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.

In this paper, we introduce a new adaptive data analysis method to study trend and instantaneous frequency of nonlinear and nonstationary data. This method is inspired by the Empirical Mode Decomposition method (EMD) and the recently developed compressed (compressive) sensing theory. The main idea is to look for the sparsest representation of multiscale data within the largest possible dictionary consisting of intrinsic mode functions of the form {a(t) cos(θ(t))}, where a ∈ V (θ), V (θ) consists of the functions smoother than cos(θ(t)) and θ   0. This problem can be formulated as a nonlinear l0 optimization problem. In order to solve this optimization problem, we propose a nonlinear matching pursuit method by generalizing the classical matching pursuit for the l0 optimization problem. One important advantage of this nonlinear matching pursuit method is it can be implemented very efficiently and is very stable to noise. Further, we provide an error analysis of our nonlinear matching pursuit method under certain scale separation assumptions. Extensive numerical examples will be given to demonstrate the robustness of our method and comparison will be made with the state-of-the-art methods. We also apply our method to study data without scale separation, and data with incomplete or under-sampled data.

In this paper, we design and analyze third order positivity-preserving discontinuous Galerkin (DG) schemes for solving the time-dependent system of Poisson–Nernst–Planck (PNP) equations, which have found much use in diverse applications. Our DG method with Euler forward time discretization is shown to preserve the positivity of cell averages at all time steps. The positivity of numerical solutions is then restored by a scaling limiter in reference to positive weighted cell averages. The method is also shown to preserve steady states. Numerical examples are presented to demonstrate the third order accuracy and illustrate the positivity-preserving property in both one and two dimensions.

We propose a class of simple and efficient numerical scheme for incompressible fluid equations with coordinate symmetry. By introducing a generalized vorticity-stream formulation, the divergence free constraints are automatically satisfied. In addition, with explicit treatment of the nonlinear terms and local vorticity boundary condition, the Navier–Stokes (MHD, respectively) equation essentially decouples into 2 (4, respectively) scalar equation and thus the scheme is very efficient. Moreover, with proper discretization of the nonlinear terms, the scheme preserves both energy and helicity identities numerically. This is achieved by recasting the nonlinear terms (convection, vorticity stretching, geometric source, Lorentz force and electro-motive force) in terms of Jacobians. This conservative property is valid even in the presence of the pole singularity for axisymmetric flows. The exact conservation of energy and helicity has effectively eliminated excessive numerical viscosity. Numerical examples have demonstrated both accuracy and efficiency of the scheme. Finally, local mesh refinement near the boundary can also be easily incorporated into the scheme without extra cost.

The immersed boundary method has evolved into one of the most useful computational methods in studying fluid structure interaction. On the other hand, the immersed boundary method is also known to suffer from a severe timestep stability restriction when using an explicit time discretization. In this paper, we propose several efficient semi-implicit schemes to remove this stiffness from the immersed boundary method for the two-dimensional Stokes flow. First, we obtain a novel unconditionally stable semi-implicit discretization for the immersed boundary problem. Using this unconditionally stable discretization as a building block, we derive several efficient semi-implicit schemes for the immersed boundary problem by applying the small scale decomposition to this unconditionally stable discretization. Our stability analysis and extensive numerical experiments show that our semi-implicit schemes offer much better stability property than the explicit scheme. Unlike other implicit or semi-implicit schemes proposed in the literature, our semi-implicit schemes can be solved explicitly in the spectral space. Thus the computational cost of our semi-implicit schemes is comparable to that of an explicit scheme, but with a much better stability property.