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 explore a unified way to construct smoothing functions for solving the absolute value equation associated with second-order cone (SOCAVE). Numerical comparisons are presented, which illustrate what kinds of smoothing functions work well along with the smoothing Newton algorithm. In particular, the numerical experiments show that the well known loss function widely used in engineering community is the worst one among the constructed smoothing functions, which indicates that the other proposed smoothing functions can be employed for solving engineering problems.

In this paper we generalize a new type of compact Hermite weighted essentially non-oscillatory (HWENO) limiter for the Runge-Kutta discontinuous Galerkin (RKDG) method, which was recently developed for structured meshes, to two dimensional unstructured meshes. The main idea of this HWENO limiter is to reconstruct the new polynomial by the usage of the entire polynomials of the DG solution from the target cell and its neighboring cells in a least squares fashion while maintaining the conservative property, then use the classical WENO methodology to form a convex combination of these reconstructed polynomials based on the smoothness indicators and associated nonlinear weights. The main advantage of this new HWENO limiter is the robustness for very strong shocks and simplicity in implementation especially for the unstructured meshes considered in this paper, since only information from the target cell and its immediate neighbors is needed. Numerical results for both scalar and system equations are provided to test and verify the good performance of this new limiter.

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In this paper, an arbitrary Lagrangian–Eulerian local discontinuous Galerkin (ALE-LDG) method for Hamilton–Jacobi equations will be developed, analyzed and numerically tested. This method is based on the time-dependent approximation space defined on the moving mesh. A priori error estimates will be stated with respect to the L∞ 􏰒(0, T ; L2)norm. In particular, the optimal (k + 1) convergence in one dimension and the suboptimal (k + 1 ) convergence in two dimensions will be proven for the semi-discrete method, when a local Lax–Friedrichs flux and piecewise polynomials of degree k on the reference cell are used. Furthermore, the validity of the geometric conservation law will be proven for the fully-discrete method. Also, the link between the piecewise constant ALE-LDG method and the monotone scheme, which converges to the unique viscosity solution, will be shown. The capability of the method will be demonstrated by a variety of one and two dimensional numerical examples with convex and noneconvex Hamiltonian.