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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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In this paper, we study the classical Allen-Cahn equations and investigate the maximum-principle-preserving (MPP) techniques. The Allen-Cahn equation has been widely used in mathematical models for problems in materials science and fluid dynamics. It enjoys the energy stability and the maximum-principle. Moreover, it is well known that the Allen-Cahn equation may yield thin interface layer, and nonuniform meshes might be useful in the numerical solutions. Therefore, we apply the local discontinuous Galerkin (LDG) method due to its flexibility on h-p adaptivity and complex geometry. However, the MPP LDG methods require slope limiters, then the energy stability may not be easy to obtain. In this paper, we only discuss the MPP technique and use numerical experiments to demonstrate the energy decay property. Moreover, due to the stiff source given in the equation, we use the conservative modified exponential Runge-Kutta methods and thus can use relatively large time step sizes. Thanks to the conservative time integration, the bounds of the unknown function will not decay. Numerical experiments will be given to demonstrate the good performance of the MPP LDG scheme.

In this paper, an analysis of the superconvergence property of the semidiscrete discontinuous Galerkin (DG) method applied to one-dimensional time-dependent nonlinear scalar conservation laws is carried out. We prove that the error between the DG solution and a particular projection of the exact solution achieves $\left(k + \frac32\right)$-th order superconvergence when upwind fluxes are used. The results hold true for arbitrary nonuniform regular meshes and for piecewise polynomials of degree $k$ ($k \ge 1$), under the condition that $|f'(u)|$ possesses a uniform positive lower bound. Numerical experiments are provided to show that the superconvergence property actually holds true for nonlinear conservation laws with general flux functions, indicating that the restriction on $f(u)$ is artificial.