Applying forces to elastic network models of large biomolecules using a haptic feedback device

Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version

Haptic molecular simulation based on force control

International audienceIn this paper, force control is proposed to connect a molecular simulator to a haptic device. Most of the works dealing with this kind of simulators use position control to manipulate the molecules, with major stability concerns. These two control modes are compared in terms of adequacy with the molecular simulator. Stability with respect to the scaling coefficients introduced to connect the macro and the nanoworlds is also considered. The theoretical results and the experiments carried out confirm that position control is sensitive to the gain tuning. Force control enables to get stable force feedback for varying gains, and is thus a promising coupling to perform manipulations on complex molecular systems

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Haptic feedback in teleoperation in Micro-and Nano-Worlds.

International audienceRobotic systems have been developed to handle very small objects, but their use remains complex and necessitates long-duration training. Simulators, such as molecular simulators, can provide access to large amounts of raw data, but only highly trained users can interpret the results of such systems. Haptic feedback in teleoperation, which provides force-feedback to an operator, appears to be a promising solution for interaction with such systems, as it allows intuitiveness and flexibility. However several issues arise while implementing teleoperation schemes at the micro-nanoscale, owing to complex force-fields that must be transmitted to users, and scaling differences between the haptic device and the manipulated objects. Major advances in such technology have been made in recent years. This chapter reviews the main systems in this area and highlights how some fundamental issues in teleoperation for micro- and nano-scale applications have been addressed. The chapter considers three types of teleoperation, including: (1) direct (manipulation of real objects); (2) virtual (use of simulators); and (3) augmented (combining real robotic systems and simulators). Remaining issues that must be addressed for further advances in teleoperation for micro-nanoworlds are also discussed, including: (1) comprehension of phenomena that dictate very small object (< 500 micrometers) behavior; and (2) design of intuitive 3-D manipulation systems. Design guidelines to realize an intuitive haptic feedback teleoperation system at the micro-nanoscale level are proposed