The immersed boundary method is one of the most useful computational methods in studying fluid structure interaction. On the other hand, the Immersed Boundary method is also known to require small time steps to maintain stability when solved with an explicit method. Many implicit or approximately implicit methods have been proposed in the literature to remove this severe time step stability constraint, but none of them give satisfactory performance. In this paper, we propose an efficient semi-implicit scheme to remove this stiffness from the immersed boundary method for the Navier–Stokes equations. The construction of our semi-implicit scheme consists of two steps. First, we obtain a semiimplicit discretization which is proved to be unconditionally stable. This unconditionally stable semi-implicit scheme is still quite expensive to implement in practice. Next, we apply the small scale decomposition to the unconditionally stable semi-implicit scheme to construct our efficient semi-implicit scheme. Unlike other implicit or semi-implicit schemes proposed in the literature, our semi-implicit scheme can be solved explicitly in the spectral space. Thus the computational cost of our semi-implicit schemes is comparable to that of an explicit scheme. Our extensive numerical experiments show that our semiimplicit scheme has much better stability property than an explicit scheme. This offers a substantial computational saving in using the immersed boundary method.

No abstract uploaded!

Comparing DNA and protein sequence groups plays an important role in biological evolutionary relationship research. Despite many methods available for sequence comparison, only a few can be used for group comparison. In this study, we propose a novel approach using convex hulls. We use statistical information contained within the sequences to represent each sequence as a point in high dimensional space. We find that the points belonging to one biological group are located in a different region of space than points belonging to other biological groups. To be more precise, the convex hull of the points from one group are disjoint from the convex hulls of points from other groups. This finding allows us to do phylogenetic analysis for groups in an efficient way. Five different theorems are presented for checking whether two convex hulls intersect or are disjoint. Test results for datasets related to HRV, HPV, Ebolavirus, PKC and protein phosphatase domains demonstrate that our method performs well and provides a new tool for studying group phylogeny. More significantly, the convex analysis presents a new way to search for sequences belonging to a biological group by examining points within the group’s convex hull.

No abstract uploaded!

We develop a theory to connect the following three areas: (a) the mean field equations on flat tori, (b) the classical Lame equations and (c) modular forms. A major theme in part I is a classification of developing maps f attached to solutions of the mean field equation according to the types of transformation laws (or monodromy) with respect to the period lattice satisfied by f.