Genomic sequence databases, like GenBank, EMBL, are widely used by molecular biologists for homology searching. Because of the long length of each genomic sequence and the increase of the size of genomic sequence databases, the importance of efficient searching methods for fast queries grows. The DNA sequences are composed of four kinds of nucleotides, and these genomic sequences can be regarded as the text strings. However, there is no concept of words in a genomic sequence, which makes the search of the genomic sequence in the genomic database much difficult. Approximate String Matching (ASM) with k errors is considered for genomic sequences, where k errors would be caused by insertion, deletion, and replacement operations. Filtration of the DNA sequence is a widely adopted technique to reduce the number of the text areas (i.e., candidates) for further verification. In most of the filter methods, they first split the database sequence into q-grams. A sequence of grams (subpatterns) which match some part of the text will be passed as a candidate. The match problem of grams with the part of the text could be speed up by using the index structure for the exact match. Candidates will then be examined by dynamic programming to get the final result. However, in the previous methods for ASM, most of them considered the local order within each gram. Only the (k + s) h-samples filter considers the global order of the sequence of matched grams. Although the (k + s) h-samples filter keeps the global order of the sequence of the grams, it still has some disadvantages. First, to be a candidate in the (k + s) h-samples filter, the number of the ordered matched grams, s, is always fixed to 2 which results in low precision. Second, the (k + s) h-samples filter uses the query time to build the index for query patterns. In this thesis, we propose a new approximate string matching method, the hash trie filter, for efficiently searching in genomic databases. We build a hash trie in the pre-computing time for the genomic sequence stored in database. Although the size q of each split grams is also decided by the same formula used in the (k + s) h-samples filter, we have proposed a different way to find the ordered subpatterns in text T. Moreover, we reduce the number of candidates by pruning some unreasonable matched positions. Furthermore, unlike the (k + s) h-samples filter which always uses s = 2 to decide whether s matched subpatterns could be a candidate or not, our method will dynamically decide s, resulting in the increase of precision. The simulation results show that our hash trie filter outperforms the (k +s) h-samples filter in terms of the response time, the number of verified candidates, and the precision under different length of the query patterns and different error levels.

This paper studies minimally-supported D-optimal designs for polynomial regression model with logarithmically concave (log-concave) weight functions. Many commonly used weight functions in the design literature are log-concave. We show that the determinant of information matrix of minimally-supported design is a log-concave function of ordered support points and the D-optimal design is unique. Therefore, the numerically D-optimal designs can be determined e¡Óciently by standard constrained concave programming algorithms.

Contemporary approach performance based engineering generally relies on the approximate procedures that are based on the use of capacity curve derived from pushover analysis. The most important parameter in the displacement-based approach is the inelastic displacement demand computed under a given seismic effect and the most common procedures employed for this estimation / the Capacity Spectrum Method and the Displacement Coefficient Method are based on bi-linearization of the capacity curve. Although there are some recommendations for this approximation, there is a vital need for rational guidelines towards the selection of the most appropriate method among several alternatives. A comprehensive research has been undertaken to evaluate the influence of several existing alternatives used for approximating the capacity curve on seismic demands. A number of frames were analyzed under a set of 100 ground motions employing OpenSees. In addition, the pushover curves obtained from nonlinear static analyses were approximated using several alternatives and the resulting curves were assigned as the force-deformation relationships of corresponding equivalent single-degree-of-freedom systems. These simplified systems were later analyzed to compute the approximate seismic response parameters. Using the results of the complex and simplified analyses, the performance of each approximation method was evaluated in estimating the &amp / #8216 / exact&amp / #8217 / inelastic deformations of the multi-degree-of-freedom systems at various degrees of inelasticity. Dependency of the errors on ductility, strength reduction factor and period was also investigated. The interpretations made and the conclusions drawn in this study is believed to clarify the rationality and accuracy of selecting the appropriate idealization of the capacity curve.

