Modeling regionalized volumetric differences in protein-ligand binding cavities

Identifying elements of protein structures that create differences in protein-ligand binding specificity is an essential method for explaining the molecular mechanisms underlying preferential binding. In some cases, influential mechanisms can be visually identified by experts in structural biology, but subtler mechanisms, whose significance may only be apparent from the analysis of many structures, are harder to find. To assist this process, we present a geometric algorithm and two statistical models for identifying significant structural differences in protein-ligand binding cavities. We demonstrate these methods in an analysis of sequentially nonredundant structural representatives of the canonical serine proteases and the enolase superfamily. Here, we observed that statistically significant structural variations identified experimentally established determinants of specificity. We also observed that an analysis of individual regions inside cavities can reveal areas where small differences in shape can correspond to differences in specificity

Topology-Adaptive Mesh Deformation for Surface Evolution, Morphing, and Multi-View Reconstruction

International audienceTriangulated meshes have become ubiquitous discrete-surface representations. In this paper we address the problem of how to maintain the manifold properties of a surface while it undergoes strong deformations that may cause topological changes. We introduce a new self-intersection removal algorithm, TransforMesh, and we propose a mesh evolution framework based on this algorithm. Numerous shape modelling applications use surface evolution in order to improve shape properties, such as appearance or accuracy. Both explicit and implicit representations can be considered for that purpose. However, explicit mesh representations, while allowing for accurate surface modelling, suffer from the inherent difficulty of reliably dealing with self-intersections and topological changes such as merges and splits. As a consequence, a majority of methods rely on implicit representations of surfaces, e.g. level-sets, that naturally overcome these issues. Nevertheless, these methods are based on volumetric discretizations, which introduce an unwanted precision-complexity trade-off. The method that we propose handles topological changes in a robust manner and removes self intersections, thus overcoming the traditional limitations of mesh-based approaches. To illustrate the effectiveness of TransforMesh, we describe two challenging applications, namely surface morphing and 3-D reconstruction

Polygon-based hidden surface elimination algorithms: serial and parallel

Chapter 1 introduces the need for rapid solutions of hidden surface elimination (HSE) problems in the interactive display of objects and scenes, as used in many application areas such as flight and driving simulators and CAD systems. It reviews the existing approaches to high-performance computer graphics and to parallel computing. It then introduces the central tenet of this thesis: that general purpose parallel computers may be usefully applied to the solution of HSE problems. Finally it introduces a set of metrics for describing sets of scene data, and applies them to the test scenes used in this thesis. Chapter 2 describes variants of several common image space hidden surface elimination algorithms, which solve the HSE problem for scenes described as collections of polygons. Implementations of these HSE algorithms on a traditional, serial, single microprocessor computer are introduced and theoretical estimates of their performance are derived. The algorithms are compared under identical conditions for various sets of test data. The results of this comparison are then placed in context with existing historical results. Chapter 3 examines the application of MIMD style parallelism to accelerate the solution of HSE problems. MIMD parallel implementations of the previously considered HSE algorithms are introduced. Their behaviour under various system configurations and for various data sets is investigated and compared with theoretical estimates. The theoretical estimates are found to match closely the experimental findings. Chapter 4 summarises the conclusions of this thesis, finding that HSE algorithms can be implemented to use an MIMD parallel computer effectively, and that of the HSE algorithms examined the z-buffer algorithm generally proves to be a good compromise solution

The evaluation of a novel haptic machining VR-based process planning system using an original process planning usability method

This thesis provides an original piece of work and contribution to knowledge by creating a new process planning system; Haptic Aided Process Planning (HAPP). This system is based on the combination of haptics and virtual reality (VR). HAPP creates a simulative machining environment where Process plans are automatically generated from the real time logging of a user’s interaction. Further, through the application of a novel usability test methodology, a deeper study of how this approach compares to conventional process planning was undertaken. An abductive research approach was selected and an iterative and incremental development methodology chosen. Three development cycles were undertaken with evaluation studies carried out at the end of each. Each study, the pre-pilot, pilot and industrial, identified progressive refinements to both the usability of HAPP and the usability evaluation method itself. HAPP provided process planners with an environment similar to which they are already familiar. Visual images were used to represent tools and material whilst a haptic interface enabled their movement and positioning by an operator in a manner comparable to their native setting. In this way an intuitive interface was developed that allowed users to plan the machining of parts consisting of features that can be machined on a pillar drill, 21/2D axis milling machine or centre lathe. The planning activities included single or multiple set ups, fixturing and sequencing of cutting operations. The logged information was parsed and output to a process plan including route sheets, operation sheets, tool lists and costing information, in a human readable format. The system evaluation revealed that HAPP, from an expert planners perspective is perceived to be 70% more satisfying to use, 66% more efficient in completing process plans, primarily due to the reduced cognitive load, is more effective producing a higher quality output of information and is 20% more learnable than a traditional process planning approach

Subdivision Surface based One-Piece Representation

Subdivision surfaces are capable of modeling and representing complex shapes of arbi-trary topology. However, methods on how to build the control mesh of a complex surfaceare not studied much. Currently, most meshes of complicated objects come from trian-gulation and simplification of raster scanned data points, like the Stanford 3D ScanningRepository. This approach is costly and leads to very dense meshes.Subdivision surface based one-piece representation means to represent the final objectin a design process with only one subdivision surface, no matter how complicated theobject\u27s topology or shape. Hence the number of parts in the final representation isalways one.In this dissertation we present necessary mathematical theories and geometric algo-rithms to support subdivision surface based one-piece representation. First, an explicitparametrization method is presented for exact evaluation of Catmull-Clark subdivisionsurfaces. Based on it, two approaches are proposed for constructing the one-piece rep-resentation of a given object with arbitrary topology. One approach is to construct theone-piece representation by using the interpolation technique. Interpolation is a naturalway to build models, but the fairness of the interpolating surface is a big concern inprevious methods. With similarity based interpolation technique, we can obtain bet-ter modeling results with less undesired artifacts and undulations. Another approachis through performing Boolean operations. Up to this point, accurate Boolean oper-ations over subdivision surfaces are not approached yet in the literature. We presenta robust and error controllable Boolean operation method which results in a one-piecerepresentation. Because one-piece representations resulting from the above two methodsare usually dense, error controllable simplification of one-piece representations is needed.Two methods are presented for this purpose: adaptive tessellation and multiresolutionanalysis. Both methods can significantly reduce the complexity of a one-piece represen-tation and while having accurate error estimation.A system that performs subdivision surface based one-piece representation was im-plemented and a lot of examples have been tested. All the examples show that our ap-proaches can obtain very good subdivision based one-piece representation results. Eventhough our methods are based on Catmull-Clark subdivision scheme, we believe they canbe adapted to other subdivision schemes as well with small modifications