A complete, self-contained mathematical framework for modelling the coupled aeroelastic and flight dynamic behaviour of free-flying flexible aircraft subject to atmospheric gust encounters is presented. The framework integrates three physical disciplines: geometrically-exact nonlinear beam theory for structural dynamics, unsteady two-dimensional strip aerodynamics based on Theodorsen thin-aerofoil theory with indicial functions for shed-wake and gust-penetration effects, and quaternion-based rigid-body flight dynamics for singularity-free attitude propagation. The coupled system is assembled into a first-order state-space form amenable to time-domain simulation, model order reduction, and control design. Detailed derivations of all coupling terms, including coordinate transformations between aerodynamic and structural frames, the Jacobian block structure, and gust input matrices, are provided. Two gust models are treated: the certification-standard discrete gust and the Von Karman continuous turbulence spectrum. The framework is verified against published benchmarks, including high-altitude long-endurance aircraft configurations and a very flexible flying-wing, demonstrating close agreement in structural frequencies, flutter speed, and static aeroelastic deflections. This paper serves as a self-contained reference for researchers implementing coupled aeroelastic-flight dynamic analysis tools for very flexible aircraft.

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