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.

In this paper, we consider a class of optimization problems of minimizing a (at least) twice continuously dierentiable function (probably nonconvex) f(x) : Rn ! R over a product of multiple balls/spheres constraints. Upon rescaling the balls/spheres, we cast without loss of generality such class of minimization problems in the following form: (BCOP) 8>< >: min x2Rn f(x) s:t: ci(x) := kx[i]k2 􀀀 1 = 0; i 2 E; ci(x) := kx[i]k2 􀀀 1  0; i 2 I; where E = f1; 2; : : : ;m1g, I = fm1 + 1;m1 + 2; : : : ;mg, x[i] 2 Rpi , x = (xT [1]; xT [2]; : : : ; xT [m])T , n = Pm i=1 pi, and k
k stands for the `2 vector norm. Here, we introduce the notation x[i] 2 Rpi to represent the ith subvector of x 2 Rn and formulate the product of multiple ball/sphere constraints as a set of equality and inequality constraints. To simplify subsequent presentation, we call the above programming the ball/sphere constrained optimization problem (BCOP). We emphasize that this problem does not allow overlap among the variables x[i] and therefore the constraints are separable. However, these variables x[i] may be linked together through the objective function f(x).

Nonlinear matrix equations are encountered in many applications of control and engineering problems. In this work, we establish a complete study for a class of nonlinear matrix equations. With the aid of Sherman Morrison Woodbury formula, we have shown that any equation in this class has the maximal positive definite solution under a certain condition. Furthermore, A thorough study of properties about this class of matrix equations is provided. An acceleration of iterative method with R-superlinear convergence with order $r>1$ is then designed to solve the maximal positive definite solution efficiently.

In this paper, we investigate the superconvergence property of the local discontinuous Galerkin (LDG) methods for solving one-dimensional linear time dependent fourth order problems. We prove that the error between the LDG solution and a particular projection of the exact solution, $\bar{e}_u$, achieves $(k+\frac32)$-th order superconvergence when polynomials of degree $k$ ($k\ge 1$) are used. Numerical experiments of $P^k$ polynomials, with $1\le k \le3$, are displayed to demonstrate the theoretical results, which show that the error $\bar{e}_u$ actually achieves $(k+2)$-th order superconvergence, indicating that the error bound for $\bar{e}_u$ obtained in this paper is sub-optimal. Initial-boundary value problems, nonlinear equations and solutions having singularities are numerically investigated to verify that the conclusions hold true for very general cases.

No abstract uploaded!