A geometrical approach to computing free-energy landscapes from short-ranged potentials

Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free-energy landscape of such systems as the range of the potential goes to zero. In this limit, the landscape is entirely defined by geometrical manifolds, plus a single control parameter. These manifolds are fundamental objects that do not depend on the details of the interaction potential and provide the starting point from which any quantity characterizing the system—equilibrium or nonequilibrium—can be computed for arbitrary potentials. To consider dynamical quantities we compute the asymptotic limit of the Fokker–Planck equation and show that it becomes restricted to the low-dimensional manifolds connected by “sticky” boundary conditions. To illustrate our theory, we compute the low-dimensional manifolds for Graphic identical particles, providing a complete description of the lowest-energy parts of the landscape including floppy modes with up to 2 internal degrees of freedom. The results can be directly tested on colloidal clusters. This limit is a unique approach for understanding energy landscapes, and our hope is that it can also provide insight into finite-range potentials.Engineering and Applied Science

Geometry videos

We present the "Geometry Video," a new data structure to encode animated meshes. Being able to encode animated meshes in a generic source-independent format allows people to share experiences. Changing the viewpoint allows more interaction than the fixed view supported by 2D video. Geometry videos are based on the "Geometry Image" mesh representation introduced by Gu et al. Our novel data structure provides a way to treat an animated mesh as a video sequence (i.e., 3D image) and is well suited for network streaming. This representation also offers the possibility of applying and adapting existing mature video processing and compression techniques (such as MPEG encoding) to animated meshes. This paper describes an algorithm to generate geometry videos from animated meshes.The main insight of this paper, is that Geometry Videos re-sample and re-organize the geometry information, in such a way, that it becomes very compressible. They provide a unified and intuitive method for level-of-detail control, both in terms of mesh resolution (by scaling the two spatial dimensions) and of frame rate (by scaling the temporal dimension). Geometry Videos have a very uniform and regular structure. Their resource and computational requirements can be calculated exactly, hence making them also suitable for applications requiring level of service guarantees.Engineering and Applied Science

Convexity-Increasing Morphs of Planar Graphs

We study the problem of convexifying drawings of planar graphs. Given any planar straight-line drawing of an internally 3-connected graph, we show how to morph the drawing to one with strictly convex faces while maintaining planarity at all times. Our morph is convexity-increasing, meaning that once an angle is convex, it remains convex. We give an efficient algorithm that constructs such a morph as a composition of a linear number of steps where each step either moves vertices along horizontal lines or moves vertices along vertical lines. Moreover, we show that a linear number of steps is worst-case optimal. To obtain our result, we use a well-known technique by Hong and Nagamochi for finding redrawings with convex faces while preserving y-coordinates. Using a variant of Tutte's graph drawing algorithm, we obtain a new proof of Hong and Nagamochi's result which comes with a better running time. This is of independent interest, as Hong and Nagamochi's technique serves as a building block in existing morphing algorithms.Comment: Preliminary version in Proc. WG 201

Discrete exterior calculus (DEC) for the surface Navier-Stokes equation

We consider a numerical approach for the incompressible surface Navier-Stokes equation. The approach is based on the covariant form and uses discrete exterior calculus (DEC) in space and a semi-implicit discretization in time. The discretization is described in detail and related to finite difference schemes on staggered grids in flat space for which we demonstrate second order convergence. We compare computational results with a vorticity-stream function approach for surfaces with genus 0 and demonstrate the interplay between topology, geometry and flow properties. Our discretization also allows to handle harmonic vector fields, which we demonstrate on a torus.Comment: 21 pages, 9 figure

Small grid embeddings of 3-polytopes

We introduce an algorithm that embeds a given 3-connected planar graph as a convex 3-polytope with integer coordinates. The size of the coordinates is bounded by $O(2^{7.55n})=O(188^{n})$. If the graph contains a triangle we can bound the integer coordinates by $O(2^{4.82n})$. If the graph contains a quadrilateral we can bound the integer coordinates by $O(2^{5.46n})$. The crucial part of the algorithm is to find a convex plane embedding whose edges can be weighted such that the sum of the weighted edges, seen as vectors, cancel at every point. It is well known that this can be guaranteed for the interior vertices by applying a technique of Tutte. We show how to extend Tutte's ideas to construct a plane embedding where the weighted vector sums cancel also on the vertices of the boundary face

The Complexity of Drawing a Graph in a Polygonal Region

We prove that the following problem is complete for the existential theory of the reals: Given a planar graph and a polygonal region, with some vertices of the graph assigned to points on the boundary of the region, place the remaining vertices to create a planar straight-line drawing of the graph inside the region. This strengthens an NP-hardness result by Patrignani on extending partial planar graph drawings. Our result is one of the first showing that a problem of drawing planar graphs with straight-line edges is hard for the existential theory of the reals. The complexity of the problem is open in the case of a simply connected region. We also show that, even for integer input coordinates, it is possible that drawing a graph in a polygonal region requires some vertices to be placed at irrational coordinates. By contrast, the coordinates are known to be bounded in the special case of a convex region, or for drawing a path in any polygonal region.Comment: Appears in the Proceedings of the 26th International Symposium on Graph Drawing and Network Visualization (GD 2018

Grid computing in image analysis

Diagnostic surgical pathology or tissue–based diagnosis still remains the most reliable and specific diagnostic medical procedure. The development of whole slide scanners permits the creation of virtual slides and to work on so-called virtual microscopes. In addition to interactive work on virtual slides approaches have been reported that introduce automated virtual microscopy, which is composed of several tools focusing on quite different tasks. These include evaluation of image quality and image standardization, analysis of potential useful thresholds for object detection and identification (segmentation), dynamic segmentation procedures, adjustable magnification to optimize feature extraction, and texture analysis including image transformation and evaluation of elementary primitives

A Survey of Methods for Volumetric Scene Reconstruction from Photographs

Scene reconstruction, the task of generating a 3D model of a scene given multiple 2D photographs taken of the scene, is an old and difficult problem in computer vision. Since its introduction, scene reconstruction has found application in many fields, including robotics, virtual reality, and entertainment. Volumetric models are a natural choice for scene reconstruction. Three broad classes of volumetric reconstruction techniques have been developed based on geometric intersections, color consistency, and pair-wise matching. Some of these techniques have spawned a number of variations and undergone considerable refinement. This paper is a survey of techniques for volumetric scene reconstruction