In recent years, artificial neural networks (ANNs) have been employed for estimation and prediction purposes in many areas of civil/structural engineering. In this thesis, multilayered feedforward backpropagation algorithm is used for the approximate analysis and calibration of RC T-beam bridges and modeling of bridge ratings of these bridges. Currently bridges are analyzed using a standard FEM program. However, when a large population of bridges is concerned, such as the one considered in this project (Pennsylvania T-beam bridge population), it is impractical to carry out FEM analysis of all bridges in the population due to the fact that development and analysis of every single bridge requires considerable time as well as effort. Rapid and acceptably approximate analysis of bridges seems to be possible using ANN approach. First part of the study describes the application of neural network (NN) systems in developing the relationships between bridge parameters and bridge responses. The NN models are trained using some training data that are obtainedfrom finite-element analyses and that contain bridge parameters as inputs and critical responses as outputs. In the second part, ANN systems are used for the calibration of the finite element model of a typical RC T-beam bridge -the Manoa Road Bridge from the Pennsylvania&rsquo / s T-beam bridge population - based on field test data. Manual calibration of these models are extremely time consuming and laborious. Therefore, a neural network- based method is developed for easy and practical calibration of these models. The ANN model is trained using some training data that are obtained from finite-element analyses and that contain modal and displacement parameters as inputs and structural parameters as outputs. After the training is completed, fieldmeasured data set is fed into the trained ANN model. Then, FE model is updated with the predicted structural parameters from the ANN model. In the final part, Neural Networks (NNs) are used to model the bridge ratings of RC T-beam bridges based on bridge parameters. Bridge load ratings are calculated more accurately by taking into account the actual geometry and detailing of the T-beam bridges. Then, ANN solution is developed to easily compute bridge load ratings.

This paper discusses the approximate and the exact n-point D-optimal design problems for the common multivariate linear and quadratic polynomial regression on some convex design spaces. For the linear polynomial regression, the design space considered are q-simplex, q-ball and convex hull of a set of finite points. It is shown that the approximate and the exact n-point D-optimal designs are concentrated on the extreme points of the design space. The structure of the optimal designs on regular polygons or regular polyhedra is also discussed. For the quadratic polynomial regression, the design space considered is a q-ball. The configuration of the approximate and the exact n-point D-optimal designs for quadratic model in two variables on a disk are investigated.

In this paper, we establish several strong convergence results of general approximate proximal algorithm and general Bregman-function-based approximate proximal algorithm for solving the generalized variational inequality problem with pseudomonotone multifunction.

The average cost of operating a queueing network depends on several factors such as the complexity of the network and the service policy used. Approximate linear programming (ALP) is a method that can be used to compute an accurate lower bound on the optimal average cost as well as generate policies to be used in operating the network. These average cost solutions and policies are dependent on the type of basis function used in the ALP. In this paper, the ALP average cost solutions and policies are analyzed for twelve networks with four different types of basis functions (quadratic, linear, pure exponential, and mixed exponential). An approximate bound on the optimality gap between the ALP average cost solution and the optimal average cost solution is computed for each system, and the size of this bound is determined relative to the ALP average cost solution. Using the same set of networks, the performance of ALP generated policies are compared to the performance of the heuristic policies first-buffer-first-served (FBFS), last-buffer-first-served (LBFS), highest-queue-first-served (HQFS), and random-queue-first-served (RQFS). In general, ALP generated average cost solutions are considerably smaller than the simulated average cost under the corresponding policy, and therefore the approximate bounds on the optimality gaps are quite large. This bound increases with the complexity of the queueing network. Some ALP generated policies are not stabilizing policies for their corresponding networks, especially those produced using pure exponential and mixed exponential basis functions. For almost all systems, at least one of the heuristic policies results in mean average cost less than or nearly equal to the smallest mean average cost of all ALP generated policies in simulation runs. This means that generally there exists a heuristic policy which can perform as well as or better than any ALP generated policy. In conclusion, a useful bound on the optimality gap between the ALP average cost solution and the optimal average cost solution cannot be computed with this method. Further, heuristic policies, which are more computationally tractable than ALP generated policies, can generally match or exceed the performance of ALP generated policies, and thus computing such policies is often unnecessary for realizing cost benefits in queueing networks. / text

