Algorithmes incrémentaux pour la théorie de la fonctionnelle de la densité

The ability to model molecular systems on a computer has become a crucial tool for chemists. Indeed molecular simulations have helped to understand and predict properties of nanoscopic world, and during the last decades have had large impact on domains like biology, electronic or materials development. Particle simulation is a classical method of molecular dynamic. In particle simulation, molecules are split into atoms, their inter-atomic interactions are computed, and their time trajectories are derived step by step. Unfortunately, inter-atomic interactions computation costs prevent large systems to be modeled in a reasonable time. In this context, our research team looks for new accurate and efficient molecular simulation models. One of our team's focus is the search and elimination of useless calculus in dynamical simulations. Hence has been proposed a new adaptively restrained dynamical model in which the slowest particles movement is frozen, computational time is saved if the interaction calculus method do not compute again interactions between static atoms. The team also developed several interaction models that benefit from a restrained dynamical model, they often updates interactions incrementally using the previous time step results and the knowledge of which particle have moved.In the wake of our team's work, we propose in this thesis an incremental First-principles interaction models. Precisely, we have developed an incremental Orbital-Free Density Functional Theory method that benefits from an adaptively restrained dynamical model. The new OF-DFT model keeps computation in Real-Space, so can adaptively focus computations where they are necessary. The method is first proof-tested, then we show its ability to speed up computations when a majority of particle are static and with a restrained particle dynamic model. This work is a first step toward a combination of incremental First-principle interaction models and adaptively restrained particle dynamic models.In the wake of our team's work, we propose in this thesis an incremental First-principles interaction models. Precisely, we have developed an incremental Orbital-Free Density Functional Theory method that benefits from an adaptively restrained dynamical model. The new OF-DFT model keeps computation in Real-Space, so can adaptively focus computations where they are necessary. The method is first proof-tested, then we show its ability to speed up computations when a majority of particle are static and with a restrained particle dynamic model. This work is a first step toward a combination of incremental First-principle interaction models and adaptively restrained particle dynamic models.L'informatique est devenue un outil incontournable de la chimie. En effet la capacité de simuler des molécules sur ordinateur a aidé à la compréhension du monde nanoscopic et à la prédiction de ses propriétés. La simulation moléculaire a eu ces dernières décennies un impact scientifique énorme en biologie, en électronique, en science des matériaux ... La simulation de particules est une des méthodes classiques de dynamique moléculaire, les molécules y sont divisées en atomes, leurs interactions relatives calculées et leurs trajectoires déduites pas à pas. Malheureusement un calcul précis des interactions entre atomes demande énormément d'opérations et donc de temps, ce qui limite la portée de la simulation moléculaire à des systèmes de taille raisonnable. C'est dans ce contexte que notre équipe recherche de nouveaux modèles de simulation moléculaire rapide et précis. Un des angles de recherche est l'élimination des calculs inutiles des simulations. L'équipe a ainsi proposé un modèle de dynamique moléculaire dite restreinte de manière adaptative dans lequel le mouvement des particules les plus lentes est bloqué. Si la simulation ne recalcule pas les interactions inchangées entre atomes bloqués, le calcul des interactions est plus rapide. L'équipe a aussi développé plusieurs modèles d'interactions plus efficaces pour des modèles de dynamique restreinte de particules, ils mettent à jour les interactions de façon incrémentale en utilisant les résultats du pas de temps précédent et la liste des particules mobiles. Dans le sillage des travaux de notre équipe de recherche, nous proposons dans cette thèse une méthode incrémentale pour calculer des interactions interatomique basées sur les modèles de Théorie de la Fonctionnelle de la Densité Sans Orbitale. La nouvelle méthode garde les calculs dans l'espace réel et peut ainsi concentrer les calculs où cela est nécessaire. Dans ce manuscrit nous vérifions cette méthode, puis nous évaluons les gains de vitesse lorsqu'une majorité de particule est bloquée, avec un modèle de dynamique restreinte. Ces travaux sont un pas vers la l'intégration de modèles d'interactions Premier-principes pour des modèles dynamiques restreint de manière adaptative

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

Adaptive Physically Based Models in Computer Graphics

International audienceOne of the major challenges in physically-based modeling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes, and particles. Applications range from fluids, through deformable bodies, to articulated solids

Matching non-uniformity for program optimizations on heterogeneous many-core systems

