This paper proposes a novel dynamic model of a Reaction Wheel Assembly (RWA) based on the Two-Input Two-Output Port framework, already presented by the authors. This method allows the user to study a complex system with a sub-structured approach: each sub-element transfers its dynamic content to the other sub-elements through local attachment points with any set of boundary conditions. An RWA is modelled with this approach and it is then used to study the impact of typical reaction wheel perturbations on a flexible satellite in order to analyze the micro-vibration content for a high accuracy pointing mission. This formulation reveals the impact of any structural design parameter and highlights the need of passive isolators to reduce the micro-vibration issues. The frequency analysis of the transfer between the disturbance sources and the line-of-sight (LOS) jitter highlights the role of the reaction wheel speed on the flexible modes migration and suggests which control strategies can be considered to mitigate the residual micro-vibration content in order to fulfil the mission performances.

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