Algorithmes adaptatifs pour la simulation moléculaire

Les simulations moléculaires sont devenues un outil essentiel en biologie, chimie et physique. Malheureusement, elles restent très couteuses. Dans cette thèse, nous proposons des algorithmes qui accélèrent les simulations moléculaires en regroupant des particules en plusieurs objets rigides. Nous étudions d'abord plusieurs algorithmes de recherche de voisins dans le cas des grands objets rigides, et démontrons que les algorithmes hiérarchiques permettent d'obtenir des accélérations importantes. En conséquence, nous proposons une technique pour construire une représentation hiérarchique d'un graphe moléculaire arbitraire. Nous démontrons l'usage de cette technique pour la mécanique adaptative en angles de torsion, une méthode de simulation qui décrit les molécules comme des objets rigides articulés. Enfin, nous introduisons ARPS - Adaptively Restrained Particle Simulations ("Simulations de particules restreintes de façon adaptative") - une méthode mathématiquement fondée capable d'activer et de désactiver les degrés de liberté en position. Nous proposons deux stratégies d'adaptation, et illustrons les avantages de ARPS sur plusieurs exemples. En particulier, nous démontrons comment ARPS permet de choisir finement le compromis entre précision et vitesse, ainsi que d'obtenir rapidement des statistiques non biaisées sur les systèmes moléculaires.Molecular simulations have become an essential tool in biology, chemistry and physics. Unfortunately, they still remain computationally challenging. In this dissertation, we propose algorithms that accelerate molecular simulations by clustering particles into rigid bodies. We first study several neighbor-search algorithms for large rigid bodies, and show that hierarchy-based algorithms may provide significant speedups. Accordingly, we propose a technique to build a hierarchical representation of an arbitrary molecular graph. We show how this technique can be used in adaptive torsion-angle mechanics, a simulation method that describes molecules as articulated rigid bodies. Finally, we introduce ARPS - Adaptively Restrained Particle Simulations - a mathematically-grounded method able to switch positional degrees of freedom on and off. We propose two switching strategies, and illustrate the advantages of ARPS on various examples. In particular, we show how ARPS allow us to smoothly trade between precision and speed, and efficiently collect unbiased statistics on molecular systems.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

A biomechanics-based articulation model for medical applications

Computer Graphics came into the medical world especially after the arrival of 3D medical imaging. Computer Graphics techniques are already integrated in the diagnosis procedure by means of the visual tridimensional analysis of computer tomography, magnetic resonance and even ultrasound data. The representations they provide, nevertheless, are static pictures of the patients' body, lacking in functional information. We believe that the next step in computer assisted diagnosis and surgery planning depends on the development of functional 3D models of human body. It is in this context that we propose a model of articulations based on biomechanics. Such model is able to simulate the joint functionality in order to allow for a number of medical applications. It was developed focusing on the following requirements: it must be at the same time simple enough to be implemented on computer, and realistic enough to allow for medical applications; it must be visual in order for applications to be able to explore the joint in a 3D simulation environment. Then, we propose to combine kinematical motion for the parts that can be considered as rigid, such as bones, and physical simulation of the soft tissues. We also deal with the interaction between the different elements of the joint, and for that we propose a specific contact management model. Our kinematical skeleton is based on anatomy. Special considerations have been taken to include anatomical features like axis displacements, range of motion control, and joints coupling. Once a 3D model of the skeleton is built, it can be simulated by data coming from motion capture or can be specified by a specialist, a clinician for instance. Our deformation model is an extension of the classical mass-spring systems. A spherical volume is considered around mass points, and mechanical properties of real materials can be used to parameterize the model. Viscoelasticity, anisotropy and non-linearity of the tissues are simulated. We particularly proposed a method to configure the mass-spring matrix such that the objects behave according to a predefined Young's modulus. A contact management model is also proposed to deal with the geometric interactions between the elements inside the joint. After having tested several approaches, we proposed a new method for collision detection which measures in constant time the signed distance to the closest point for each point of two meshes subject to collide. We also proposed a method for collision response which acts directly on the surfaces geometry, in a way that the physical behavior relies on the propagation of reaction forces produced inside the tissue. Finally, we proposed a 3D model of a joint combining the three elements: anatomical skeleton motion, biomechanical soft tissues deformation, and contact management. On the top of that we built a virtual hip joint and implemented a set of medical applications prototypes. Such applications allow for assessment of stress distribution on the articular surfaces, range of motion estimation based on ligament constraint, ligament elasticity estimation from clinically measured range of motion, and pre- and post-operative evaluation of stress distribution. Although our model provides physicians with a number of useful variables for diagnosis and surgery planning, it should be improved for effective clinical use. Validation has been done partially. However, a global clinical validation is necessary. Patient specific data are still difficult to obtain, especially individualized mechanical properties of tissues. The characterization of material properties in our soft tissues model can also be improved by including control over the shear modulus

