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Fast Algorithms (fast + algorithms)

Distribution by Scientific Domains

Chemistry	33%

Selected Abstracts

A software system for rigid-body modelling of solution scattering data

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000
M.B. Kozin
A computer system for rigid body modelling against solution scattering data is described. Fast algorithms to compute scattering from a complex of two arbitrary positioned subunits are implemented and coupled with the graphics program ASSA (Kozin, Volkov & Svergun, 1997, J. Appl. Cryst.30, 811-815). Mutual positions and orientations of the subunits (represented by low-resolution envelopes or by atomic models) can be determined by interactively fitting the experimental scattering curve from the complex. The system runs on the major Unix platforms (SUN, SGI and DEC workstations). [source]

A Primer on Topological Persistence

COMPUTER GRAPHICS FORUM, Issue 3 2006
Herbert Edelsbrunner
The idea of topological persistence is to look at homological features that persist along a nested sequence of topo-logical spaces. As a typical example, we may take the sequence of sublevel sets of a function. The combinatorial characterization of persistence in terms of pairs of critical values and fast algorithms computing these pairs make this idea practical and useful in dealing with the pervasive phenomenon of noise in geometric and visual data. This talk will 1. recall the relatively short history of persistence and some of its older roots; 2. introduce the concept intuitively while pointing out where algebra is needed to solidify the more difficult steps; 3. discuss a few applications to give a feeling of the potential of the method in dealing with noise and scale. Besides the initial concept, the talk will touch upon recent extensions and their motivation. [source]

Drawing for Illustration and Annotation in 3D

COMPUTER GRAPHICS FORUM, Issue 3 2001
David Bourguignon
We present a system for sketching in 3D, which strives to preserve the degree of expression, imagination, and simplicity of use achieved by 2D drawing. Our system directly uses user-drawn strokes to infer the sketches representing the same scene from different viewpoints, rather than attempting to reconstruct a 3D model. This is achieved by interpreting strokes as indications of a local surface silhouette or contour. Strokes thus deform and disappear progressively as we move away from the original viewpoint. They may be occluded by objects indicated by other strokes, or, in contrast, be drawn above such objects. The user draws on a plane which can be positioned explicitly or relative to other objects or strokes in the sketch. Our system is interactive, since we use fast algorithms and graphics hardware for rendering. We present applications to education, design, architecture and fashion, where 3D sketches can be used alone or as an annotation of an existing 3D model. [source]

On the fast search algorithms for vector quantization encoding

INTERNATIONAL JOURNAL OF IMAGING SYSTEMS AND TECHNOLOGY, Issue 5 2002
Wen-Shiung Chen
Abstract One of the major difficulties arising in vector quantization (VQ) is high encoding time complexity. Based on the well-known partial distance search (PDS) method and a special order of codewords in VQ codebook, two simple and efficient methods are introduced in fast full search vector quantization to reduce encoding time complexity. The exploitation of the "move-to-front" method, which may get a smaller distortion as early as possible, combined with the PDS algorithm, is shown to improve the encoding efficiency of the PDS method. Because of the feature of energy compaction in DCT domain, search in DCT domain codebook may be further speeded up. The experimental results show that our fast algorithms may significantly reduce search time of VQ encoding. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 12, 204,210, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.10030 [source]

Extension theorems for Stokes and Lamé equations for nearly incompressible media and their applications to numerical solution of problems with highly discontinuous coefficients

NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS, Issue 2 2002
N. S. Bakhvalov
Abstract We prove extension theorems in the norms described by Stokes and Lamé operators for the three-dimensional case with periodic boundary conditions. For the Lamé equations, we show that the extension theorem holds for nearly incompressible media, but may fail in the opposite limit, i.e. for case of absolutely compressible media. We study carefully the latter case and associate it with the Cosserat problem. Extension theorems serve as an important tool in many applications, e.g. in domain decomposition and fictitious domain methods, and in analysis of finite element methods. We consider an application of established extension theorems to an efficient iterative solution technique for the isotropic linear elasticity equations for nearly incompressible media and for the Stokes equations with highly discontinuous coefficients. The iterative method involves a special choice for an initial guess and a preconditioner based on solving a constant coefficient problem. Such preconditioner allows the use of well-known fast algorithms for preconditioning. Under some natural assumptions on smoothness and topological properties of subdomains with small coefficients, we prove convergence of the simplest Richardson method uniform in the jump of coefficients. For the Lamé equations, the convergence is also uniform in the incompressible limit. Our preliminary numerical results for two-dimensional diffusion problems show fast convergence uniform in the jump and in the mesh size parameter. Copyright © 2002 John Wiley & Sons, Ltd. [source]

UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009
Xavier Siebert
Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30,10,Å range and sometimes even beyond 10,Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/. [source]