Numerical and Geometric Optimizations for Surface and Tolerance Modeling

Optimization techniques are widely used in many research and engineering areas. This dissertation presents numerical and geometric optimization methods for solving geometric and solid modeling problems. Geometric optimization methods are designed for manufacturing process planning, which optimizes the process by changing dependency relationships among geometric primitives from the original design diagram. Geometric primitives are used to represent part features, and dependencies in the dimensions between parts are represented by a topological graph. The ordering of these dependencies can have a significant effect on the tolerance zones in the part. To obtain tolerance zones from the dependencies, the conventional parametric method of tolerance analysis is de-composed into a set of geometric computations, which are combined and cascaded to obtain the tolerance zones in the geometric representations. Geometric optimization is applied to the topological graph in order to find a solution that provides not only an optimal dimensioning scheme but also an optimal plan for manufacturing the physical part. The applications of our method include tolerance analysis, dimension scheme optimization, and process planning. Two numerical optimization methods are proposed for local and global surface parameterizations. One is the nonlinear optimization, which is used for building the local field-aware parameterization. Given a local chart of the surface, a two-phase method is proposed, which generates a folding-free parameterization while still being aware of the geodesic metric. The parameterization method is applied in a view-dependent 3D painting system, which constitutes a local, adaptive and interactive painting environment. The other is the mixed-integer quadratic optimization, which is used for generating a quad mesh from a given triangular mesh. With a given cross field, the computation of parametric coordinates is formulated to be a mixed-integer optimization problem, which parameterizes the surface with good quality by adding redundant integer variables. The mixed integer system is solved more efficiently by an improved adaptive rounding solver. To obtain the final quadrangular mesh, an isoline tracing method and a breadth-first traversal mesh generation method are proposed so that the final mesh result has face information, which is useful for further model processing

Hybrid phase-change Lattice Boltzmann simulation of vapor condensation on vertical subcooled walls

Saturated vapor condensation on homogenous and heterogeneous subcooled walls is presented in this study by adopting a hybrid phase-change multiple-relaxation-time Lattice Boltzmann model. The effects of wall wettability on the condensation process, including droplets’ growth, coalescence and falling, and the influence of vapor flow to condensation are investigated. The results demonstrate that the heat fluxes around the triple-phase contact lines are higher than that in other cold areas in homogeneous subcooled walls, which actually indicates the fact that filmwise condensation is preventing the continuous condensation process. Furthermore, the dropwise condensation can be formed more easily on the heterogeneous surface with a mixed surface wettability. At last, the dynamic process of condensation of continuous vapor flow is also investigated by considering the homogenous and heterogeneous subcooled surfaces. The results show that the heterogeneous surface with mixed wettability doesn’t contribute to the formation, growth of droplets, when compared to the homogeneous surface. It is expected that this study can bring more attentions to simulate condensation using multiphase LBM for complex geometries in heat transfer community

Identification of genes regulated by Wnt/β-catenin pathway and involved in apoptosis via microarray analysis

BACKGROUND: Wnt/β-catenin pathway has critical roles in development and oncogenesis. Although significant progress has been made in understanding the downstream signaling cascade of this pathway, little is known regarding Wnt/β-catenin pathway modification of the cellular apoptosis. METHODS: To identify potential genes regulated by Wnt/β-catenin pathway and involved in apoptosis, we used a stably integrated, inducible RNA interference (RNAi) vector to specific inhibit the expression and the transcriptional activity of β-catenin in HeLa cells. Meanwhile, we designed an oligonucleotide microarray covering 1384 apoptosis-related genes. Using oligonucleotide microarrays, a series of differential expression of genes was identified and further confirmed by RT-PCR. RESULTS: Stably integrated inducible RNAi vector could effectively suppress β-catenin expression and the transcriptional activity of β-catenin/TCF. Meanwhile, depletion of β-catenin in this manner made the cells more sensitive to apoptosis. 130 genes involved in some important cell-apoptotic pathways, such as PTEN-PI3K-AKT pathway, NF-κB pathway and p53 pathway, showed significant alteration in their expression level after the knockdown of β-catenin. CONCLUSION: Coupling RNAi knockdown with microarray and RT-PCR analyses proves to be a versatile strategy for identifying genes regulated by Wnt/β-catenin pathway and for a better understanding the role of this pathway in apoptosis. Some of the identified β-catenin/TCF directed or indirected target genes may represent excellent targets to limit tumor growth

The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Screening of Bioactive Ingredients in Ligusticum Chuanxiong Hort for Protection against Myocardial Ischemia

Background/Aims: To study the spectrum-effect relationship and effective components of Ligusticum Chuanxiong Hort. (LCH) on the protection of canine myocardial ischemia. Methods: Fingerprint spectrum of LCH extracts was developed using high performance liquid chromatography (HPLC), and a canine model of acute myocardial ischemia was established by ligating the coronary artery. Bivariate correlation analysis and multivariate regression analysis were used to correlate the pharmacodynamics of LCH extract and its common peaks in HPLC. Results: The bioactive components of LCH were ligustrazine, ferulic acid, cnidilide and ligustilide. Ligustrazine and ferulic acid could significantly reduce serum lactic acid in canine model of acute myocardial ischemia, while ligustilide could significantly reduce the elevation of serum free fatty acid. Conclusions: The spectrum-effect relationship study shows that the effective components of LCH are ligustrazine, ferulic acid, cnidilide and ligustilide, which have protective effect on myocardial ischemia