Epidemiological models traditionally make the assumption that populations are homogeneous. By relaxing that assumption, models often become more complicated, but better representations of the real world. Here we describe new computational tools for studying heterogeneous populations, and we examine consequences of two particular types of heterogeneity: that people are not all equally likely to interact, and that people are not all equally likely to become infected if exposed to a pathogen. Contact network epidemiology provides a robust and flexible paradigm for thinking about heterogeneous populations. Despite extensive mathematical and algorithmic methods, however, we lack a programming framework for working with epidemiological contact networks and for the simulation of disease transmission through such networks. We present EpiFire, a C++ applications programming interface and graphical user interface, which includes a fast and efficient library for generating, analyzing and manipulating networks. EpiFire also provides a variety of traditional and network-based epidemic simulations. Heterogeneous population structure may cause multi-wave epidemics, but urban populations are generally assumed to be too well mixed to have such structure. Multi-wave epidemics are not predicted by simple models, and are particularly problematic for public health officials deploying limited resources. Using a unique empirical interaction network for 103,000 people in Montreal, Canada, we show that large, urban populations may feature sufficient community structure to drive multi-wave dynamics, and that highly connected individuals may play an important role in whether communities are synchronized. Finally, we show that heterogeneous immunity is an important determinant of influenza epidemic size. While many epidemic models assume a homogeneously susceptible population and describe dynamics for one season, the trans-seasonal dynamics of partially immunizing diseases likely play a critical role in determining both future epidemic size and pathogen evolution. We present a multi-season network model of a population exposed to a pathogen conferring partial cross-immunity that decays over time. We fit the model to 25 years of influenza-like illness epidemic data from France using a novel Bayesian technique. Using conservative priors, we estimate important epidemiological quantities that are consistent with empirical studies. / text

At the core of evolutionary biology stands the study of divergence between populations and the formation of new species. This dissertation applies a diverse array of theoretical and statistical approaches to study how chromosomes evolve. In the first chapter, I build models that predict the amount of neutral genetic variation in chromosomal inversions involved in local adaptation, providing a foundation for future studies on the role of these rearrangements in population divergence. In the second chapter, I use a large dataset of the geographic variation in frequency of a chromosomal inversion to infer natural selection and non-random mating, revealing that this inversion could be implicated in strong reproductive isolation between subpopulations of a single species. In the third chapter, I use coalescent models for recombining sex chromosomes coupled with approximate Bayesian computation to estimate the recombination rate between X and Y chromosomes in European tree frogs. This novel approach allows me to infer a rate so low that would have been hard to detect with empirical methods. In the fourth chapter, I study the theoretical conditions that favor the evolution of a chromosome fusion that reduces recombination between locally adapted alleles. / text

In this thesis, a capacitor semi-active hybrid energy storage system for electric vehicle is proposed. A DC-to-DC bi-directional converter is required to couple the supercapacitor to the system DC bus. Through literature reviews, it was decided that a dual-bridge resonant converter with HF transformer isolation is best suited for the hybrid energy storage application. First, a dual-bridge series resonant converter with capacitive output filter is proposed. Modified gating scheme is applied to the converter instead of the 50% duty cycle gating scheme. Comparing to the 50% duty cycle gating scheme where only four switches work in ZVS, The modified gating scheme allows all eight switches working in ZVS at design point with high load level, and seven switches working in ZVS under other conditions. Next, a dual-bridge LCL-type series resonant converter with capacitive output filter is proposed. Similarly, the modified gating scheme is applied to the converter. This converter shows further improvement in ZVS ability. Operating principles, design examples, simulation results and experimental results of the two newly proposed converters are also presented. In the last part of the thesis, a capacitor semi-active hybrid energy storage system is built to test if the proposed converters are compatible to the system. The dual-bridge LCL-type series resonant converter is placed in parallel to the supercapacitor. The simulation and experimental results of the hybrid energy storage system match closely to the theoretical waveforms. / Graduate