Fast Collision Culling in Large-Scale Environments Using GPU Mapping Function

International audienceThis paper presents a novel and efficient GPU-based parallel algorithm to cull non-colliding object pairs in very large-scale dynamic simulations. It allows to cull objects in less than 25ms with more than 100K objects. It is designed for many-core GPU and fully exploits multi-threaded capabilities and data-parallelism. In order to take advantage of the high number of cores, a new mapping function is defined that enables GPU threads to determine the objects pair to compute without any global memory access. These new optimized GPU kernel functions use the thread indexes and turn them into a unique pair of objects to test. A square root approximation technique is used based on Newton's estimation, enabling the threads to only perform a few atomic operations. A first characterization of the approximation errors is presented, enabling the fixing of incorrect computations. The I/O GPU streams are optimized using binary masks. The implementation and evaluation is made on largescale dynamic rigid body simulations. The increase in speed is highlighted over other recently proposed CPU and GPU-based techniques. The comparison shows that our system is, in most cases, faster than previous approaches

Statistical and Directable Methods for Large-Scale Rigid Body Simulation

This dissertation describes several techniques to improve performance and controllability of large-scale rigid body simulations. We first describe a statistical simulation method that replaces certain stages of rigid body simulation with a statistically- based approximation. We begin by collecting statistical data regarding changes in linear and angular momentum for collisions of a given object. From the data, we extract a statistical ”signature” for the object, giving a compact representation of the object’s response to collision events. During object simulation, both the collision detection and the collision response calculations are replaced by simpler calculations based on the statistical signature. In addition, based on our statistical simulator, we develop a mixed rigid body simulator that combines an impulse-based with a statistically-based collision response method. This allows us to maintain high accuracy in important parts of the scene while achieving greater efficiency by simplifying less important parts of the simulation. The resulting system gives speedups of more than an order of magnitude on several large rigid body simulations while maintaining high accuracy in key places and capturing overall statistical behavior in other places. Also, we introduce two methods for directing pile behavior to form the desired shapes. To fill up the space inside the desired shapes and maintain the stability of the desired pile shapes, our methods analyze the configurations and status of all objects and properly select some candidates to have their degrees of freedom (DOFs) reduced. Our first method utilizes the idea of angles of repose to perform the analysis. According to the desired angle of repose, we create an additional spatial structure to track the piling status and select suitable objects to reduce their DOFs. In our second method, we adapt equilibrium analysis in a local scheme to find “stable” objects of the stacking structure. Then, we restrict their DOFs by adding constraints on them for stabilizing the structure. Overall, our directing methods generate a wider variety of piled structures than possible with strict physically-based simulation

Sphere encapsulated oriented-discrete orientation polytopes (S-dop) collision culling for multi-, rigid body dynamic

This paper discusses on sphere encapsulated oriented-discrete orientation polytopes (therefore will be referred to as S-Dop) collision culling for multiple rigid body simulation. In order to improve performance of the whole simulation system, there are available options in sacrificing the accuracy over speed by using certain approximation techniques. The aim of this research is to achieve excellent performance through implementation of suitable culling technique, without jeopardizing the resulting behavior so that the simulation will still be physically plausible. The basic idea is to identify the highly probable pairs to collide and test the pair with a more accurate collision test in broad-phase collision detection, before the pair is passed to a more costly stage. Results from the experiments showed that there are a number of ways to implement the sphere encapsulated or-Dops (S-Dop) collision culling on a multiple rigid body simulation depending on the level of performance needed