Virtual articulation and kinematic abstraction in robotics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 279-292).This thesis presents the theory, implementation, novel applications, and experimental validation of a general-purpose framework for applying virtual modifications to an articulated robot, or virtual articulations. These can homogenize various aspects of a robot and its task environment into a single unified model which is both qualitatively high-level and quantitatively functional. This is the first framework designed specifically for the mixed real/virtual case. It supports arbitrary topology spatial kinematics, a broad catalog of joints, on-line structure changes, interactive kinostatic simulation, and novel kinematic abstractions, where complex subsystems are simplified with virtual replacements in both space and time. Decomposition algorithms, including a novel method of hierarchical subdivision, enable scaling to large closed-chain mechanisms with 100s of joints. Novel applications are presented in two areas of current interest: operating high- DoF kinematic manipulation and inspection tasks, and analyzing reliable kinostatic locomotion strategies based on compliance and proprioception. In both areas virtual articulations homogeneously model the robot and its task environment, and abstractions structure complex models. For high-DoF operations the operator attaches virtual joints as a novel interface metaphor to define task motion and to constrain coordinated motion (by virtually closing kinematic chains); virtual links can represent task frames or serve as intermediate connections for virtual joints. For compliant locomotion, virtual articulations model relevant compliances and uncertainties, and temporal abstractions model contact state evolution.(cont.) Results are presented for experiments with two separate robotic systems in each area. For high-DoF operations, NASA/JPL's 36 DoF ATHLETE performs previously challenging coordinated manipulation/inspection moves, and a novel large-scale (100s of joints) simulated modular robot is conveniently operated using spatial abstractions. For compliant locomotion, two experiments are analyzed that each achieve high reliability in uncertain tasks using only compliance and proprioception: a novel vertical structure climbing robot that is 99.8% reliable in over 1000 motions, and a mini-humanoid that steps up an uncertain height with 90% reliability in 80 trials. In both cases virtual articulation models capture the essence of compliant/proprioceptive strategies at a higher level than basic physics, and enable quantitative analyses of the limits of tolerable uncertainty that compare well to experiment.by Marsette Arthur Vona, III.Ph.D

Scaling Robot Motion Planning to Multi-core Processors and the Cloud

Imagine a world in which robots safely interoperate with humans, gracefully and efficiently accomplishing everyday tasks. The robot's motions for these tasks, constrained by the design of the robot and task at hand, must avoid collisions with obstacles. Unfortunately, planning a constrained obstacle-free motion for a robot is computationally complex---often resulting in slow computation of inefficient motions. The methods in this dissertation speed up this motion plan computation with new algorithms and data structures that leverage readily available parallel processing, whether that processing power is on the robot or in the cloud, enabling robots to operate safer, more gracefully, and with improved efficiency. The contributions of this dissertation that enable faster motion planning are novel parallel lock-free algorithms, fast and concurrent nearest neighbor searching data structures, cache-aware operation, and split robot-cloud computation. Parallel lock-free algorithms avoid contention over shared data structures, resulting in empirical speedup proportional to the number of CPU cores working on the problem. Fast nearest neighbor data structures speed up searching in SO(3) and SE(3) metric spaces, which are needed for rigid body motion planning. Concurrent nearest neighbor data structures improve searching performance on metric spaces common to robot motion planning problems, while providing asymptotic wait-free concurrent operation. Cache-aware operation avoids long memory access times, allowing the algorithm to exhibit superlinear speedup. Split robot-cloud computation enables robots with low-power CPUs to react to changing environments by having the robot compute reactive paths in real-time from a set of motion plan options generated in a computationally intensive cloud-based algorithm. We demonstrate the scalability and effectiveness of our contributions in solving motion planning problems both in simulation and on physical robots of varying design and complexity. Problems include finding a solution to a complex motion planning problem, pre-computing motion plans that converge towards the optimal, and reactive interaction with dynamic environments. Robots include 2D holonomic robots, 3D rigid-body robots, a self-driving 1/10 scale car, articulated robot arms with and without mobile bases, and a small humanoid robot.Doctor of Philosoph

