Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.National Library of Medicine (LM05205-13

Binaural Cues for Distance and Direction of Nearby Sound Sources

To a first-order approximation, binaural localization cues are ambiguous: a number of source locations give rise to nearly the same interaural differences. For sources more than a meter from the listener, binaural localization cues are approximately equal for any source on a cone centered on the interaural axis (i.e., the well-known "cones of confusion"). The current paper analyzes simple geometric approximations of a listener's head to gain insight into localization performance for sources near the listener. In particular, if the head is treated as a rigid, perfect sphere, interaural intensity differences (IIDs) can be broken down into two main components. One component is constant along the cone of confusion (and thus co varies with the interaural time difference, or ITD). The other component is roughly constant for a sphere centered on the interaural axis and depends only on the relative pathlengths from the source to the two ears. This second factor is only large enough to be perceptible when sources are within one or two meters of the listener. These results are not dramatically different if one assumes that the ears are separated by 160 degrees along the surface of the sphere (rather than diametrically opposite one another). Thus, for sources within a meter of the listener, binaural information should allow listeners to locate sources within a volume around a circle centered on the interaural axis, on a "doughnut of confusion." The volume of the doughnut of confusion increases dramatically with angle between source and the interaural axis, degenerating to the entire median plane in the limit.Air Force Office of Scientific Research (F49620-98-1-0108

