Optimal Point Placement for Mesh Smoothing

We study the problem of moving a vertex in an unstructured mesh of triangular, quadrilateral, or tetrahedral elements to optimize the shapes of adjacent elements. We show that many such problems can be solved in linear time using generalized linear programming. We also give efficient algorithms for some mesh smoothing problems that do not fit into the generalized linear programming paradigm.Comment: 12 pages, 3 figures. A preliminary version of this paper was presented at the 8th ACM/SIAM Symp. on Discrete Algorithms (SODA '97). This is the final version, and will appear in a special issue of J. Algorithms for papers from SODA '9

Conforming restricted Delaunay mesh generation for piecewise smooth complexes

A Frontal-Delaunay refinement algorithm for mesh generation in piecewise smooth domains is described. Built using a restricted Delaunay framework, this new algorithm combines a number of novel features, including: (i) an unweighted, conforming restricted Delaunay representation for domains specified as a (non-manifold) collection of piecewise smooth surface patches and curve segments, (ii) a protection strategy for domains containing curve segments that subtend sharply acute angles, and (iii) a new class of off-centre refinement rules designed to achieve high-quality point-placement along embedded curve features. Experimental comparisons show that the new Frontal-Delaunay algorithm outperforms a classical (statically weighted) restricted Delaunay-refinement technique for a number of three-dimensional benchmark problems.Comment: To appear at the 25th International Meshing Roundtabl

Local statistics for random domino tilings of the Aztec diamond

We prove an asymptotic formula for the probability that, if one chooses a domino tiling of a large Aztec diamond at random according to the uniform distribution on such tilings, the tiling will contain a domino covering a given pair of adjacent lattice squares. This formula quantifies the effect of the diamond's boundary conditions on the behavior of typical tilings; in addition, it yields a new proof of the arctic circle theorem of Jockusch, Propp, and Shor. Our approach is to use the saddle point method to estimate certain weighted sums of squares of Krawtchouk polynomials (whose relevance to domino tilings is demonstrated elsewhere), and to combine these estimates with some exponential sum bounds to deduce our final result. This approach generalizes straightforwardly to the case in which the probability distribution on the set of tilings incorporates bias favoring horizontal over vertical tiles or vice versa. We also prove a fairly general large deviation estimate for domino tilings of simply-connected planar regions that implies that some of our results on Aztec diamonds apply to many other similar regions as well.Comment: 42 pages, 7 figure

Once punctured disks, non-convex polygons, and pointihedra

We explore several families of flip-graphs, all related to polygons or punctured polygons. In particular, we consider the topological flip-graphs of once-punctured polygons which, in turn, contain all possible geometric flip-graphs of polygons with a marked point as embedded sub-graphs. Our main focus is on the geometric properties of these graphs and how they relate to one another. In particular, we show that the embeddings between them are strongly convex (or, said otherwise, totally geodesic). We also find bounds on the diameters of these graphs, sometimes using the strongly convex embeddings. Finally, we show how these graphs relate to different polytopes, namely type D associahedra and a family of secondary polytopes which we call pointihedra.Comment: 24 pages, 6 figure

Rooting a phylogenetic tree with nonreversible substitution models

BACKGROUND: We compared two methods of rooting a phylogenetic tree: the stationary and the nonstationary substitution processes. These methods do not require an outgroup. METHODS: Given a multiple alignment and an unrooted tree, the maximum likelihood estimates of branch lengths and substitution parameters for each associated rooted tree are found; rooted trees are compared using their likelihood values. Site variation in substitution rates is handled by assigning sites into several classes before the analysis. RESULTS: In three test datasets where the trees are small and the roots are assumed known, the nonstationary process gets the correct estimate significantly more often, and fits data much better, than the stationary process. Both processes give biologically plausible root placements in a set of nine primate mitochondrial DNA sequences. CONCLUSIONS: The nonstationary process is simple to use and is much better than the stationary process at inferring the root. It could be useful for situations where an outgroup is unavailable

Identifying combinations of tetrahedra into hexahedra: a vertex based strategy

Indirect hex-dominant meshing methods rely on the detection of adjacent tetrahedra an algorithm that performs this identification and builds the set of all possible combinations of tetrahedral elements of an input mesh T into hexahedra, prisms, or pyramids. All identified cells are valid for engineering analysis. First, all combinations of eight/six/five vertices whose connectivity in T matches the connectivity of a hexahedron/prism/pyramid are computed. The subset of tetrahedra of T triangulating each potential cell is then determined. Quality checks allow to early discard poor quality cells and to dramatically improve the efficiency of the method. Each potential hexahedron/prism/pyramid is computed only once. Around 3 millions potential hexahedra are computed in 10 seconds on a laptop. We finally demonstrate that the set of potential hexes built by our algorithm is significantly larger than those built using predefined patterns of subdivision of a hexahedron in tetrahedral elements.Comment: Preprint submitted to CAD (26th IMR special issue