As computing enters an era of heterogeneity and massive parallelism, it exhibits a distinct feature: the deepening non-uniform relations among the computing elements in both hardware and software. Besides traditional non-uniform memory accesses, much deeper non-uniformity shows in a processor, runtime, and application, exemplified by the asymmetric cache sharing, memory coalescing, and thread divergences on multicore and many-core processors. Being oblivious to the non-uniformity, current applications fail to tap into the full potential of modern computing devices.;My research presents a systematic exploration into the emerging property. It examines the existence of such a property in modern computing, its influence on computing efficiency, and the challenges for establishing a non-uniformity--aware paradigm. I propose several techniques to translate the property into efficiency, including data reorganization to eliminate non-coalesced accesses, asynchronous data transformations for locality enhancement and a controllable scheduling for exploiting non-uniformity among thread blocks. The experiments show much promise of these techniques in maximizing computing throughput, especially for programs with complex data access patterns

Haptic holography : an early computational plastic

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2001.Includes bibliographical references (p. 135-148).This dissertation introduces haptic holography, a combination of computational modeling and multimodal spatial display, as an early computationalplastic In this work, we combine various holographic displays with a force feedback device to image free-standing material surfaces with programmatically prescribed behavior. We present three implementations, Touch, Lathe, and Poke, each named for the primitive functional affordance it offers. In Touch, we present static holographic images of simple geometry, reconstructed in front of the hologram plane (in the viewer's space), and precisely co-located with a force model of the same geometry. These images can be visually inspected and haptically explored using a hand-held interface. In Lathe, we again display holo-haptic images of simple geometry, this time allowing those images to be reshaped by haptic interaction in a dynamic but constrained manner. Finally in Poke, we present a holo-haptic image that permits arbitrary reshaping of its reconstructed surface. As supporting technology, we offer a new technique for incrementally computing and locally updating interference-modeled holographic fringe patterns. This technique permits electronic holograms to be updated arbitrarily and interactively, marking a long-held goal in display holography. As a broader contribution, we offer a new behavior-based spatial framework, based on both perception and action, for informing the design of spatial interactive systems.Wendy J. Plesniak.Ph.D

Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics

International audienceAdaptively Restrained Molecular dynamics (ARMD) allows users to perform more integration steps in wall-clock time by switching on and off positional degrees of freedoms. This article presents new, single-pass incremental force updates algorithms to efficiently simulate a system using ARMD. We assessed different algorithms for speedup measurements and implemented them in the LAMMPS MD package. We validated the single-pass incremental force update algorithm on four different benchmarks using diverse pair potentials. The proposed algorithm allows us to perform simulation of a system faster than traditional MD in both NVE and NVT ensembles. Moreover, ARMD using the new single-pass algorithm speeds up the convergence of observables in wall-clock time

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Methods for increasing model accuracy and simulation time scales of biological processes with molecular dynamics

This dissertation presents three research projects on novel methods in computational bio- physics. Each of these projects introduces methodologies to extend the capabilities of molecular dynamics simulations in one way or another. In the first chapter, molecular dynamics simulations and the central role they play in the field of structural biology is introduced to give the reader some background on the common basis of the projects. The second chapter describes the first of these projects, where the molecular dynamics flexible fitting method for refining molecular structures of macromolecules using experimental electron density data is extended to be able to handle high-resolution density data, which are becoming increasingly commonplace. The third chapter focuses on adaptive multilevel splitting, a replica-based sampling technique that was employed in molecular dynamics simulations to measure the rate of drug molecule dissociation, a process that occurs on the order of milliseconds and above, which is out of the reach of typical molecular dynamics simulations. In the final chapter, a kinetic model of diffusion is introduced. This model allows simulation of the diffusion of small molecules in arbitrary potentials, for example, those that characterize the space around and within a membrane protein channel. The adaptive discretization scheme allows simulations between the micro- to millisecond time scales, which are typical of diffusive processes. This collection of projects is a snapshot of the diversity and versatility of current problems in structural biology that can be addressed by molecular dynamics simulations. I hope to instill in the reader a sense of how method development in molecular dynamics will expand the contributions of the field to both scientific and practical pursuits in biology

Underwater Vehicles

For the latest twenty to thirty years, a significant number of AUVs has been created for the solving of wide spectrum of scientific and applied tasks of ocean development and research. For the short time period the AUVs have shown the efficiency at performance of complex search and inspection works and opened a number of new important applications. Initially the information about AUVs had mainly review-advertising character but now more attention is paid to practical achievements, problems and systems technologies. AUVs are losing their prototype status and have become a fully operational, reliable and effective tool and modern multi-purpose AUVs represent the new class of underwater robotic objects with inherent tasks and practical applications, particular features of technology, systems structure and functional properties