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.

Most biochemical processes involve macromolecules in solution. The corresponding electrostatics is of central importance for understanding their structures and functions. An accurate and efficient numerical scheme is introduced to evaluate the corresponding electrostatic potential and force by solving the governing Poisson-Boltzmann equation. This paper focuses on the following issues: (i) the point charge singularity problem, (ii) the dielectric discontinuity problem across a molecular surface, and (iii) the infinite domain problem. Green's function associated with the point charges plus a harmonic function is introduced as the zeroth order approximation to the solution to solve the point charge singularity problem. A jump condition capturing finite difference scheme is adopted to solve the discontinuity problem across molecule surfaces, where a body-fitting grid is used. The infinite domain problem is solved by mapping the outer infinite domain into a finite domain. The corresponding stiffness matrix is symmetric and positive definite, therefore, fast algorithm such as preconditioned conjugate gradient method can be applied for inner iteration. Finally, the resulting scheme is second order accurate for both the potential and its gradient.

In this paper, we propose a novel and simple technique to construct effective difference schemes for solving systems of singularly perturbed convection-diffusionreaction equations, whose solutions may display boundary or interior layers. We illustrate the technique by taking the Il’in-Allen-Southwell scheme for 1-D scalar equations as a basis to derive a formally second-order scheme for 1-D coupled systems and then extend the scheme to 2-D case by employing an alternating direction approach. Numerical examples are given to demonstrate the high performance of the obtained scheme on uniform meshes as well as piecewise-uniform Shishkin meshes.

A new class of high order weighted essentially non-oscillatory (WENO) schemes [J. Comput. Phys., 318 (2016), 110-121] is applied to solve Euler equations with steady state solutions. It is known that the classical WENO schemes [J. Comput. Phys., 126 (1996), 202-228] might suffer from slight post-shock oscillations. Even though such post-shock oscillations are small enough in magnitude and do not visually affect the essentially non-oscillatory property, they are truly responsible for the residue to hang at a truncation error level instead of converging to machine zero. With the application of this new class of WENO schemes, such slight post-shock oscillations are essentially removed and the residue can settle down to machine zero in steady state simulations. This new class of WENO schemes uses a convex combination of a quartic polynomial with two linear polynomials on unequal size spatial stencils in one dimension and is extended to two dimensions in a dimension-by-dimension fashion. By doing so, such WENO schemes use the same information as the classical WENO schemes in [J. Comput. Phys., 126 (1996), 202-228] and yield the same formal order of accuracy in smooth regions, yet they could converge to steady state solutions with very tiny residue close to machine zero for our extensive list of test problems including shocks, contact discontinuities, rarefaction waves or their interactions, and with these complex waves passing through the boundaries of the computational domain.

To avoid the order reduction when third order implicit-explicit Runge-Kutta time discretization is used together with the local discontinuous Galerkin (LDG) spatial discretization, for solving convection-diffusion problems with time-dependent Dirichlet boundary conditions, we propose a strategy of boundary treatment at each intermediate stage in this paper. The proposed strategy can achieve optimal order of accuracy by numerical verification. Also by suitably setting numerical flux on the boundary in the LDG methods, and by establishing an important relationship between the gradient and interface jump of the numerical solution with the independent numerical solution of the gradient and the given boundary conditions, we build up the unconditional stability of the corresponding scheme, in the sense that the time step is only required to be upper bounded by a suitable positive constant, which is independent of the mesh size.