Mathematische Modellierung von Lymphozyten-vermittelten Immunantworten

The adaptive immune response is crucial for defence of organisms against infections. There are two main cell populations of the adaptive immune system, T and B lymphocytes, bearing specific receptors which allow to recognise infection and cancer antigens. Although these cells may play a beneficial role in viral or bacterial infection, in some cases, like autoimmune diseases or organ transplantation, T and B cell responses are undesired. Chronic graft rejection is associated with the production of donor-specific antibodies by B cells, and is the main reason for late graft failure. Immune cell clusters called tertiary lymphoid organs (TLOs), which develop at chronic inflammation sites, are shown to be related to graft rejection in mice. The stability of these clusters depends on the interactions of lymphocytes with stromal cells via chemokine and cell surface proteins, which is modelled in chapter 3. In addition, I implemented a 3D agent-based off-lattice model, which allows to describe cell migration, chemokine diffusion and receptor internalisation dynamics. I show that chemokine degradation by proteolysis does not influ- ence its concentration in the vicinity of a secreting cell. In addition, I study how consumption of the chemokine may change its gradient or even invert it at certain model parameters. In chapter 4, I model interaction of germinal centres (GCs). GCs are organized clusters of immune and stromal cells in secondary and tertiary lymphoid tissue, which are responsible for the generation of B cell clones producing high affinity antibodies. Injected antibodies are shown to mask antigen which is presented to B cells in GCs. It motivates to consider GCs as a system of agents interacting via antibodies. Simulation of a system of interacting GCs suggested the possibility for early GCs to suppress development of the later ones. I hope to provoke new experiments in order to investigate influence of antibodies on the GC reaction course, which might find an application in different clinical conditions. Besides antibody responses, a cytotoxic T cell (CTL) activity might also find application in clinics. In chapter 5, I estimated killing rates for CTLs in different experimental set-ups. Using the data from in vivo microscopy about target cell fate depending on the contacts with CTLs I show that previous contacts dramatically increase the probability of target cells to die. This kind of modelling may be used for optimization of T cell-based therapies.Die adaptive Immunantwort ist essentiell für die Verteidigung des Organismus gegen Infektionen. Es gibt zwei wesentliche Zellpopulationen des adaptiven Immunsystems, die T- und B-Lymphozyten, welche spezifische Rezeptoren tragen, die ihnen erlauben, Antigene in Infektionen und Krebs zu erkennen. Obwohl diese Zellen bei Infektionskrankheiten hilfreich sind, ist der Immunantwort unter bestimmten Bedingungen unerwünscht. Chronische Transplantatabstoßung geht mit der Produktion spezifischer Antikörper gegen das Spendergewebe einher und ist der Haupgrund für spätes Transplantatatversagen. Verbünde von Immunzellen, genannt tertiäre lymphoide Organe (TLO), die sich an chronischen Entzündungsherden bilden, stehen mit der Transplantatabstoßung in Mäusen im Zusammenhang. Ihre Stabilität hängt von über Chemokine und Oberflächenproteine vermittelten Interaktionen ab, die in Kapitel 3 modelliert werden. Ich zeige hier, dass die Degradation von Chemokin durch Proteolyse dessen Konzentration in der Umgebung einer chemokinproduzierenden Zelle nicht beeinflusst. Weiterhin untersuche ich, wie der Verbrauch von Chemokin dessen Gradienten unter bestimmten Modellparametern verändern oder sogar umkehren kann. In Kapitel 4 modelliere ich Interaktionen zwischen Keimzentren (GC). GC sind organisierte Verbünde von Immun- und Stromazellen in lymphoiden Gewebe, die für die Bildung von B-Zell-Klonen verantwortlich sind, die hochaffine Antikörper produzieren. Es konnte nachgewiesen werden, dass injizierte Antikörper das im GC den B-Zellen präsentierte Antigen bedecken. Dies legt nahe, GC als ein System von interagierenden Akteuren zu betrachten. Simulationen eines Systems interagierender GC weisen darauf hin, dass früh gebildete GC sich später bildende GC unterdrücken könnten. Neben der Antikörperantwort kann auch die Aktivität cytotoxischer T-Zellen (CTL) für die klinische Anwendung relevant sein. In Kapitel 5 schätze ich die Rate ab, mit der CTL in verschiedenen Experimenten Zellen eliminieren. Anhand von mittels in vivo-Mikroskopie generierten Daten zur weiteren Entwicklung von Zellen abhängig von der Zahl der Kontakte mit CTL weise ich nach, dass ein früherer Kontakt mit CTL die Wahrscheinlichkeit für eine Zelle massiv erhöht, bei einem erneuten CTL-Kontakt zu sterben. Dieser Modellierungsansatz könnte für die Optimierung von auf T-Zellen basierten Therapien genutzt werden

