Large-n conditional facedness m_n of 3D Poisson-Voronoi cells

We consider the three-dimensional Poisson-Voronoi tessellation and study the average facedness m_n of a cell known to neighbor an n-faced cell. Whereas Aboav's law states that m_n=A+B/n, theoretical arguments indicate an asymptotic expansion m_n = 8 + k_1 n^{-1/6} +.... Recent new Monte Carlo data due to Lazar et al., based on a very large data set, now clearly rule out Aboav's law. In this work we determine the numerical value of k_1 and compare the expansion to the Monte Carlo data. The calculation of k_1 involves an auxiliary planar cellular structure composed of circular arcs, that we will call the Poisson-Moebius diagram. It is a special case of more general Moebius diagrams (or multiplicatively weighted power diagrams) and is of interest for its own sake. We obtain exact results for the total edge length per unit area, which is a prerequisite for the coefficient k_1, and a few other quantities in this diagram.Comment: 18 pages, 5 figure

Metric combinatorics of convex polyhedra: cut loci and nonoverlapping unfoldings

This paper is a study of the interaction between the combinatorics of boundaries of convex polytopes in arbitrary dimension and their metric geometry. Let S be the boundary of a convex polytope of dimension d+1, or more generally let S be a `convex polyhedral pseudomanifold'. We prove that S has a polyhedral nonoverlapping unfolding into R^d, so the metric space S is obtained from a closed (usually nonconvex) polyhedral ball in R^d by identifying pairs of boundary faces isometrically. Our existence proof exploits geodesic flow away from a source point v in S, which is the exponential map to S from the tangent space at v. We characterize the `cut locus' (the closure of the set of points in S with more than one shortest path to v) as a polyhedral complex in terms of Voronoi diagrams on facets. Analyzing infinitesimal expansion of the wavefront consisting of points at constant distance from v on S produces an algorithmic method for constructing Voronoi diagrams in each facet, and hence the unfolding of S. The algorithm, for which we provide pseudocode, solves the discrete geodesic problem. Its main construction generalizes the source unfolding for boundaries of 3-polytopes into R^2. We present conjectures concerning the number of shortest paths on the boundaries of convex polyhedra, and concerning continuous unfolding of convex polyhedra. We also comment on the intrinsic non-polynomial complexity of nonconvex polyhedral manifolds.Comment: 47 pages; 21 PostScript (.eps) figures, most in colo

The still-Life density problem and its generalizations

A "still Life" is a subset S of the square lattice Z^2 fixed under the transition rule of Conway's Game of Life, i.e. a subset satisfying the following three conditions: 1. No element of Z^2-S has exactly three neighbors in S; 2. Every element of S has at least two neighbors in S; 3. Every element of S has at most three neighbors in S. Here a ``neighbor'' of any x \in Z^2 is one of the eight lattice points closest to x other than x itself. The "still-Life conjecture" is the assertion that a still Life cannot have density greater than 1/2 (a bound easily attained, for instance by {(x,y): x is even}). We prove this conjecture, showing that in fact condition 3 alone ensures that S has density at most 1/2. We then consider variations of the problem such as changing the number of allowed neighbors or the definition of neighborhoods; using a variety of methods we find some partial results and many new open problems and conjectures.Comment: 29 pages, including many figures drawn as LaTeX "pictures

Local Anisotropy of Fluids using Minkowski Tensors

Statistics of the free volume available to individual particles have previously been studied for simple and complex fluids, granular matter, amorphous solids, and structural glasses. Minkowski tensors provide a set of shape measures that are based on strong mathematical theorems and easily computed for polygonal and polyhedral bodies such as free volume cells (Voronoi cells). They characterize the local structure beyond the two-point correlation function and are suitable to define indices $0\leq \beta_\nu^{a,b}\leq 1$ of local anisotropy. Here, we analyze the statistics of Minkowski tensors for configurations of simple liquid models, including the ideal gas (Poisson point process), the hard disks and hard spheres ensemble, and the Lennard-Jones fluid. We show that Minkowski tensors provide a robust characterization of local anisotropy, which ranges from $\beta_\nu^{a,b}\approx 0.3$ for vapor phases to $\beta_\nu^{a,b}\to 1$ for ordered solids. We find that for fluids, local anisotropy decreases monotonously with increasing free volume and randomness of particle positions. Furthermore, the local anisotropy indices $\beta_\nu^{a,b}$ are sensitive to structural transitions in these simple fluids, as has been previously shown in granular systems for the transition from loose to jammed bead packs

Cell shape analysis of random tessellations based on Minkowski tensors

To which degree are shape indices of individual cells of a tessellation characteristic for the stochastic process that generates them? Within the context of stochastic geometry and the physics of disordered materials, this corresponds to the question of relationships between different stochastic models. In the context of image analysis of synthetic and biological materials, this question is central to the problem of inferring information about formation processes from spatial measurements of resulting random structures. We address this question by a theory-based simulation study of shape indices derived from Minkowski tensors for a variety of tessellation models. We focus on the relationship between two indices: an isoperimetric ratio of the empirical averages of cell volume and area and the cell elongation quantified by eigenvalue ratios of interfacial Minkowski tensors. Simulation data for these quantities, as well as for distributions thereof and for correlations of cell shape and volume, are presented for Voronoi mosaics of the Poisson point process, determinantal and permanental point processes, and Gibbs hard-core and random sequential absorption processes as well as for Laguerre tessellations of polydisperse spheres and STIT- and Poisson hyperplane tessellations. These data are complemented by mechanically stable crystalline sphere and disordered ellipsoid packings and area-minimising foam models. We find that shape indices of individual cells are not sufficient to unambiguously identify the generating process even amongst this limited set of processes. However, we identify significant differences of the shape indices between many of these tessellation models. Given a realization of a tessellation, these shape indices can narrow the choice of possible generating processes, providing a powerful tool which can be further strengthened by density-resolved volume-shape correlations.Comment: Chapter of the forthcoming book "Tensor Valuations and their Applications in Stochastic Geometry and Imaging" in Lecture Notes in Mathematics edited by Markus Kiderlen and Eva B. Vedel Jense

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure