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This paper presents for the first time the transient simulation of the 3-D mode converter with surface deformation. The simulation results were obtained by solving the Maxwell equations directly on a 3-D domain with a discontinuous Galerkin method. The presented full-wave simulation was possible only through the use of an advanced highly scalable numerical method operating on a large-scale high-performance computing system. Moreover, the properties of the Maxwell solver with respect to accuracy and computation time are discussed for the application to a smooth-wall waveguide where an analytical solution is available.