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Full spectrum of a large sparse $\top$-palindromic quadratic eigenvalue problem ($\top$-PQEP) is considered arguably for the first time in this article. Such a problem is posed by calculation of surface Green's functions (SGFs) of mesoscopic transistors with a tremendous non-periodic cross-section. For this problem, general purpose eigensolvers are not efficient, nor is advisable to resort to the decimation method \etc to obtain the Wiener-Hopf factorization. After reviewing some rigorous understanding of SGF calculation from the perspective of $\top$-PQEP and nonlinear matrix equation, we present our new approach to this problem. In a nutshell, the unit disk where the spectrum of interest lies is broken down adaptively into pieces small enough that they each can be locally tackled by the generalized $\top$-skew-Hamiltonian implicitly restarted shift-and-invert Arnoldi (G$\top$SHIRA) algorithm with suitable shifts and other parameters, and the eigenvalues missed by this divide-and-conquer strategy can be recovered thanks to the accurate estimation provided by our newly developed scheme. Notably the novel non-equivalence deflation is proposed to avoid as much as possible duplication of nearby known eigenvalues when a new shift of G$\top$SHIRA is determined. We demonstrate our new approach by calculating the SGF of a realistic nanowire whose unit cell is described by a matrix of size $4000\times 4000$ at the density functional tight binding level, corresponding to a $8\times 8\; \mbox{nm}^{2}$ cross-section. We believe that quantum transport simulation of realistic nano-devices in the mesoscopic regime will greatly benefit from this work.

This work is devoted to the numerical computation of complex band structure $\k=\k(\omega)\in\mathbb C^3$ for positive $\omega$ of three dimensional isotropic dispersive or non-dispersive photonic crystals from the perspective of structured quadratic eigenvalue problems (QEPs). Our basic strategy is to fix two degrees of freedom in $\k\in\mathbb C^3$ and to view the remaining one as the eigenvalue of a quadratic operator pencil derived from Maxwell's equations. Then Yee's scheme is employed to discretize $\nabla\times$ and $\k\times$ operators in this quadratic operator pencil. Distinct from the others' works which either ignore or directly exploit the Hamiltonian structure of the spectrum of the resulting QEP, we reformulate this QEP into an equivalent $\top$-palindromic QEP to facilitate the use of superior structure-preserving algorithms. Ultimately we rely on the structured Arnoldi algorithm, namely the G$\top$SHIRA algorithm, to compute eigenvalues of a $\top$-skew-Hamiltonian pair which are near or in $[-2,2]$, a much narrower region than the whole positive real axis in the origin problem. Moreover, to accelerate the inner iterations of the G$\top$SHIRA algorithm, we propose the preconditioning technique, making most of the eigenmatrix, which can essentially be seen as the Kronecker product of three discrete Fourier transformation matrices, of the commutative discretized $\partial_x,\partial_y,\partial_z$ operators. The advantage of our method is discussed in detail and corroborated by several numerical results.