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#### Minimal model for the secondary structures and conformational conversions in proteins

(University of Waterloo, 2005)

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express

**α**-helix and**β**-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a**β**-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both**α**-helix and**β**-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of**β**-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between**α**-helix and**β**-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined....#### Design and Characterization of Silicon-on-Insulator Passive Polarization Converter with Finite-Element Analysis

(University of Waterloo, 2005)

As optical fiber systems evolve to higher data rates, the importance of polarization control and manipulation steadily increases. Polarization manipulating devices, such as polarization splitters and converters, can be realized by introducing material anisotropy or geometric asymmetry. Compared to active devices, passive polarization converters are more simply fabricated and controlled; therefore they have attracted increasing attention during the past two decades. However, materials employed in previous polarization rotating waveguides are mainly limited to low index-contrast III-V semiconductors such as InP and GaAs. Such III-V devices possess large radiation loss, large curvature loss, and low coupling efficiency to single-mode fibers; in addition, due to the weak optical confinement, the device spacing has to be large, which prevents high-density and large-scale integration in optoelectronic integrated circuits (OEIC) and planar lightwave circuits (PLC). <br /><br /> In this dissertation, the silicon-on-insulator (SOI) technology is introduced to the design and fabrication of passive polarization rotators (PR). Efficient and accurate full-vectorial finite-element eigenmode solvers as well as propagation schemes for characterizing novel SOI PRs are developed because commercial software packages based on finite-difference techniques are inefficient in dealing with arbitrary waveguide geometries. <br /><br /> A set of general design procedures are accordingly developed to design a series of slanted-angle polarization converters, regardless of the material system (SOI or III-V), outer-slab layer configuration (symmetric or asymmetric), and longitudinal loading (single- or multi-section). In particular, our normalized design charts and simple empirical formula for SOI polarization converters are applicable to a wide range of silicon-guiding-film thickness, e. g. , from 1 to 30 μm, enabling fast and accurate polarization rotator design on most commercial SOI wafers. With these procedures, in principle 100% polarization conversion efficiency can be achieved by optimizing waveguide geometric parameters. <br /><br /> A novel configuration with asymmetric external waveguiding layers is proposed, which is advantageous for fabrication procedure, manufacturing tolerance, single-mode region, and conversion efficiency. By etching along the crystallographic plane, the angled-facet can be perfectly fabricated. Completely removing external waveguiding layer beside the sloped sidewall not only simplifies production procedures but also enhances fabrication tolerances. <br /><br /> To accurately and efficiently characterize asymmetric slanted-angle SOI polarization converters, adaptive mesh generation procedures are incorporated into our finite-element method (FEM) analysis. In addition, anisotropic perfectly-matched-layer (PML) boundary condition (BC) is employed in the beam propagation method (BPM) in order to effectively suppress reflections from the edges of the computation window. For the BPM algorithm, the power conservation is strictly monitored, the non-unitarity is thoroughly analyzed, and the inherent numerical dissipation is reduced by adopting the quasi-Crank-Nicholson scheme and adaptive complex reference index. <br /><br /> Advantages of SOI polarization rotators over III-V counterparts are studied through comprehensive research on power exchange, single-mode condition, fabrication tolerance, wavelength stability, bending characteristics, loss and coupling properties. The performance of SOI PRs is stable for wavelengths in the ITU-T

**C**-band and**L**-band, making such devices quite suitable for DWDM applications. Due to the flexible cross-section of SOI polarization converters, the coupling loss to laser diodes and single mode fibers (SMF) can be designed to be very small and can be further reduced by a tapered waveguide with cross-sections always satisfying the single-mode criteria. Slanted-angle SOI polarization rotators display asymmetric bending characteristics and permit extremely small curvatures with negligible radiation loss when the angled-facet is located at the outer bend radius. Moreover, SOI polarization rotators can be manufactured with low-price processing techniques that are fully compatible with CMOS integrated circuits (IC) technology, and thus can be integrated on both photonic and electronic chips. <br /><br /> Experimental verifications have shown good agreement with theoretical analysis and have confirmed the promising characteristics of our novel asymmetric SOI polarization converters. Similar asymmetric-outer-slab geometry has recently been employed by peer researchers to fabricate high performance III-V polarization rotators. We therefore believe that results in this dissertation will contribute much to related research fields....#### Transparent Decision Support Using Statistical Evidence

(University of Waterloo, 2005)

An automatically trained, statistically based, fuzzy inference system that functions as a classifier is produced. The hybrid system is designed specifically to be used as a decision support system. This hybrid system ...

