In this thesis, rapid transfer alignment algorithm for a helicopter launched guided munition is studied. Transfer alignment is the process of initialization of a guided munition&rsquo / s inertial navigation system with the aid of the carrier platform&rsquo / s navigation system, which is generally done by comparing the navigation data of missile and carrier&rsquo / s navigation data. In the literature, there are different studies of transfer alignment, especially for aircraft launched munitions. One important problem in transfer alignment is the attitude uncertainty of lever arm between munition&rsquo / s and carrier&rsquo / s navigation systems. In order to overcome this problem, most of the studies in the literature do not use carrier&rsquo / s attitude data in the transfer alignment, only velocity data is used. In order to estimate attitude and related inertial sensor errors, specific maneuvers of carrier platform are required which can take 1-5 minutes. The purpose of this thesis is to compensate the errors arising from the dynamics of the Helicopter, lever arm, mechanical vibration effects and inertial sensor error amplification, thus designing a transfer alignment algorithm under real environment conditions. The algorithm design begins with observability analysis, which is not done for helicopter transfer alignment in literature. In order to make proper compensations, characterization and modeling of vibration and lever arm environment is done for the helicopter. Also, vibration based errors of MEMS based inertial sensors are experimentally shown. The developed transfer alignment algorithm is tested by simulated and experimental data

The objective of this thesis is to develop high dielectric constant nanoparticle dispersion for switchable aircraft antenna systems. Two steps were designed to achieve the objective. First, obtain high dielectric, high aspect ratio nanoparticles and disperse them in dielectric oil medium. Second, manipulate the particle-oil dispersion using an external alternating current (AC) electric field to increase the effective dielectric constant. In order to obtain high dielectric dispersions, different sizes and shapes of titanium dioxide (TiO2) and barium titanate (BaTiO3) nanoparticles were purchased and measured. However, after a number of experiments detailed in the thesis, it was found that none of the commercially available nanoparticles could satisfy our requirements for a minimum effective dielectric constant. Thus, to achieve the goals above, we synthesized high aspect ratio BaTiO3 nanowires with BaC2O4 and TiO2 powders as precursors using a molten salt method. The as-synthesized BaTiO3 nanowires were characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), and energy dispersive spectroscopy (EDS) mapping. The nanowires have a diameter ranging from 100 nm to 300 nm, and their lengths range from 1.5 micrometers to 5 micrometers. Mechanical stirring and bath sonication were used to obtain even colloidal dispersions. Different concentrations of BaTiO3 nanoparticles well dispersed in the oil medium were successfully manipulated using AC electric field. To monitor the change in microstructure of BaTiO3 nanoparticles, optical microscopy was used to observe the alignment of particles in the sample under the applied electric field. Various parameters including the magnitude, frequency, and duration of the electric field, and the concentration of BaTiO3 nanoparticles were investigated to achieve the optimal alignment of nanoparticles. The experimental results were validated by theoretical analysis using Maxwell-Garnett mixing rule. It was demonstrated that the effective dielectric constant of the colloidal dispersions would increase with the increase of the magnitude, frequency and duration of applied electric field. Synthesized BaTiO3 nanowire-based dispersions exhibit significant enhancement of the effective dielectric constant compared to other colloidal materials. The effective dielectric constant of 5 wt percent BaTiO3-oil dispersions could reach up to 10 when aligned at 1000 V/mm electric field at 1 kHz frequency for 1 hour.

This thesis addresses assembly issues encountered in optical and fluidic microsystem applications. In optics, the first subject concerns the active alignment of components in optical fibersystems. A solution for reducing the cost of optical component assembly while retaining submicron accuracy is to integrate the alignment mechanism onto the optical substrate. A polymer V-shaped actuator is presented that can carry the weight of the large components - on a micromechanical scale - and that can generate movement with six degrees of freedom. The second subject in optics is the CMOS-compatible fabrication of monocrystalline silicon micromirror arrays that are intended to serve as CMOS-controlled high-quality spatial light modulators in maskless microlithography systems. A wafer-level assembly method is presented that is based on adhesive wafer bonding whereby a monocrystalline layer is transferred onto a substrate wafer in a CMOS-compatible process without needing bond alignment. In fluidics, a hybrid assembly method is introduced that combines two separately micromachined structures to create hotwire anemometers that protrude from a surface with minimum interference with the air flow. The assembled sensor enables one to make accurate time-resolved measurements of the wall shear stress, a quantity that has previously been hard to measure with high time resolution. Also in the field of hotwire anemometers, a method using a hotwire anemometer array is presented for measuring the mass flow, temperature and composition of a gas in a duct. In biochemistry, a bio-analysis chip is presented. Single nucleotide polymorphism scoring is performed using dynamic allele-specific hybridization (DASH). Using monolayers of beads, multiplexing based on single-bead analysis is achieved at heating rates more than 20 times faster than conventional DASH provides. Space and material e±ciency in packaging are the focus of the other two projects in fluidics. The first introduces an assembly based on layering conductive adhesives for the fabrication of miniature polymer electrolyte membrane fuel cells. The fuel cells made with this low-cost approach perform among the best of their type to date. The second project concerns a new cross-flow microvalve concept. Intended as a step towards the mass production of large-flow I/P converters, the silicon footprint area is minimized by an out-of-plane moving gate and in-plane, half-open pneumatic channels. / QC 20101019