Micromechanics of passive and active inclusions in granular media

Passive and active inclusions in granular materials play an increasingly important role in the development of sustainable infrastructure. Passive inclusions, such as geogrids, have been shown to augment the service life of roadways and reduce aggregate consumption in pavement base layers. This is possible due to the aggregate-geogrid composite action, that results in the redistribution of traffic loads. The present study presents three-dimensional models that simulate the cyclic-loading behavior of geogrid-reinforced base layers using the discrete element method. It introduces a new framework by which upper and lower performance bounds are established by simulating unreinforced and perfectly reinforced aggregate bases. The model works as a tool for systematic prototyping of new geogrid geometries and mechanical properties. Furthermore, important insights into how aggregate morphology works in combination with different geogrids were obtained via a parametric study. The sustainability of linear infrastructure can also be improved with the use of active inclusions for thorough soil exploration and characterization. Self-motile probes are an emergent technology that will enable multidirectional testing of soils in situ. The locomotion systems of several of these technologies have been inspired by annelid peristalsis. Annelids such as the earthworm Lumbricus terrestris use synchronized muscle expansion and contraction to anchor portions of their segmented bodies while other portions push into the medium. In this doctoral work, the peristaltic locomotion and the design of burrowing robots are investigated on multiple fronts. First, the anchorage mechanism developed by expanded segments is studied by conducting pullout experiments in sand and numerical modeling using the discrete element method. The results revealed the expansion ratio to be critical in the development of anchorage resistance by promoting different soil responses. Subsequently, the effect of tip shape in reducing penetration resistance to enable greater advancement into granular beds is investigated using experiments and numerical modeling with the discrete element method. Results reveal that under low interface friction, penetration resistance can be decreased threefold by utilizing sharper tips. Later, the soil response to the anchor–push mechanism employed is investigated utilizing robotic analogs and X-ray micro-tomography. Results revealed a significant contrast between the soil response in loose and dense materials. Finally, a transparent synthetic soil testbed is developed. It enables the prototyping and testing of burrowing devices with real-time imaging. Results demonstrate the ability of the setup to provide important insight into geometrical aspects of robot designs that improve their advancement and overall performance.Ph.D

Model Simplification for Efficient Collision Detection in Robotics

Motion planning for industrial robots is a computationally intensive task due to the massive number of potential motions between any two configurations. Calculating all possibilities is generally not feasible. Instead, many motion planners sample a sub-set of the available space until a viable solution is found. Simplifying models to improve collision detection performance, a significant component of motion planning, results in faster and more capable motion planners. Several approaches for simplifying models to improve collision detection performance have been presented in the literature. However, many of them are sub-optimal for an industrial robotics application due to input model limitations, accuracy sacrifices, or the probability of increasing false negatives during collision queries. This thesis focuses on the development of model simplification approaches optimised for industrial robotics applications. Firstly, a new simplification approach, the Bounding Sphere Simplification (BSS), is presented that converts triangle-mesh inputs to a collection of spheres for efficient collision and distance queries. Additionally, BSS removes small features and generates an output model less prone to false negatives

Virtual Assembly and Disassembly Analysis: An Exploration into Virtual Object Interactions and Haptic Feedback

In recent years, researchers have developed virtual environments, which allow more realistic human-computer interactions and have become increasingly popular for engineering applications such as computer-aided design and process evaluation. For instance, the demand for product service, remanufacture, and recycling has forced companies to consider ease of assembly and disassembly during the design phase of their products. Evaluating these processes in a virtual environment during the early stages of design not only increases the impact of design modifications on the final product, but also eliminates the time, cost, and material associated with the construction of physical prototypes. Although numerous virtual environments for assembly analysis exist or are under development, many provide only visual feedback. A real-time haptic simulation test bed for the analysis of assembly and disassembly operations has been developed, providing the designer with force and tactile feedback in addition to traditional visual feedback. The development such a simulation requires the modeling of collisions between virtual objects, which is a computationally expensive process. Also, the demands of a real-time simulation incorporating haptic feedback introduce additional complications for reliable collision detection. Therefore, the first objective of this work was to discover ways in which current collision detection libraries can be improved or supplemented to create more robust interaction between virtual objects. Using the simulation as a test bed, studies were then conducted to determine the potential usefulness of haptic feedback for analysis of assembly and disassembly operations. The following significant contributions were accomplished: (1) a simulation combining the strengths of an impulse-based simulation with a supplemental constraint maintenance scheme for modeling object interactions, (2) a toolkit of supplemental techniques to support object interactions in situations where collision detection algorithms commonly fail, (3) a haptic assembly and disassembly simulation useful for experimentation, and (4) results from a series of five experimental user studies with the focus of determining the effectiveness of haptic feedback in such a simulation. Additional contributions include knowledge of the usability and functionality of current collision detection libraries, the limitations of haptic feedback devices, and feedback from experimental subjects regarding their comfort and overall satisfaction with the simulation.Ph.D.Committee Chair: Bras, Bert; Committee Member: Baker, Nelson; Committee Member: Griffin, Paul; Committee Member: Paredis, Chris; Committee Member: Rosen, Davi

Design and development of a VR system for exploration of medical data using haptic rendering and high quality visualization

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