A new method of quality improvement for quadrilateral mesh based on small polygon reconnection

In this paper, a new method of topological cleanup for quadrilateral mesh is presented. The method first selects a patch of mesh around an irregular node. It then seeks the best connection of the selected patch according to its irregular valence using a new topological operation： small polygon reconnection （SPR）. By replacing the original patch with an optimal one that has less irregular valence, mesh quality can be improved. Three applications based on the proposed approach are enumerated： （1） improving the quality of a quadrilateral mesh, （2） converting a triangular mesh to a quadrilateral one, and （3） adapting a triangle generator to a quadrilateral one. The presented method is highly effective in all three applications.

Improving the Quality of Conforming Triangular Meshes by Topological Clean up and DSI

A new method as a post-processing step is presented to improve the shape quality of triangular meshes, which uses a topological clean up procedure and discrete smoothing interpolate (DSI) algorithm together. This method can improve the angle distribution of mesh element. while keeping the resulting meshes conform to the predefined constraints which are inputted as a PSLG.

Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation

We consider the design of an effective and reliable adaptive finite element method(AFEM)for the nonlinear Poisson-Boltzmann equation(PBE).We first examine the two-term regularization technique for the continuous problem recently proposed by Chen,Holst and Xu based on the removal of the singular electrostatic potential inside biomolecules;this technique made possible the development of the first complete solution and approximation theory for the Poisson-Boltzmann equation,the first provably convergent discretization and also allowed for the development of a provably convergent AFEM.However,in practical implementation,this two-term regularization exhibits numerical instability.Therefore,we examine a variation of this regularization technique which can be shown to be less susceptible to such instability.We establish a priori estimates and other basic results for the continuous regularized problem,as well as for Galerkin finite element approximations.We show that the new approach produces regularized continuous and discrete problemswith the samemathematical advantages of the original regularization.We then design an AFEM scheme for the new regularized problem and show that the resulting AFEM scheme is accurate and reliable,by proving a contraction result for the error.This result,which is one of the first results of this type for nonlinear elliptic problems,is based on using continuous and discrete a priori L¥estimates.To provide a high-quality geometric model as input to the AFEM algorithm,we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures,based on the intrinsic local structure tensor of the molecular surface.All of the algorithms described in the article are implemented in the Finite Element Toolkit(FETK),developed and maintained at UCSD.The stability advantages of the new regularization scheme are demonstrated with FETK through comparisons with the original regularization approach for a model problem.The convergence and accuracy of the overall AFEMalgorithmis also illustrated by numerical approximation of electrostatic solvation energy for an insulin protein.

Numerical simulations of 2-D floating body driven by regular waves

An improved meshing method based on Fluent is used to update the computational meshes in solving the Navier-Stokes （N-S） equations for viscous and incompressible free surface flows with the volume of fluid （VOF） method. To maintain the mesh quality when updating meshes for a moving structure, the computational domain is separated into several parts and each part corre- sponds to a specific type of body motion. The numerical results of the interaction between the floating body and the regular waves agree well with the experimental data. A total of eight typical motion types are simulated separately to understand the correlation between the motion types and the wave transmission as well as the forces acting on the floating body. Numerical experiments show that the wave transmission increases in the case of sway and heave motions and decreases in the case of pitch motion as compared with the stationary case. It is also found that the sway motion reduces the horizontal wave force acting on the floating body, while the heave motion enhances the vertical wave force.