In this paper, we propose and analyze a novel stabilized finite element method (FEM) for the system of generalized Stokes equations arising from the time-discretization of transient Stokes problem. The system involves a small viscosity, which is proportional to the inverse of large Reynolds number, and a large reaction coefficient, which is the inverse of small time step. The proposed stabilized FEM employs the $C^0$ piecewise linear elements for both velocity field and pressure on the same mesh and uses the residuals of the momentum equation and the divergence-free equation to define the stabilization terms. The stabilization parameters are fixed and element-independent, without a comparison of the viscosity, the reaction coefficient and the mesh size. Using the finite element solution of an auxiliary boundary value problem as the interpolating function for velocity and the $H^1$-seminorm projection for pressure, instead of the usual nodal interpolants, we derive error estimates for the stabilized finite element approximations to velocity and pressure in the $L^2$ and $H^1$ norms and most importantly, we explicitly establish the dependence of error bounds on the viscosity, the reaction coefficient and the mesh size. Our analysis reveals that this stabilized FEM is particularly suitable for the generalized Stokes system with a small viscosity and a large reaction coefficient, which has never been achieved before in the error analysis of other stabilization methods in the literature. We then numerically confirm the effectiveness of the proposed stabilized FEM. Comparisons made with other existing stabilization methods show that the newly proposed method can attain better accuracy and stability.

A spectral collocation scheme for the three-dimensional incompressible \(({\varvec{u}},p)\) formulation of the Navier鈥揝tokes equations, in domains \(\varOmega \) with a non-periodic boundary condition, is described. The key feature is the high order approximation, by means of a local Hermite interpolant, of a Neumann boundary condition for use in the numerical solution of the pressure Poisson system. The time updates of the velocity \({\varvec{u}}\) and pressure \(p\) are decoupled as a result of treating the pressure gradient in the momentum equation explicitly in time. The pressure update is computed from a pressure Poisson equation. Extension of the overall methodology to the Boussinesq system is also described. The uncoupling of the pressure and velocity time updates results in a highly efficient scheme that is simple to implement and well suited for simulating moderate to high Reynolds and Rayleigh number flows. Accuracy checks are presented, along with simulations of the lid-driven cavity flow and a differentially heated cavity flow, to demonstrate the scheme produces accurate three-dimensional results at a reasonable computational cost.

Gibbs phenomenon is the particular manner how a global spectral approximation of a piecewise analytic function behaves at the jump discontinuity. The truncated spectral series has large oscillations near the jump, and the overshoot does not decay as the number of terms in the truncated series increases. There is therefore no convergence in the maximum norm, and convergence in smooth regions away from the discontinuity is also slow. In earlier work, a methodology is proposed to completely overcome this difficulty in the context of spectral collocation methods, resulting in the recovery of exponential accuracy from collocation point values of a piecewise analytic function. In this paper, we extend this methodology to handle spectral collocation methods for functions which are analytic in the open interval but have singularities at end-points. With this extension, we are able to obtain exponential accuracy from collocation point values of such functions. Similar to earlier work, the proof is constructive and uses the Gegenbauer polynomials $C^\lambda_n(x)$. The result implies that the Gibbs phenomenon can be overcome for smooth functions with endpoint singularities.

This is an extension of our earlier work \cite{DS} in which a high order stable method was constructed for solving hyperbolic conservation laws on arbitrarily distributed point clouds. %The initial condition is given on such a point cloud, %and the algorithm solves for point values of the solution at %later time also on this point cloud. An algorithm of building a suitable polygonal mesh based on the random points was given and the traditional discontinuous Galerkin (DG) method was adopted on the constructed polygonal mesh. Numerical results in \cite{DS} show that the current scheme will generate spurious numerical oscillations when dealing with solutions containing strong shocks. In this paper, we adapt a simple weighted essentially non-oscillatory (WENO) limiter, originally designed for DG schemes on two-dimensional unstructured triangular meshes \cite{ZZSQ}, to our high order method on polygonal meshes. The objective of this simple WENO limiter is to simultaneously maintain uniform high order accuracy of the original method in smooth regions and control spurious numerical oscillations near discontinuities. The WENO limiter we adopt is particularly simple to implement and will not harm the conservativeness and compactness of the original method. Moreover, we also extend the maximum-principle-satisfying limiter for the scalar case and the positivity-preserving limiter for the Euler system to our method. Numerical results for both scalar equations and Euler systems of compressible gas dynamics are provided to illustrate the good behavior of these limiters.

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.