Simulating molecular docking with haptics

Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually the binding site, and guide the molecules to their binding pose. Despite a forty-year research e�ort however, the docking community has been slow to adopt this technology. Proprietary, unreleased software, expensive haptic hardware and limits on processing power are the main reasons for this. Another signi�cant factor is the size of the molecules simulated, limited to small molecules. The focus of the research described in this thesis is the development of an interactive haptics-assisted docking application that addresses the above issues, and enables the rigid docking of very large biomolecules and the study of the underlying interactions. Novel methods for computing the interaction forces of binding on the CPU and GPU, in real-time, have been developed. The force calculation methods proposed here overcome several computational limitations of previous approaches, such as precomputed force grids, and could potentially be used to model molecular exibility at haptic refresh rates. Methods for force scaling, multipoint collision response, and haptic navigation are also reported that address newfound issues, particular to the interactive docking of large systems, e.g. force stability at molecular collision. The i ii result is a haptics-assisted docking application, Haptimol RD, that runs on relatively inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary hardware)

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

Argonne National Laboratory annual report of laboratory directed research and development program activities for FY 1995.

The purposes of Argonne's Laboratory Directed Research and Development (LDRD) Program are to encourage the development of novel concepts, enhance the Laboratory's R&D capabilities, and further the development of its strategic initiatives