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.

This is part II of our paper in which we propose and develop a dynamically bi-orthogonal method (DyBO) to study a class of time-dependent stochastic partial differential equations (SPDEs) whose solutions enjoy a low-dimensional structure. In part I of our paper [9], we derived the DyBO formulation and proposed numerical algorithms based on this formulation. Some important theoretical results regarding consistency and bi-orthogonality preservation were also established in the first part along with a range of numerical examples to illustrate the effectiveness of the DyBO method. In this paper, we focus on the computational complexity analysis and develop an effective adaptivity strategy to add or remove modes dynamically. Our complexity analysis shows that the ratio of computational complexities between the DyBO method and a generalized polynomial chaos method (gPC) is roughly of order O ((m/N p) 3) for a

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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.

In this paper, we focus on error estimates to smooth solutions of semi-discrete discontinuous Galerkin (DG) methods with quadrature rules for scalar conservation laws. The main techniques we use are energy estimate and Taylor expansion first introduced by Zhang and Shu. We show that, with ${P}^k$ (piecewise polynomials of degree $k$) finite elements in 1D problems, if the quadrature over elements is exact for polynomials of degree $(2k)$, error estimates of $O(h^{k+1/2})$ are obtained for general monotone fluxes, and optimal estimates of $O(h^{k+1})$ are obtained for upwind fluxes. For multidimensional problems, if in addition quadrature over edges is exact for polynomials of degree $(2k+1)$, error estimates of $O(h^k)$ are obtained for general monotone fluxes, and $O(h^{k+1/2})$ are obtained for monotone and sufficiently smooth numerical fluxes. Numerical results validate our analysis.