Reflection of electromagnetic waves from a periodic grating can be described in terms of a discrete coupled multichannel scattering problem. By modeling the grating as a space- and frequency-dependent dielectric, it is possible to use a variable phase method, applied to a generalized Helmholtz equation incorporating both transverse and longitudinal modes, to efficiently compute the scattering -matrix. The projection onto transverse modes of this result, evaluated for imaginary wave vector, provides the information necessary for a Casimir energy calculation. This approach is of particular interest for gratings with deep corrugations, which can limit the applicability of techniques based on the Rayleigh expansion. We demonstrate the method by calculating the Casimir interaction energy between sinusoidal grating profiles as a function of separation and lateral displacement.

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