Hierarchical Variance Reduction Techniques for Monte Carlo Rendering

Ever since the first three-dimensional computer graphics appeared half a century ago, the goal has been to model and simulate how light interacts with materials and objects to form an image. The ultimate goal is photorealistic rendering, where the created images reach a level of accuracy that makes them indistinguishable from photographs of the real world. There are many applications ñ visualization of products and architectural designs yet to be built, special effects, computer-generated films, virtual reality, and video games, to name a few. However, the problem has proven tremendously complex; the illumination at any point is described by a recursive integral to which a closed-form solution seldom exists. Instead, computer simulation and Monte Carlo methods are commonly used to statistically estimate the result. This introduces undesirable noise, or variance, and a large body of research has been devoted to finding ways to reduce the variance. I continue along this line of research, and present several novel techniques for variance reduction in Monte Carlo rendering, as well as a few related tools. The research in this dissertation focuses on using importance sampling to pick a small set of well-distributed point samples. As the primary contribution, I have developed the first methods to explicitly draw samples from the product of distant high-frequency lighting and complex reflectance functions. By sampling the product, low noise results can be achieved using a very small number of samples, which is important to minimize the rendering times. Several different hierarchical representations are explored to allow efficient product sampling. In the first publication, the key idea is to work in a compressed wavelet basis, which allows fast evaluation of the product. Many of the initial restrictions of this technique were removed in follow-up work, allowing higher-resolution uncompressed lighting and avoiding precomputation of reflectance functions. My second main contribution is to present one of the first techniques to take the triple product of lighting, visibility and reflectance into account to further reduce the variance in Monte Carlo rendering. For this purpose, control variates are combined with importance sampling to solve the problem in a novel way. A large part of the technique also focuses on analysis and approximation of the visibility function. To further refine the above techniques, several useful tools are introduced. These include a fast, low-distortion map to represent (hemi)spherical functions, a method to create high-quality quasi-random points, and an optimizing compiler for analyzing shaders using interval arithmetic. The latter automatically extracts bounds for importance sampling of arbitrary shaders, as opposed to using a priori known reflectance functions. In summary, the work presented here takes the field of computer graphics one step further towards making photorealistic rendering practical for a wide range of uses. By introducing several novel Monte Carlo methods, more sophisticated lighting and materials can be used without increasing the computation times. The research is aimed at domain-specific solutions to the rendering problem, but I believe that much of the new theory is applicable in other parts of computer graphics, as well as in other fields

Modelling and simulation of flexible instruments for minimally invasive surgical training in virtual reality

Improvements in quality and safety standards in surgical training, reduction in training hours and constant technological advances have challenged the traditional apprenticeship model to create a competent surgeon in a patient-safe way. As a result, pressure on training outside the operating room has increased. Interactive, computer based Virtual Reality (VR) simulators offer a safe, cost-effective, controllable and configurable training environment free from ethical and patient safety issues. Two prototype, yet fully-functional VR simulator systems for minimally invasive procedures relying on flexible instruments were developed and validated. NOViSE is the first force-feedback enabled VR simulator for Natural Orifice Transluminal Endoscopic Surgery (NOTES) training supporting a flexible endoscope. VCSim3 is a VR simulator for cardiovascular interventions using catheters and guidewires. The underlying mathematical model of flexible instruments in both simulator prototypes is based on an established theoretical framework – the Cosserat Theory of Elastic Rods. The efficient implementation of the Cosserat Rod model allows for an accurate, real-time simulation of instruments at haptic-interactive rates on an off-the-shelf computer. The behaviour of the virtual tools and its computational performance was evaluated using quantitative and qualitative measures. The instruments exhibited near sub-millimetre accuracy compared to their real counterparts. The proposed GPU implementation further accelerated their simulation performance by approximately an order of magnitude. The realism of the simulators was assessed by face, content and, in the case of NOViSE, construct validity studies. The results indicate good overall face and content validity of both simulators and of virtual instruments. NOViSE also demonstrated early signs of construct validity. VR simulation of flexible instruments in NOViSE and VCSim3 can contribute to surgical training and improve the educational experience without putting patients at risk, raising ethical issues or requiring expensive animal or cadaver facilities. Moreover, in the context of an innovative and experimental technique such as NOTES, NOViSE could potentially facilitate its development and contribute to its popularization by keeping practitioners up to date with this new minimally invasive technique.Open Acces