Robust object-based algorithms for direct shadow simulation

En informatique graphique, les algorithmes de générations d'ombres évaluent la quantité de lumière directement perçue par une environnement virtuel. Calculer précisément des ombres est cependant coûteux en temps de calcul. Dans cette dissertation, nous présentons un nouveau système basé objet robuste, qui permet de calculer des ombres réalistes sur des scènes dynamiques et ce en temps interactif. Nos contributions incluent notamment le développement de nouveaux algorithmes de génération d'ombres douces ainsi que leur mise en oeuvre efficace sur processeur graphique. Nous commençons par formaliser la problématique du calcul d'ombres directes. Tout d'abord, nous définissons ce que sont les ombres directes dans le contexte général du transport de la lumière. Nous étudions ensuite les techniques interactives qui génèrent des ombres directes. Suite à cette étude nous montrons que mêmes les algorithmes dit physiquement réalistes se reposent sur des approximations. Nous mettons également en avant, que malgré leur contraintes géométriques, les algorithmes d'ombres basées objet sont un bon point de départ pour résoudre notre problématique de génération efficace et robuste d'ombres directes. Basé sur cette observation, nous étudions alors le système basé objet existant et mettons en avant ses problèmes de robustesse. Nous proposons une nouvelle technique qui améliore la qualité des ombres générées par ce système en lui ajoutant une étape de mélange de pénombres. Malgré des propriétés et des résultats convaincants, les limitations théoriques et de mise en oeuvre limite la qualité générale et les performances de cet algorithme. Nous présentons ensuite un nouvel algorithme d'ombres basées objet. Cet algorithme combine l'efficacité de l'approche basée objet temps réel avec la précision de sa généralisation au rendu hors ligne. Notre algorithme repose sur l'évaluation locale du nombre d'objets entre deux points : la complexité de profondeur. Nous décrivons comment nous utilisons cet algorithme pour échantillonner la complexité de profondeur entre les surfaces visibles d'une scène et une source lumineuse. Nous générons ensuite des ombres à partir de cette information soit en modulant l'éclairage direct soit en intégrant numériquement l'équation d'illumination directe. Nous proposons ensuite une extension de notre algorithme afin qu'il puisse prendre en compte les ombres projetées par des objets semi-opaque. Finalement, nous présentons une mise en oeuvre efficace de notre système qui démontre que des ombres basées objet peuvent être générées de façon efficace et ce même sur une scène dynamique. En rendu temps réel, il est commun de représenter des objets très détaillés encombinant peu de triangles avec des textures qui représentent l'opacité binaire de l'objet. Les techniques de génération d'ombres basées objet ne traitent pas de tels triangles dit "perforés". De par leur nature, elles manipulent uniquement les géométries explicitement représentées par des primitives géométriques. Nous présentons une nouvel algorithme basé objet qui lève cette limitation. Nous soulignons que notre méthode peut être efficacement combinée avec les systèmes existants afin de proposer un système unifié basé objet qui génère des ombres à la fois pour des maillages classiques et des géométries perforées. La mise en oeuvre proposée montre finalement qu'une telle combinaison fournit une solution élégante, efficace et robuste à la problématique générale de l'éclairage direct et ce aussi bien pour des applications temps réel que des applications sensibles à la la précision du résultat.Direct shadow algorithms generate shadows by simulating the direct lighting interaction in a virtual environment. The main challenge with the accurate direct shadow problematic is its computational cost. In this dissertation, we develop a new robust object-based shadow framework that provides realistic shadows at interactive frame rate on dynamic scenes. Our contributions include new robust object-based soft shadow algorithms and efficient interactive implementations. We start, by formalizing the direct shadow problematic. Following the light transport problematic, we first formalize what are robust direct shadows. We then study existing interactive direct shadow techniques and outline that the real time direct shadow simulation remains an open problem. We show that even the so called physically plausible soft shadow algorithms still rely on approximations. Nevertheless we exhibit that, despite their geometric constraints, object-based approaches seems well suited when targeting accurate solutions. Starting from the previous analyze, we investigate the existing object-based shadow framework and discuss about its robustness issues. We propose a new technique that drastically improve the resulting shadow quality by improving this framework with a penumbra blending stage. We present a practical implementation of this approach. From the obtained results, we outline that, despite desirable properties, the inherent theoretical and implementation limitations reduce the overall quality and performances of the proposed algorithm. We then present a new object-based soft shadow algorithm. It merges the efficiency of the real time object-based shadows with the accuracy of its offline generalization. The proposed algorithm lies onto a new local evaluation of the number of occluders between $two$ points (\ie{} the depth complexity). We describe how we use this algorithm to sample the depth complexity between any visible receiver and the light source. From this information, we compute shadows by either modulate the direct lighting or numerically solve the direct illumination with an accuracy depending on the light sampling strategy. We then propose an extension of our algorithm in order to handle shadows cast by semi opaque occluders. We finally present an efficient implementation of this framework that demonstrates that object-based shadows can be efficiently used on complex dynamic environments. In real time rendering, it is common to represent highly detailed objects with few triangles and transmittance textures that encode their binary opacity. Object-based techniques do not handle such perforated triangles. Due to their nature, they can only evaluate the shadows cast by models whose their shape is explicitly defined by geometric primitives. We describe a new robust object-based algorithm that addresses this main limitation. We outline that this method can be efficiently combine with object-based frameworks in order to evaluate approximative shadows or simulate the direct illumination for both common meshes and perforated triangles. The proposed implementation shows that such combination provides a very strong and efficient direct lighting framework, well suited to many domains ranging from quality sensitive to performance critical applications

Efficient algorithms for occlusion culling and shadows

The goal of this research is to develop more efficient techniques for computing the visibility and shadows in real-time rendering of three-dimensional scenes. Visibility algorithms determine what is visible from a camera, whereas shadow algorithms solve the same problem from the viewpoint of a light source. In rendering, a lot of computational resources are often spent on primitives that are not visible in the final image. One visibility algorithm for reducing the overhead is occlusion culling, which quickly discards the objects or primitives that are obstructed from the view by other primitives. A new method is presented for performing occlusion culling using silhouettes of meshes instead of triangles. Additionally, modifications are suggested to occlusion queries in order to reduce their computational overhead. The performance of currently available graphics hardware depends on the ordering of input primitives. A new technique, called delay streams, is proposed as a generic solution to order-dependent problems. The technique significantly reduces the pixel processing requirements by improving the efficiency of occlusion culling inside graphics hardware. Additionally, the memory requirements of order-independent transparency algorithms are reduced. A shadow map is a discretized representation of the scene geometry as seen by a light source. Typically the discretization causes difficult aliasing issues, such as jagged shadow boundaries and incorrect self-shadowing. A novel solution is presented for suppressing all types of aliasing artifacts by providing the correct sampling points for shadow maps, thus fully abandoning the previously used regular structures. Also, a simple technique is introduced for limiting the shadow map lookups to the pixels that get projected inside the shadow map. The fillrate problem of hardware-accelerated shadow volumes is greatly reduced with a new hierarchical rendering technique. The algorithm performs per-pixel shadow computations only at visible shadow boundaries, and uses lower resolution shadows for the parts of the screen that are guaranteed to be either fully lit or fully in shadow. The proposed techniques are expected to improve the rendering performance in most real-time applications that use 3D graphics, especially in computer games. More efficient algorithms for occlusion culling and shadows are important steps towards larger, more realistic virtual environments.reviewe

