Dynamics and kinematics of viral protein linear nano-actuators for bio-nano robotic systems

Dynamic and kinematic analysis is performed to predict and verify the performance of a new nanoscale biomolecular motor: The Viral Protein Linear (VPL) Motor. The motor is based on a conformational change observed in a family of viral envelope proteins when subjected to a changing pH environment. The conformational change produces a motion of about 10 nm, making the VPL a basic linear actuator which can be further interfaced with other organic/inorganic nanoscale components such as DNA actuators and carbon nanotubes. The proteins used in the motor are subjected to Molecular Dynamics simulation using the software called CHARMm (Chemistry at Harvard Molecular Mechanics). The results of dynamics are further verified by performing a set of kinematic simulations using direct and inverse kinematics methods.