MoMA-LigPath: A web server to simulate protein-ligand unbinding

Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity. However, obtaining information about these interactions with experimental or computational methods remains difficult. The computational tool presented in this paper, MoMA-LigPath, is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space. Such a purely geometric approach, together with the efficiency of the exploration algorithm, enables the simulation of ligand unbinding within very short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide very useful information about protein-ligand interactions. When needed, this approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. MoMA-LigPath is available at http://moma.laas.fr. The web server is free and open to all users, with no login requirement

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

SOUK: Social Observation of hUman Kinetics

International audienceSimulating human-centered pervasive systems requires accurate assumptions on the behavior of human groups. Recent models consider this behavior as a combination of both social and spatial factors. Yet, establishing accurate traces of human groups is difficult: current techniques capture either positions, or contacts, with a limited accuracy. In this paper we introduce a new technique to capture such behaviors. The interest of this approach lies in the unprecedented accuracy at which both positions and orientations of humans, even gathered in a crowd, are captured. From the mobility to the topological connectivity, the open-source framework we developed offers a layered approach that can be tailored, allowing to compare and reason about models and traces. We introduce a new trace of 50 individuals on which the validity and accuracy of this approach is demonstrated. To showcase the interest of our software pipeline, we compare it against the random waypoint model. Our fine-grain analyses, that take into account social interactions between users, show that the random way point model is not a reasonable approximation of any of the phenomena we observed

A UML-based method for risk analysis of human-robot interactions

International audienceSafety is a major concern for robots that interact physically with humans. We propose a risk analysis method based on deviation analysis of system usage scenarios that allows the identification of major risks. Scenarios are described with the common Unified Modeling Language (UML), and risk analysis is performed with the guideword-based collab-orative method HAZOP (HAZard OP-erability). We adapt HAZOP attributes and guidewords for generic interpretation of UML use-case and sequence diagrams describing human-robot interactions. This approach has been systematically applied for the analysis of two quite different robots working in a human environment: a mobile manipulator and a robotic strolling assistant. When applied, the method gave conclusive evidence that the modeled systems were not safe. A CASE tool to support this method is also presented

Data Backup for Mobile Nodes : a Cooperative Middleware and Experimentation Platform

In this paper, we present a middleware for dependable mobile systems and an experimentation platform for its evaluation. The middleware proposed is based on three original building blocks: a Proximity Map, a Trust and Cooperation Oracle, and a Cooperative Data Backup service. A Distributed Black-box is used as an illustrative application and evaluated on top of the proposed mobile platform