How round is a protein? Exploring protein structures for globularity using conformal mapping.

We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry

3D ball skinning using PDEs for generation of smooth tubular surfaces

We present an approach to compute a smooth, interpolating skin of an ordered set of 3D balls. By construction, the skin is constrained to be C-1 continuous, and for each ball, it is tangent to the ball along a circle of contact. Using an energy formulation, we derive differential equations that are designed to minimize the skin's surface area, mean curvature, or convex combination of both. Given an initial skin, we update the skin's parametric representation using the differential equations until convergence occurs. We demonstrate the method's usefulness in generating interpolating skins of balls of different sizes and in various configurations

3D ball skinning using PDEs for generation of smooth tubular surfaces

We present an approach to compute a smooth, interpolating skin of an ordered set of 3D balls. By construction, the skin is constrained to be C1 continuous, and for each ball, it is tangent to the ball along a circle of contact. Using an energy formulation, we derive differential equations that are designed to minimize the skin’s surface area, mean curvature, or convex combination of both. Given an initial skin, we update the skin’s parametric representation using the differential equations until convergence occurs. We demonstrate the method’s usefulness in generating interpolating skins of balls of different sizes and in various configurations

Variational skinning of an ordered set of discrete 2D balls

This paper considers the problem of computing an interpolating envelope of an ordered set of 2D balls. By construction, the envelope is constrained to be C1 continuous, and for each ball, it touches the ball at a point and is tangent to the ball at the point of contact. Using an energy formulation, we derive differential equations that are designed to minimize the envelope’s arc length and/or curvature subject to these constraints. Given an initial envelope, we update the envelope’s parameters using the differential equations until convergence occurs. We demonstrate the method’s usefulness in generating interpolating envelopes of balls of different sizes and in various configurations

Algorithms for meshing smooth surfaces and their volumes

Ph.DDOCTOR OF PHILOSOPH

Molecular Surface Mesh Generation by Filtering Electron Density Map

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface

Dense point sets have sparse Delaunay triangulations

The spread of a finite set of points is the ratio between the longest and shortest pairwise distances. We prove that the Delaunay triangulation of any set of n points in R^3 with spread D has complexity O(D^3). This bound is tight in the worst case for all D = O(sqrt{n}). In particular, the Delaunay triangulation of any dense point set has linear complexity. We also generalize this upper bound to regular triangulations of k-ply systems of balls, unions of several dense point sets, and uniform samples of smooth surfaces. On the other hand, for any n and D=O(n), we construct a regular triangulation of complexity Omega(nD) whose n vertices have spread D.Comment: 31 pages, 11 figures. Full version of SODA 2002 paper. Also available at http://www.cs.uiuc.edu/~jeffe/pubs/screw.htm

SHAPE DEFORMATION FOR OBJECTS OF GREATLY DISSIMILAR SHAPES WITH SMOOTH MANIFOLD

Ph.DDOCTOR OF PHILOSOPH