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.

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.

The convergence of a fourth order finite difference method for the 2-D unsteady, viscous incompressible Boussinesq equations, based on the vorticity-stream function formulation, is established in this article. A compact fourth order scheme is used to discretize the momentum equation, and long-stencil fourth order operators are applied to discretize the temperature transport equation. A local vorticity boundary condition is used to enforce the no-slip boundary condition for the velocity. One-sided extrapolation is used near the boundary, dependent on the type of boundary condition for the temperature, to prescribe the temperature at ‘‘ghost’’ points lying outside of the computational domain. Theoretical results of the stability and accuracy of the method are also provided. In numerical experiments the method has been shown to be capable of producing highly resolved solutions at a reasonable computational cost.

Using the vorticity and stream function variables is an effective way to compute 2-D incompressible flow due to the facts that the incompressibility constraint for the velocity is automatically satisfied, the pressure variable is eliminated, and high order schemes can be efficiently implemented. However, a difficulty arises in a multi-connected computational domain in determining the constants for the stream function on the boundary of the “holes”. This is an especially challenging task for the calculation of unsteady flows, since these constants vary with time to reflect the total fluxes of the flow in each sub-channel. In this paper, we propose an efficient method in a finite difference setting to solve this problem and present some numerical experiments, including an accuracy check of a Taylor vortex-type flow, flow past a non-symmetric square, and flow in a heat exchanger.

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.