Reconstructing the evolutionary history of a set of species is a fundamental problem in biology. This thesis concerns computational problems that arise in different settings and stages of phylogenetic tree reconstruction, but also in other contexts. The contributions include: • A new distance-based tree reconstruction method with optimal reconstruction radius and optimal runtime complexity. Included in the result is a greatly simplified proof that the NJ algorithm also has optimal reconstruction radius. (co-author Jens Lagergren) • NP-hardness results for the most common variations of Multiple Alignment. In particular, it is shown that SP-score, Star Alignment, and Tree Alignment, are NP hard for all metric symbol distances over all binary or larger alphabets. • A 1.375-approximation algorithm for Sorting By Transpositions (SBT). SBT is the problem of sorting a permutation using as few block-transpositions as possible. The complexity of this problem is still open and it was a ten-year-old open problem to improve the best known 1.5-approximation ratio. The 1.375-approximation algorithm is based on a new upper bound on the diameter of 3-permutations. Moreover, a new lower bound on the transposition diameter of the symmetric group is presented and the exact transposition diameter of simple permutations is determined. (co-author Tzvika Hartman) • Approximation, fixed-parameter tractable, and fast heuristic algorithms for two variants of the Ancestral Maximum Likelihood (AML) problem: when the phylogenetic tree is known and when it is unknown. AML is the problem of reconstructing the most likely genetic sequences of extinct ancestors along with the most likely mutation probabilities on the edges, given the phylogenetic tree and sequences at the leafs. (co-author Tamir Tuller) • An algorithm for computing the number of mutational events between aligned DNA sequences which is several hundred times faster than the famous Phylip packages. Since pairwise distance estimation is a bottleneck in distance-based phylogeny reconstruction, the new algorithm improves the overall running time of many distancebased methods by a factor of several hundred. (co-author Jens Lagergren) / QC 20110121

Aim: Based on a case study of UNICEF Supply Division (SD), this thesis seeks to investigate how non-profit organizations use scorecards and if the use of scorecards in non-profit organizations results in strategic alignment.   Method: The theoretical framework for this case study consists primarily of the strategic performance management tool known as the Balanced Scorecard, which consists of interlinked measures, derived from the organization's strategy. For the case study, primary data, both qualitative and quantitative, was collected by means of semi structured interviews with members of senior management and a survey which was sent out to the whole organization. Abductive reasoning was applied in the analysis.   Result & Conclusions: The case study organization's scorecard focuses mainly on a selection of process measures and is perceived by staff and management as a good diagnostic tool for processes. The organization thus has implemented a more operational adaption of the scorecard. A weak match between the organization's strategy and selected measures in its scorecard in combination with limited incentives for achieving set targets suggest that strategic alignment is likely to be low.   Suggestions for future research: The scope of the thesis is limited to UNICEF Supply Division. Comparative studies of other UN agencies would increase the reliability of the study. Future research may also try to address, more in-depth, how non-profit organizations can implement more strategic, as opposed to operational performance management systems.   Contribution of the thesis: While the findings of this study mirror prior findings on Balanced Scorecard use in the non-profit sector, it has given the case study organization valuable insight on important measurement parameters, strategy mapping and other areas of improvement.

The human protein kinase superfamily consists of over 500 members that individually control specific aspects of cell behavior and collectively control the complete range of cellular processes. That such a large group of proteins is able to uniquely diversify and establish individual identities while retaining common enzymatic function and significant sequence/structural conservation is remarkable. The means by which this is achieved is poorly understood, and we have begun to examine the issue by performing a comparative analysis of the catalytic domain of protein kinases. A novel approach for protein structural alignment has revealed a high degree of similarity found across the kinase superfamily, with variability confined largely to a single region thought to be involved in substrate binding. The similarity detected is not limited to amino acids, but includes a group of conserved water molecules that play important structural roles in stabilizing critical residues and the fold of the kinase domain. The development of a novel technique for identifying kinase substrates on a large scale directly from cell lysate has revealed that substrate specificity is not what discriminates the closely related p38α and β mitogen-activated protein kinases. Instead cellular localization appears to be their distinguishing characteristic, at least during myoblast differentiation. Together these results highlight the extent of conservation, as well as the minimal variability, that is found in the catalytic domain of all protein kinase superfamily members, and that while distantly related kinases may be distinguished by substrate specificity, closely related kinases are likely to be distinguished by other factors. Although these results focus on representative members of the kinase superfamily, they give insight as to how all protein kinases likely diversified and established unique non-redundant identities. In addition, the novel techniques developed and presented here for structural alignment and substrate discovery offer new tools for studying molecular biology and cell signaling.

