IM-UFF: extending the Universal Force Field for interactive molecular modeling

International audienceThe universal force field (UFF) is a broadly applicable classical force field that contains parameters for almost every atom type of the periodic table. This force field is non-reactive, i.e. the topology of the system under study is considered as fixed and no creation or breaking of covalent bonds is possible. This paper introduces interactive modeling-UFF (IM-UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physics based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience available at http://www.samson-connect.net

Generating conformational transition paths with low potential-energy barriers for proteins

International audienceThe knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation

The CUIK suite: Analyzing the motion closed-chain multibody systems

Many situations in robotics require the analysis of the motions of complex multibody systems. These are sets of articulated bodies arising in a variety of devices, including parallel manipulators, multifingered hands, or reconfigurable mechanisms, but they appear in other domains too as mechanical models of molecular compounds or nanostructures. Closed kinematic chains arise frequently in such systems, either due to their morphology or due to geometric or contact constraints to fulfill during operation, giving rise to configuration spaces of an intricate structure. Despite appearing very often in practice, there is a lack of general software tools to analyze and represent such configuration spaces. Existing packages are oriented either to open-chain systems or to specific robot types, which hinders the analysis and development of innovative manipulators. This article describes the CUIK suite, a software toolbox for the kinematic analysis of general multibody systems. The implemented tools can isolate the valid configurations, determine the motion range of the whole multibody system or of some of its parts, detect singular configurations leading to control or dexterity issues, or find collision-and singularity-free paths between configurations. The toolbox has applications in robot design and programming and is the result of several years of research and development within the Kinematics and Robot Design group at IRI, Barcelona. It is available under GPLv3 license from http://www.iri.upc.edu/cuik.This work has been partially supported by the Spanish Ministry of Economy and Competitiveness under project DPI2010-18449, by a Juan de la Cierva fellowship supporting Montserrat Manubens, and by a CSIC JAE-Doc fellowship partially funded by the ESF supporting Leonard Jaillet.Peer Reviewe

ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways

International audienceThis article proposes a method to efficiently generate approximate ligand unbind-ing pathways. It combines an efficient tree-based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is com-putationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state-of-the-art approaches. We show that the method is time-efficient and produces pathways in good agreement with other state-of-the-art solutions. These paths can serve as first approximations that can be used, analyzed or improved with more specialized methods

Méthodes probabilistes pour la planification réactive de mouvements

Current motion planning techniques are now capable of planning motions for complex mechanisms in cluttered environments. Nevertheless the adaptation of these planners to scenes with both static and mobile obstacles has been limited so far. One of the reasons is the cost to reflect during queries the dynamic changes of the scene into the data structure preprocessed to capture the free configuration space connectivity. Our main contribution is the proposition of a new planner able to deal with static and mobile obstacles. This hybrid planner combines the PRM framework, originally designed for solving multiple-query problems and that we extended for operating in dynamic scenes with improved diffusion techniques designed to solve single queries without requiring any preprocessing. In practice this planner is also based on several lazy evaluation mechanisms to improve the efficiency of the approach. The design of this new planer has led to the main following development: - The proposition of an original architecture for this planner dedicated to changing environments. This architecture include several lazy evaluation mechanisms to make the planner really efficient. - A new diffusion planner to locally reconnect portions of the roadmap broken by mobile obstacles. We call it Dynamic-Domain RRT planner. This new extension of the original RRT method is able to automatically balance refinement of already explored regions and expansion toward new unknown regions. - Two methods to create cyclic roadmaps to initialise the planner. The first one use the assumption that mobile obstacles are confined to some regions of the space to build roadmap specifically to changes of the obstacles positions. The second one is a general method to capture the connectivity but also the homotopical classes of the free configuration space in a condensed data structure. All these methods are implemented within the software platform Move3D developed at LAAS and evaluated on different kind o f complex 3D examples.Les techniques de planification de mouvement actuelles sont maintenant capables de résoudre des problèmes mettant en jeu des mécanismes complexes plongés au sein d'environnements encombrés. Néanmoins, l'adaptation de ces planificateurs à des scènes comprenant à la fois des obstacles statiques et des obstacles mobiles s'est avérée limitée jusqu'ici. Une des raisons en est le coût associé à la mise à jour des structures de données qui sont précalculées pour capturer la connexité de l'espace libre. Notre contribution principale concerne la proposition d'un nouveau planificateur capable de traiter des problèmes comprenant à la fois obstacles statiques et obstacles mobiles. Ce planificateur hybride combine deux grandes familles de techniques. D'une part les techniques dites PRM, initialement conçues pour résoudre des problèmes à requêtes multiples et que nous avons étendu à des problèmes de scènes dynamiques. D'autre part, de nouvelles techniques de diffusion, alors que celles-ci sont généralement dédiées aux problèmes simple requête ne nécessitant aucune opération de prétraitement. Les principaux développements accompagnant la construction de ce planificateur sont les suivants : - La proposition d'une architecture originale pour le planificateur dédié aux environnements changeants. Cette architecture inclut notamment plusieurs mécanismes dits d' "évaluation paresseuse" qui permettent de minimiser les test de collision et ainsi d'assurer de bonnes performances. - Le développement d'une nouvelle méthode de diffusion permettant de reconnecter localement certaines portions du réseau invalidées par la présence des obstacles mobiles. Cette méthode, appelée RRT à Domaine Dynamique correspond en fait une extension des planificateur bien connus à bases de RRTs. Un des intérêt propre à notre approche est d'équilibrer automatiquement deux comportements propres au planificateur : l'exploration vers des régions encore inconnues et l'affinage du modèle des régions de l'espac e déjà explorées. - Deux méthodes originales de création de réseaux cycliques qui servent à initialiser notre planificateur. La première assume que les obstacles mobiles sont confinés dans une région donnée, pour construire un réseau adapté aux différents types de changements de position possibles. La seconde est une méthode qui construit des réseaux appelés "réseaux de rétraction". A l'aide d'une structure de donnée de faible taille, cette structure parvient à capturer les différentes variétés de chemins de l'espace, à travers notamment chacune des classes d'homotopie de l'espace libre. Toutes ces méthodes sont implémentées au sein de la plate-forme de travail Move3D développée au LAAS-CNRS et sont évaluées sur différents types de systèmes mécaniques plongés au sein d'environnements 3D

