ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations

International audienceThe amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

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Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange

10 simple rules to create a serious game, illustrated with examples from structural biology

Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games, games that allow people to produce and/or analyze scientific data. Interestingly, it is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience ( Phylo , DocMolecules , HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games

Dynamique Moléculaire Interactive

Interactive Molecular Dynamics (IMD) is a real-time simulation technique that allows scientists to interact with virtual molecular systems. Users can observe a simulation in progress in real time and manipulate the motion of individual atoms and molecules by applying forces, and receive feedback on the dynamic response of these systems in interactive time. The development of IMD has been influenced by technological and algorithmic advances in simulation tools as well as advances in human-computer interaction, including haptic devices or augmented and virtual reality approaches, and increasingly affordable devices. Scientific and practical applications include mechanobiology research, determination of experimental structures, and nanoscale property visualization for dissemination. IMD has made significant advances in performance, visualization, and data analysis.La dynamique moléculaire interactive (IMD) est une technique de simulation en temps réel qui permet aux scientifiques d'interagir avec des systèmes moléculaires virtuels. Les utilisateurs peuvent observer une simulation en cours en temps réel et manipuler le mouvement d'atomes et de molécules individuels en appliquant des forces, et recevoir des retours sur la réponse dynamique de ces systèmes en temps interactif. Le développement de l'IMD a été influencé par les avancées technologiques et algorithmiques dans les outils de simulation ainsi que par les avancées dans l'interaction homme-machine, y compris les dispositifs haptiques ou les approches de réalité augmentée et virtuelle, des appareils de plus en plus abordables. Les applications scientifiques et pratiques comprennent la recherche en mécanobiologie, la détermination des structures expérimentales et la visualisation des propriétés à l'échelle nanométrique pour la diffusion. IMD a fait des progrès significatifs dans la performance, la visualisation et l'analyse des données

Wielding the power of interactive molecular simulations

International audienceSince the dawn of the computer age, scientists have designed devices to represent molecular structures and developed tools to simulate their dynamic behavior in silico. To this day, these tools remain central to our understanding of biomolecular phenomena. In contrast to other fields such as fluid mechanics or meteorology, the observation of molecular motions at the atomic level remains a major experimental challenge. Continuous advances in computer graphics and numerical computation, combined with the emergence of human-computer interaction approaches, led to the methodology of so-called "interactive molecular simulations", characterized by two main features. First, the possibility to visualize a running simulation in interactive time, i.e. compatible with human perception. Second, the possibility to manipulate the simulation interactively by imposing a force, changing a biophysical property, or editing runtime parameters on the fly. Such simulations are still little used in computational biology, where it is more common to run a series of offline simulations and then visualize and analyze the results. However, interactive molecular simulation tools promise to handle time-consuming tasks such as the modeling of particularly complex biomolecular structures more efficiently or to support approaches such as Rational Drug Design with regard to pharmaceutical applications

Using Conceptual Graphs to embed expert knowledge in VR Interactions: Application to Structural Biology

International audienceTo manage expert knowledge in VR interactions, we propose a software architecture based on semantic representation with Conceptual Graphs. We applied it on structural biology analysis. We define three semantic layers. The first layer embeds basic and specific domain knowledge (objects of interest). The second one describes the available tools in the application (visual representations). The third layer contains facts coming from VR interactions. Operations such as merging, projection, specialization and generalization allow us to build pattern conceptual graphs. They are translated using application specific wrapper into command interpretable by our targeted application. One goal is to release experts from the technical aspects of commands, and allow them to use their field terminology as vocal commands, in order to concentrate on the exploration task

Interface moléculaire tangible, modulaire, articulée, sans fil et sans marqueur, basée sur l’internet des objets

International audienceRational drug design, as car or building design, implies a detailed understanding of proteins’ behavior. Proteins are the building blocks the workers, the messengers, the transporters involved in the cell machinery and its components, and targeted by drugs. However, one of the major obstacles to this approach lies in the limitations of the human-computer interfaces to manipulate complex, three-dimensional, flexible objects during a simulation in progress. To address this problem, we designed a tangible molecular interface, allowing the manipulation of a modular and �exible physical molecular model, to build and manipulate a virtual molecular twin from this physical model, synchronized thanks to embedded sensors. We propose to present this tangible interface, allowing to open the discussion on the perspectives concerning this prototype.Concevoir de manière rationnelle des médicaments, comme on conçoit une voiture ou un bâtiment, implique une compréhension fine du fonctionnement des protéines, protéines constituant les briques, les ouvriers, les messagers, transporteurs, nécessaires au fonctionnement de la cellule et de ses composants, et ciblées par les médicaments. Cependant, un des freins majeurs à cette approche appelée Rational Drug Design, réside dans les limitations des interfaces humain-machine pour manipuler des objets moléculaires, complexes, tridimensionnels et flexibles. Pour avancer sur cette problématique, nous avons conçus une interface tangible moléculaire, permettant la manipulation directe d’un modèle physique moléculaire modulaire et flexible, outillé par des capteurs électroniques, pour construire et manipuler le jumeau virtuel moléculaire de ce modèle physique. Nous proposons d’en faire la démonstration, en suscistant la discussion sur les perspectives d’évolution de notre prototype