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The seismic performance of long, embedded tunnels can be significantly influenced by spatial variation in ground motion, particularly when the tunnel length approaches the wavelength of seismic waves. This study presents an integrated two-stage modelling approach to evaluate the effect of global (alignment-scale) effects on the local (lining-scale) seismic response of the 27 km circular large hadron collider (LHC) tunnel at CERN. A beam on non-linear Winkler foundation (BNWF) model is first used to simulate the effects of asynchronous wave passage and alignment curvature under three-dimensional (3D) seismic scenarios. The results reveal that asynchronous excitation induces wave-like differential displacements and non-planar forces, particularly intensified at tunnel–cavern interfaces due to stiffness contrasts. These global actions are then applied as dynamic boundary conditions in high-fidelity 3D non-linear finite-element analyses (FEA) of a critical tunnel section. The 3D FEA captures detailed local responses within the reinforced concrete lining, revealing that conventional two-dimensional plane-strain models underestimate hoop forces and overlook alignment-induced amplifications of seismic actions. The results demonstrate the necessity of accounting for alignment effects in seismic tunnel design and demonstrate the effectiveness of the proposed BNWF–FEA hybrid methodology.

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