Well-posedness and Robust Preconditioners for the Discretized Fluid-Structure Interaction Systems

In this paper we develop a family of preconditioners for the linear algebraic systems arising from the arbitrary Lagrangian-Eulerian discretization of some fluid-structure interaction models. After the time discretization, we formulate the fluid-structure interaction equations as saddle point problems and prove the uniform well-posedness. Then we discretize the space dimension by finite element methods and prove their uniform well-posedness by two different approaches under appropriate assumptions. The uniform well-posedness makes it possible to design robust preconditioners for the discretized fluid-structure interaction systems. Numerical examples are presented to show the robustness and efficiency of these preconditioners.Comment: 1. Added two preconditioners into the analysis and implementation 2. Rerun all the numerical tests 3. changed title, abstract and corrected lots of typos and inconsistencies 4. added reference

Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses

Although an exchange of genetic information by recombination plays an important role in the evolution of viruses, it is not clear how it generates diversity. {\it Geminiviruses} are plant viruses which have ambisense single-stranded circular DNA genomes and one of the most economically important plant viruses in agricultural production. Small circular single-stranded DNA satellites, termed DNA-$\beta$, have recently been found associated with some geminivirus infections. In this paper we analyze a satellite molecule DNA-$\beta$ of geminiviruses for recombination events using phylogenetic and statistical analysis and we find that one strain from ToLCMaB has a recombination pattern and is possibly recombinant molecule between two strains from two species, PaLCuB-[IN:Chi:05] (major parent) and ToLCB-[IN:CP:04] (minor parent).Comment: 8 figures and 2 tables. To appear in Frontiers in Systems Biolog

Gene specific co-regulation discovery: an improved approach

[Abstract]: Discovering gene co-regulatory relationships is a new but important research problem in DNA microarray data analysis. The problem of gene specific co-regulation discovery is to, for a particular gene of interest, called the target gene, identify its strongly co-regulated genes and the condition subsets where such strong gene co-regulations are observed. The study on this problem can contribute to a better understanding and characterization of the target gene. The existing method, using the genetic algorithm (GA), is slow due to its expensive fitness evaluation and long individual representation. In this paper, we propose an improved method for finding gene specific co-regulations. Compared with the current method, our method features a notably improved effciency. We employ kNN Search Table to substantially speed up fitness evaluation in the GA. We also propose a more compact representation scheme for encoding individuals in the GA, which contributes to faster crossover and mutation operations. Experimental results with a real-life gene mi-croarray data set demonstrate the improved effciency of our technique compared with the current method