Festschrift zum 60. Geburtstag von Wolfgang Strasser

Die vorliegende Festschrift ist Prof. Dr.-Ing. Dr.-Ing. E.h. Wolfgang Straßer zu seinem 60. Geburtstag gewidmet. Eine Reihe von Wissenschaftlern auf dem Gebiet der Computergraphik, die alle aus der "Tübinger Schule" stammen, haben - zum Teil zusammen mit ihren Schülern - Aufsätze zu dieser Schrift beigetragen. Die Beiträge reichen von der Objektrekonstruktion aus Bildmerkmalen über die physikalische Simulation bis hin zum Rendering und der Visualisierung, vom theoretisch ausgerichteten Aufsatz bis zur praktischen gegenwärtigen und zukünftigen Anwendung. Diese thematische Buntheit verdeutlicht auf anschauliche Weise die Breite und Vielfalt der Wissenschaft von der Computergraphik, wie sie am Lehrstuhl Straßer in Tübingen betrieben wird. Schon allein an der Tatsache, daß im Bereich der Computergraphik zehn Professoren an Universitäten und Fachhochschulen aus Tübingen kommen, zeigt sich der prägende Einfluß Professor Straßers auf die Computergraphiklandschaft in Deutschland. Daß sich darunter mehrere Physiker und Mathematiker befinden, die in Tübingen für dieses Fach gewonnen werden konnten, ist vor allem seinem Engagement und seiner Ausstrahlung zu verdanken. Neben der Hochachtung vor den wissenschaftlichen Leistungen von Professor Straßer hat sicherlich seine Persönlichkeit einen entscheidenden Anteil an der spontanten Bereischaft der Autoren, zu dieser Festschrift beizutragen. Mit außergewöhnlich großem persönlichen Einsatz fördert er Studenten, Doktoranden und Habilitanden, vermittelt aus seinen reichen internationalen Beziehungen Forschungskontakte und schafft so außerordentlich gute Voraussetzungen für selbständige wissenschafliche Arbeit. Die Autoren wollen mit ihrem Beitrag Wolfgang Straßer eine Freude bereiten und verbinden mit ihrem Dank den Wunsch, auch weiterhin an seinem fachlich wie menschlich reichen und bereichernden Wirken teilhaben zu dürfen

Simulation of nonverbal social interaction and small groups dynamics in virtual environments

How can the behaviour of humans who interact with other humans be simulated in virtual environments? This thesis investigates the issue by proposing a number of dedicated models, computer languages, software architectures, and specifications of computational components. It relies on a large knowledge base from the social sciences, which offers concepts, descriptions, and classifications that guided the research process. The simulation of nonverbal social interaction and group dynamics in virtual environments can be divided in two main research problems: (1) an action selection problem, where autonomous agents must be made capable of deciding when, with whom, and how they interact according to individual characteristics of themselves and others; and (2) a behavioural animation problem, where, on the basis of the selected interaction, 3D characters must realistically behave in their virtual environment and communicate nonverbally with others by automatically triggering appropriate actions such as facial expressions, gestures, and postural shifts. In order to introduce the problem of action selection in social environments, a high-level architecture for social agents, based on the sociological concepts of role, norm, and value, is first discussed. A model of action selection for members of small groups, based on proactive and reactive motivational components, is then presented. This model relies on a new tagbased language called Social Identity Markup Language (SIML), allowing the rich specification of agents' social identities and relationships. A complementary model controls the simulation of interpersonal relationship development within small groups. The interactions of these two models create a complex system exhibiting emergent properties for the generation of meaningful sequences of social interactions in the temporal dimension. To address the issues related to the visualization of nonverbal interactions, results are presented of an evaluation experiment aimed at identifying the application requirements through an analysis of how real people interact nonverbally in virtual environments. Based on these results, a number of components for MPEG-4 body animation, AML — a tag-based language for the seamless integration and synchronization of facial animation, body animation, and speech — and a high-level interaction visualization service for the VHD++ platform are described. This service simulates the proxemic and kinesic aspects of nonverbal social interactions, and comprises such functionalities as parametric postures, adapters and observation behaviours, the social avoidance of collisions, intelligent approach behaviours, and the calculation of suitable interaction distances and angles