. Regions around the tubular holes are represented by hexahedral elements, and tetrahedral elements tessellate the rest of the domain. The procedure consists of three steps. Firstly, surfaces of tubular holes are recognized and discretized, and then the hexahedr...