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This paper addresses the issue of flight control of high frequency time-varying dynamics of biologically motivated flapping-wing micro air vehicle (FWMAV). A control scheme based on time-averaging theory is presented for the control of longitudinal dynamics of FWMAV. The time averaging results in a simplified model which approximates the high frequency time varying dynamics of the original system. A differential flatness based non-linear controller is designed for the time-averaged system and successfully applied to the time-varying system for trajectory tracking.