1,466 research outputs found
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
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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
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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
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
Molecular Skin Surface-Based Transformation Visualization between Biological Macromolecules
Molecular skin surface (MSS), proposed by Edelsbrunner, is a C2 continuous smooth surface modeling approach of biological macromolecules. Compared to the traditional methods of molecular surface representations (e.g., the solvent exclusive surface), MSS has distinctive advantages including having no self-intersection and being decomposable and transformable. For further promoting MSS to the field of bioinformatics, transformation between different MSS representations mimicking the macromolecular dynamics is demanded. The transformation process helps biologists understand the macromolecular dynamics processes visually in the atomic level, which is important in studying the protein structures and binding sites for optimizing drug design. However, modeling the transformation between different MSSs suffers from high computational cost while the traditional approaches reconstruct every intermediate MSS from respective intermediate union of balls. In this study, we propose a novel computational framework named general MSS transformation framework (GMSSTF) between two MSSs without the assistance of union of balls. To evaluate the effectiveness of GMSSTF, we applied it on a popular public database PDB (Protein Data Bank) and compared the existing MSS algorithms with and without GMSSTF. The simulation results show that the proposed GMSSTF effectively improves the computational efficiency and is potentially useful for macromolecular dynamic simulations
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