Positioning, immobilization, and organ motion are some of the major concerns in all imaging modalities. With synchrotron X-ray imaging, alignment of the region of interest to the beam is usually done inside the experimental hutch. However, because specimen alignment can be time consuming; such a system is wasteful of valuable beam time. For the purposes of the Biomedical Imaging and Therapy (BMIT) beamlines at the Canadian Light Source, we propose an effective and versatile means of positioning a wide range of subjects (human and animal) with a wide range of sizes using a laser-based fiducial system to define the region of interest (ROI) before imaging; i.e., outside the experimental hutch. This system will allow the beam path through a specific region of interest to be modeled outside the imaging hutch in a way that it can be reproduced relative to the fixed X-ray beamline inside the hutch. The model will include an indication of the center of the beam and a rectangular area around the target delineating the limits of the area to be imaged (i.e., encompassing the region of interest). The rectangular field of view would be projected on the incoming (entrance) side of the subject as well as the outgoing (exit) side of the subject, and these projections must be coaxial with each other and parallel with the X-ray beam. This method is user friendly, allows mistake to be corrected before experiment and most importantly saves time.

Game balance is the problem of determining the fairness of actions or sets of actions in competitive, multiplayer games. This problem primarily arises in the context of designing board and video games. Traditionally, balance has been achieved through large amounts of play-testing and trial-and-error on the part of the designers. In this thesis, it is our intent to lay down the beginnings of a framework for a formal and analytical solution to this problem, combining techniques from game theory and machine learning. We first develop a set of game-theoretic definitions for different forms of balance, and then introduce the concept of a strategic abstraction. We show how machine classification techniques can be used to identify high-level player strategy in games, using the two principal methods of sequence alignment and Naive Bayes classification. Bioinformatics sequence alignment, when combined with a 3-nearest neighbor classification approach, can, with only 3 exemplars of each strategy, correctly identify the strategy used in 55\% of cases using all data, and 77\% of cases on data that experts indicated actually had a strategic class. Naive Bayes classification achieves similar results, with 65\% accuracy on all data and 75\% accuracy on data rated to have an actual class. We then show how these game theoretic and machine learning techniques can be combined to automatically build matrices that can be used to analyze game balance properties.

Ciliates are a class of organisms which undergo a genetic process called gene descrambling after mating. In order to better understand the problem, a literature review of past works has been presented in this thesis. This includes a brief summary of both the relevant biology and bioinformatics literature. Then, a formal definition of scrambling systems is developed which attempts to model the problem of sequence alignment between scrambled and descrambled genes. With this system, sequences can be classified into relevant functional segments. It also provides a framework whereby we can compare various ciliate sequence alignment algorithms. After that, a new method of predicting the various functional segments is studied. This method shows better coverage, and usually a better labelling score with certain parameters. Then we discuss several recent hypotheses as to how ciliates naturally descramble genes. An algorithm suite is developed to test these hypotheses. With the tests, we are able to computationally check which factors are potentially the most important. According to the current results with 247 pointer sequences of 13 micronuclear genes, examining repeats which are the same distance together with either the sequence or the size, as the real pointers, is almost always enough information to guide descrambling. Indeed, the real pointer sequence is the unique repeat 92.7% and 94.3% of the time within the 247 pointers, from the left and right respectively, using only the pointer distance and the pointer sequence information.

Shack-Hartmann wavefront sensors are commonly used in optical alignment, ophthalmology, astronomy, adaptive optics and commercial optical testing. Wavefront error measurement yields Zernike polynomials which provide useful data for alignment correction calculations. In this thesis a practical alignment method of a helmet visor is proposed based on the wavefront error measurements. The optical system is modeled in Zemax software in order to collect the Zernike polynomial data necessary to relate the error measurements to the positioning of the visor. An artificial neural network based computer program is designed and trained with the data obtained from Zernike simulation in Zemax software and then the program is able to find how to invert the misalignments in the system. The performance of this alignment correction method is compared with the optical test setup measurements.