The Iray Light Transport Simulation and Rendering System

While ray tracing has become increasingly common and path tracing is well understood by now, a major challenge lies in crafting an easy-to-use and efficient system implementing these technologies. Following a purely physically-based paradigm while still allowing for artistic workflows, the Iray light transport simulation and rendering system allows for rendering complex scenes by the push of a button and thus makes accurate light transport simulation widely available. In this document we discuss the challenges and implementation choices that follow from our primary design decisions, demonstrating that such a rendering system can be made a practical, scalable, and efficient real-world application that has been adopted by various companies across many fields and is in use by many industry professionals today

3D simulation of complex shading affecting PV systems taking benefit from the power of graphics cards developed for the video game industry

Shading reduces the power output of a photovoltaic (PV) system. The design engineering of PV systems requires modeling and evaluating shading losses. Some PV systems are affected by complex shading scenes whose resulting PV energy losses are very difficult to evaluate with current modeling tools. Several specialized PV design and simulation software include the possibility to evaluate shading losses. They generally possess a Graphical User Interface (GUI) through which the user can draw a 3D shading scene, and then evaluate its corresponding PV energy losses. The complexity of the objects that these tools can handle is relatively limited. We have created a software solution, 3DPV, which allows evaluating the energy losses induced by complex 3D scenes on PV generators. The 3D objects can be imported from specialized 3D modeling software or from a 3D object library. The shadows cast by this 3D scene on the PV generator are then directly evaluated from the Graphics Processing Unit (GPU). Thanks to the recent development of GPUs for the video game industry, the shadows can be evaluated with a very high spatial resolution that reaches well beyond the PV cell level, in very short calculation times. A PV simulation model then translates the geometrical shading into PV energy output losses. 3DPV has been implemented using WebGL, which allows it to run directly from a Web browser, without requiring any local installation from the user. This also allows taken full benefits from the information already available from Internet, such as the 3D object libraries. This contribution describes, step by step, the method that allows 3DPV to evaluate the PV energy losses caused by complex shading. We then illustrate the results of this methodology to several application cases that are encountered in the world of PV systems design.Comment: 5 page, 9 figures, conference proceedings, 29th European Photovoltaic Solar Energy Conference and Exhibition, Amsterdam, 201

Provably Safe Robot Navigation with Obstacle Uncertainty

As drones and autonomous cars become more widespread it is becoming increasingly important that robots can operate safely under realistic conditions. The noisy information fed into real systems means that robots must use estimates of the environment to plan navigation. Efficiently guaranteeing that the resulting motion plans are safe under these circumstances has proved difficult. We examine how to guarantee that a trajectory or policy is safe with only imperfect observations of the environment. We examine the implications of various mathematical formalisms of safety and arrive at a mathematical notion of safety of a long-term execution, even when conditioned on observational information. We present efficient algorithms that can prove that trajectories or policies are safe with much tighter bounds than in previous work. Notably, the complexity of the environment does not affect our methods ability to evaluate if a trajectory or policy is safe. We then use these safety checking methods to design a safe variant of the RRT planning algorithm.Comment: RSS 201