Path planning with loop closure constraints using an atlas-based RRT

Presentado al 15th International Symposium on Robotics Research celebrado en USA del 28 de agosto al 1 de septiembre de 2011.In many relevant path planning problems, loop closure constraints reduce the configuration space to a manifold embedded in the higher-dimensional joint ambient space. Whereas many progresses have been done to solve path planning problems in the presence of obstacles, only few work consider loop closure constraints. In this paper we present the AtlasRRT algorithm, a planner specially tailored for such constrained systems that builds on recently developed tools for higher-dimensional continuation. These tools provide procedures to define charts that locally parametrize manifolds and to coordinate them forming an atlas. AtlasRRT simultaneously builds an atlas and a Rapidly-Exploring Random Tree (RRT), using the atlas to sample relevant configurations for the RRT, and the RRT to devise directions of expansion for the atlas. The new planner is advantageous since samples obtained from the atlas allow a more efficient extension of the RRT than state of the art approaches, where samples are generated in the joint ambient space.This work has been partially supported by the Spanish Ministry of Science and Innovation under project DPI2010-18449.Peer Reviewe

Randomized path planning on manifolds based on higher-dimensional continuation

Despite the significant advances in path planning methods, highly constrained problems are still challenging. In some situations, the presence of constraints defines a configuration space that is a non-parametrizable manifold embedded in a high-dimensional ambient space. In these cases, the use of sampling-based path planners is cumbersome since samples in the ambient space have low probability to lay on the configuration space manifold. In this paper, we present a new path planning algorithm specially tailored for highly constrained systems. The proposed planner builds on recently developed tools for higher-dimensional continuation, which provide numerical procedures to describe an implicitly defined manifold using a set of local charts. We propose to extend these methods focusing the generation of charts on the path between the two configurations to connect and randomizing the process to find alternative paths in the presence of obstacles. The advantage of this planner comes from the fact that it directly operates into the configuration space and not into the higher-dimensional ambient space, as most of the existing methods do. © 2012 SAGE Publications.This work has been partially supported by the Spanish Ministry of Science and Innovation under project DPI2010-18449.Peer Reviewe

A PRM-based motion planner for dynamically changing environments

This paper presents a path planner for robots operating in dynamically changing environments with both static and moving obstacles. The proposed planner is based on probabilistic path planning techniques and it combines techniques originally designed for solving multiple-query and single-query problems. The planner first starts with a preprocessing stage that constructs a roadmap of valid paths with respect to the static obstacles. It then uses lazy-evaluation mechanisms combined with a single-query technique as local planner in order to rapidly update the roadmap according to the dynamic changes. This allows to answer queries quickly when the moving obstacles have little impact on the free-space connectivity. When the solution can not be found in the updated roadmap, the planner initiates a reinforcement stage that possibly results into the creation of cycles representing alternative paths that were not already stored in the roadmap. Simulation results show that this combination of techniques yields to efficient global planner capable of solving with a real-time performance problems in geometrically complex environments with moving obstacles

Path Deformation Roadmaps

This paper describes a new approach to sampling-based motion planning with PRM methods. Our aim is to compute good quality roadmaps that encode the multiply connectedness of the Cspace inside low redundancy graphs, yet representative of the different varieties of free paths. The proposed approach relies on a notion of path deformability indicating whether or not a given path can be continuously deformed to another existing one. By considering a simpler form of deformation than the one allowed between homotopic paths, we propose a method that extends the Visibility-PRM technique [12] to construct compact roadmaps that encode a richer and more suitable information than representative paths of the homotopy classes. The Path Deformation Roadmaps also contain additional useful cycles between paths in the same homotopy class that can be hardly deformed into each other. First experiments presented in the paper show that our technique enables small roadmaps to reliably and efficiently capture the multiply-connectedness of the space in various problems