Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality

Authors:
Mustapha Hamdi;Antoine Ferreira;Gaurav Sharma;Constantinos Mavroidis
Affiliations:
Laboratoire Vision et Robotique, ENSI Bourges-University of Orléans, 18000 Bourges, France;Laboratoire Vision et Robotique, ENSI Bourges-University of Orléans, 18000 Bourges, France;Computational Bionano Robotics Laboratory, Northeastern University, Boston, MA-02120, USA;Computational Bionano Robotics Laboratory, Northeastern University, Boston, MA-02120, USA
Venue:
Microelectronics Journal
Year:
2008

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Abstract

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive bio-nanorobotic prototyping. Using simulated bio-nano environments in VR, the operator can design and characterize through physical simulation and 3D visualization the behavior of protein-based components and structures. The main novelty of the proposed simulations is based on the characterization of stiffness performances of passive joints-based proteins (@a-helix deca-alanine, repressor of primer protein and immunoglobulin protein) and active joints-based viral protein motor (VPL) in their native environment. Their use as elementary bio-nanorobotic components are also simulated and the results discussed.