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.

Two nonlinear diffusion equations for thin film epitaxy, with or without slope selection, are studied in this work. The nonlinearity models the Ehrlich–Schwoebel effect – the kinetic asymmetry in attachment and detachment of adatoms to and from terrace boundaries. Both perturbation analysis and numerical simulation are presented to show that such an atomistic effect is the origin of a nonlinear morphological instability, in a rough-smooth-rough pattern, that has been experimentally observed as transient in an early stage of epitaxial growth on rough surfaces. Initial-boundary-value problems for both equations are proven to be well-posed, and the solution regularity is also obtained. Galerkin spectral approximations are studied to provide both a priori bounds for proving the well-posedness and numerical schemes for simulation. Numerical results are presented to confirm part of the analysis and to explore the difference between the two models on coarsening dynamics.

We present a new formulaiton of the incompressible Navier-Stokes equation in terms of an auxiliary field that differs from the velocity by a gauge transformation. The gauge freedom allows us to assign simple and specific boundary conditions for both the auxiliary field and the gauge field, thus eliminating the issue of pressure boundary condition in the usual primitive variable formulation. The resulting dynamic and kinematic equations can then be solved by standard methods for heat and Poisson equations. A normal mode analysis suggests that in contrast to the classical projection method, the gauge method does not suffer from the problem of numerical boundary layers. Thus the subtleties on the spatial discretization for the projection methods are removed. Consequently, the projection step in the gauge method can be accomplished by standard Poissin solves. We demonstrate the efficiency and accuracy of the gauge method by several numerical examples, including the flow past cylinder.

In this paper we study the effects of small viscosity term and the far-field boundary conditions for systems of convection-diffusion equations in the zero viscosity limit. The far-field boundary conditions are classified and the corresponding solution structures are analyzed. It is confirmed that the Neumann type of far-field boundary condition is preferred. On the other hand, we also identify a class of improperly coupled boundary conditions which lead to catastrophic reflection waves dominating the inlet in the zero viscosity limit. The analysis is performed on the linearized convection-diffusion model which well describes the behavior at the far field for many physical and engineering systems such as fluid dynamical equations and electro-magnetic equations. The results obtained here should provide some theoretical guidance for designing effective far field boundary conditions.

In this paper, we give a systematic study of the boundary layer behavior for linear convection-diffusion equation in the zero viscosity limit. We analyze the boundary layer structures in the viscous solution and derive the boundary condition satisfied by the viscosity limit as a solution of the inviscid equation. The results confirm that the Neumann type of far-field boundary condition is preferred in the outlet and characteristic boundary condition. Under some appropriate regularity and compatibility conditions on the initial and boundary data, we obtain optimal error estimates between the full viscous solution and the inviscid solution with suitable boundary layer corrections. These results hold in arbitrary space dimensions and similar statements also hold for the strip problem. This model well describes the behavior at the far-field for many physical and engineering systems such as fluid dynamical equation and electro-magnetic equation. The results obtained here should provide some theoretical guidance for designing effective far-field boundary conditions.