We present a new Matched Interface and Boundary (MIB) regularization method for treating charge singularity in solvated biomolecules whose electrostatics are described by the Poisson–Boltzmann (PB) equation. In a regularization method, by decomposing the potential function into two or three components, the singular component can be analytically represented by the Green’s function, while other components possess a higher regularity. Our new regularization combines the efficiency of two-component schemes with the accuracy of the three-component schemes. Based on this regularization, a new MIB finite difference algorithm is developed for solving both linear and nonlinear PB equations, where the nonlinearity is handled by using the inexact-Newton’s method. Compared with the existing MIB PB solver based on a three-component regularization, the present algorithm is simpler to implement by circumventing the work to solve a boundary value Poisson equation inside the molecular interface and to compute related interface jump conditions numerically. Moreover, the new MIB algorithm becomes computationally less expensive, while maintains the same second order accuracy. This is numerically verified by calculating the electrostatic potential and solvation energy on the Kirkwood sphere on which the analytical solutions are available and on a series of proteins with various sizes.

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Homotopy continuation is an efficient tool for solving polynomial systems. Its efficiency relies on utilizing adaptive stepsize and adaptive precision path tracking, and endgames. In this article, we apply homotopy continuation to solve steady state problems of hyperbolic conservation laws. A third-order accurate finite difference weighted essentially non-oscillatory (WENO) scheme with Lax-Friedrichs flux splitting is utilized to derive the difference equation. This new approach is free of the CFL condition constraint. Extensive numerical examples in both scalar and system test problems in one and two dimensions demonstrate the efficiency and robustness of the new method.

In this paper, we adapt a simple weighted essentially non-oscillatory (WENO) limiter, originally designed for discontinuous Galerkin (DG) schemes, to the correction procedure via reconstruction (CPR) framework for solving conservation laws. The objective of this simple WENO limiter is to simultaneously maintain uniform high order accuracy of the CPR framework in smooth regions and control spurious numerical oscillations near discontinuities. The WENO limiter we adopt in this paper is particularly simple to implement and will not harm the conservativeness of the CPR framework. Also, it uses information only from the target cell and its immediate neighbors, thus can maintain the compactness of the CPR framework. Since the CPR framework with the WENO limiter does not in general preserve positivity of the solution, we also extend the positivity preserving limiters to the CPR framework. Numerical results in one and two dimensions are provided to illustrate the good behavior of this procedure.

We propose a simple fast spectral method for the Boltzmann collision operator with general collision kernels. In contrast to the direct spectral method [L. Pareschi and G. Russo, SIAM J. Numer. Anal., 37 (2000), pp. 1217–1245; I. M. Gamba and S. H. Tharkabhushanam, J. Comput. Phys., 228 (2009), pp. 2012–2036], which requires O(N6) memory to store precomputed weights and has O(N6) numerical complexity, the new method has complexity O(MN4 log N), where N is the number of discretization points in each of the three velocity dimensions and M is the total number of discretization points on the sphere and M ≪ N2. Furthermore, it requires no precomputation for the variable hard sphere model and only O(MN4) memory to store precomputed functions for more general collision kernels. Although a faster spectral method is available [C. Mouhot and L. Pareschi, Math. Comp., 75 (2006), pp. 1833–1852] (with complexity O(MN3 logN)), it works only for hard sphere molecules, thus limiting its use for practical problems. Our new method, on the other hand, can apply to arbitrary collision kernels. A series of numerical tests is performed to illustrate the efficiency and accuracy of the proposed method.