21531236
Towards Unsupervised Segmentation of Semi-rigid Low-Resolution Molecular Surfaces
In this paper, we study a particular type of surface segmentation problem motivated by molecular biology applications. In particular, two input surfaces are given, coarsely modeling two different conformations of a molecule undergoing a semi-rigid deformation. The molecule consists of two subunits that move in a roughly rigid manner. The goal is to segment the input surfaces into these semi-rigid subcomponents. The problem is closely related to non-rigid surface registration problems, although considering only a special type of deformation that exists commonly in macromolecular movements (such as the popular hinge motion). We present and implement an efficient paradigm for this problem, which combines several existing and new ideas. We demonstrate the performance of our new algorithm by some preliminary experimental results in segmenting low-resolution molecular surfaces.
15443235
Computing the Writhing Number of a Polygonal Knot
AbstractThe writhing number measures the global geometry of
 a closed space curve or knot.
 We show that this measure is related to the average winding number
 of its Gauss map.
 Using this relationship, we give an algorithm for computing
 the writhing number for a polygonal knot with n edges
 in time roughly proportional to n1.6.
 We also implement a different, simple algorithm and provide
 experimental evidence for its practical efficiency.


2273352
Near-Linear Time Approximation Algorithms for Curve Simplification
AbstractWe consider the problem of approximating a polygonal
 curve P under a given error criterion by another
 polygonal curve P’ whose vertices are a
 subset of the vertices of P. The goal is to minimize
 the number of vertices of P’ while ensuring that the
 error between P’ and P is below a certain threshold.
 We consider two different error measures: 
 Hausdorff and Frechet. For both error criteria, we present
 near-linear time approximation algorithms that, given a
 parameter ε > 0, compute a simplified polygonal
 curve P’ whose error is less than ε and
 size at most the size of an optimal simplified
 polygonal curve with error ε/2. We consider
 monotone curves in ℝ2 in the case of the Hausdorff error measure
 under the uniform distance metric
 and arbitrary curves in any dimension for the Frechet error measure
 under Lp metrics. 
 We present
 experimental results demonstrating that our algorithms
 are simple and fast, and produce close to optimal
 simplifications in practice.
312809
Segmenting molecular surfaces
This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of the scalar function. The segmentation is obtained by associating segments with local minima/maxima. Controlled simplification of the function merges segments resulting in a hierarchical segmentation of the molecular surface. This segmentation is used to identify rigid components of protein molecules and to study the role of cavities and protrusions in protein-protein interactions.
378133
LFM-Pro: a tool for detecting significant local structural sites in proteins
MOTIVATION
The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.


RESULTS
We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.


AVAILABILITY
The software and the datasets are freely available for academic research use at http://bioinfo.ceng.metu.edu.tr/Pub/LFMPro.
37729130
Extreme Elevation on a 2-Manifold
Given a smoothly embedded 2-manifold in ${\Bbb R}^3,$ we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.
10668110
Evaluating the effects of real world distraction on user performance in virtual environments
Although many virtual environment (VE) technologies such as the four-screen CAVE™ are described as immersive, users can still perceive distractions from the real world. This exposure to real-world distraction may reduce users' sense of presence, and if presence is correlated with performance as some have claimed, the real-world distractions may also hinder performance. Thus, VE designers may want to consider ways to reduce real-world distraction. This paper presents an experiment to investigate the effect of reduced visual stimulus in the peripheral area on user performance and the usability of an immersive VE. We carefully designed three tasks that cause different levels of awareness of the real-world distraction. Using these tasks, we evaluated users' performance and preference in two conditions. The low-stimulus condition was created by hanging a black cloth across the missing back wall of a CAVE. The high-stimulus condition was created by projected animations and real human motion outside the CAVE. The experiments show that reduced distraction may have a positive or negative effect on user performance, depending on the specific tasks and environments.
793367
3D Brain surface matching based on geodesics and local geometry
The non-rigid registration of surfaces is a complex and difficult task for which there are many important applications, such as comparing shape between deformable objects and comparing associated function. This paper presents a new approach for brain surface matching by determining the correspondence of 3D point sets between pairs of surfaces. The algorithm is based on shape using a combination of geodesic distance and surface curvature. There are two major procedures involved. An initial sparse set of corresponding points is first generated by matching local geometrical features. Geodesic distance interpolation is then employed hierarchically in order to capture the complex surface. By this scheme, surface correspondence and triangulation are computed simultaneously. Experiments applied to human cerebral cortical surfaces are shown to evaluate the approach. It is shown that the proposed method performs well for both surface matching and surface shape recovery.
5267319
Volumetric harmonic brain mapping
We developed two different techniques to study volume mapping problem in Computer Graphics. The first one is to find a harmonic map from a 3 manifold to a 3D solid sphere and the second is a sphere carving algorithm which calculates the simplicial decomposition of volume adapted to surfaces. In this paper, we apply these two techniques to brain mapping problem. We use a tetrahedral mesh to represent the brain volume. The experimental results on both synthetic and brain volume data are reported. We suggest that 3D harmonic mapping of brain volumes to a solid sphere can provide a canonical coordinate system for feature identification and segmentation, as well as anatomical normalization.
7477567
Design formalism for collaborative assembly design
Abstract Joints in product design are common because of the limitations of component geometric configurations and material properties, and the requirements of inspection, accessibility, repair, and portability. Collaborative product design is emerging as a viable alternative to the traditional design process. The collaborative assembly design (AsD) methodologies are needed for distributed product development. Existing AsD methodologies have limitations in capturing the non-geometric aspects of designer's intent on joining and are not efficient for a collaborative design environment. This paper introduces an AsD formalism and associated AsD tools to capture joining relations and spatial relationship implications. This AsD formalism allows the joining relations to be modeled symbolically for computer interpretation, and the model can be used for inferring mathematical and physical implications. An AsD model generated from the AsD formalism is used to exchange AsD information transparently in a collaborative AsD environment. An assembly relation model and a generic assembly relationship diagram are to capture assembly and joining information concisely and persistently. As a demonstration, the developed AsD formalism and AsD tools are applied on a connector assembly with arc weld and rivet joints.
7392070
System and Transport Interface of H.264/AVC Scalable Extension
The scalable extension of H.264/AVC, known as scalable video coding or SVC, has recently been the main focus of the Joint Video Team. The higher level syntax of SVC follows the design principles of H.264/AVC. This allows the work towards an optimized file format and RTF payload format to be conducted in parallel with the core SVC specification. This paper provides an overview of the system and transport interface design of SVC, including the SVC high-level syntax and functionalities, SVC file format, and SVC RTF payload format.