Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality

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 3-D 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 (α-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.