#### Experimental and Modelling Investigation of a Novel Tetrafunctional Initiator in Free Radical Polymerization

(University of Waterloo, 2005)

An experimental and modelling investigation of a tetrafunctional initiator designed for free radical polymerizations is presented. Multifunctional initiators are believed to provide two advantages over traditional ...

#### The Continuum Architecture: Towards Enabling Chaotic Ubiquitous Computing

(University of Waterloo, 2005)

Interactions in the style of the ubiquitous computing paradigm are possible today, but only in handcrafted environments within one administrative and technological realm. This thesis describes an architecture (called ...

#### Reconstruction and Visualization of Polyhedra Using Projections

(University of Waterloo, 2005)

Two types of problems are studied in this thesis: reconstruction and visualization of polygons and polyhedra. <br /><br /> Three problems are considered in reconstruction of polygons and polyhedra, given a set of projection characteristics. The first problem is to reconstruct a closed convex polygon (polyhedron) given the number of visible edges (faces) from each of a set of directions

**S**. The main results for this problem include the necessary and sufficient conditions for the existence of a polygon that realizes the projections. This characterization gives an algorithm to construct a feasible polygon when it exists. The other main result is an algorithm to find the maximum and minimum size of a feasible polygon for the given set**S**. Some special cases for non-convex polygons and for perspective projections are also studied. <br /><br /> For reconstruction of polyhedra, it is shown that when the projection directions are co-planar, a feasible polyhedron (i. e. a polyhedron satisfying the projection properties) can be constructed from a feasible polygon and vice versa. When the directions are covered by two planes, if the number of visible faces from each of the directions is at least four, then an algorithm is presented to decide the existence of a feasible polyhedron and to construct one, when it exists. When the directions see arbitrary number of faces, the same algorithm works, except for a particular sub-case. <br /><br /> A polyhedron is, in general, called equiprojective, if from any direction the size of the projection or the projection boundary is fixed, where the "size" means the number of vertices, edge, or faces. A special problem on reconstruction of polyhedra is to find all equiprojective polyhedra. For the case when the size is the number of vertices in the projection boundary, main results include the characterization of all equiprojective polyhedra and an algorithm to recognize them, and finding the minimum equiprojective polyhedra. Other measures of equiprojectivity are also studied. <br /><br /> Finally, the problem of efficient visualization of polyhedra under given constraints is considered. A user might wish to find a projection that highlights certain properties of a polyhedron. In particular, the problem considered is given a set of vertices, edges, and/or faces of a convex polyhedron, how to determine all projections of the polyhedron such that the elements of the given set are on the projection boundary. The results include efficient algorithms for both perspective and orthogonal projections, and improved adaptive algorithm when only edges are given and they form disjoint paths. A related problem of finding all projections where the given edges, faces, and/or vertices are not on the projection boundary is also studied....#### Modeling and Design of Photoconductive and Superconductive Terahertz Photomixer Sources

(University of Waterloo, 2005)

Terahertz technology is a fast growing field with variety of applications in biology and medicine, medical imaging, material spectroscopy and sensing, monitoring and spectroscopy in pharmaceutical industry, security, and ...

#### Remote Sensing for Large-Area, Multi-Jurisdictional Habitat Mapping

(University of Waterloo, 2005)

A framework designed to guide the effective use of remote sensing in large-area, multi-jurisdictional habitat mapping studies has been developed. Based on hierarchy theory and the remote sensing scene model, the approach ...

#### Future climate change impacts on the boreal forest in northwestern Ontario. Implications for the forestry sector and the local community.

(University of Waterloo, 2005)

A large body of research has documented evidence of climate change impact already occurring on different systems on earth, future impacts can be expected. Accordingly, research is urgently needed to analyze the potential ...

#### Enhancements to Hidden Markov Models for Gene Finding and Other Biological Applications

(University of Waterloo, 2005)

In this thesis, we present enhancements of hidden Markov models for the problem of finding genes in DNA sequences. Genes are the parts of DNA that serve as a template for synthesis of proteins. Thus, gene finding ...