In recent years, the field of bioinformatics has exploded in a scale that is unprecedented. The amount of data generated from different genome projects demands a new and efficient way of information storage and retrieval. The analysis and management of the protein structure information has become one of the main focuses. It is well-known that a protein’s functions differ depending on its structure’s position in 3-dimensional space. Due to the fact that protein structures are exceedingly large, complex, and multi-dimensional, there is a need for a data model that can fulfill the requirements of storing protein structures in accordance to its spatial arrangement and topological relationships and, at the same time, provide tools to analyze the information stored. With the emergence of spatial database, first used in the field of Geographical Information Systems, the data model for protein structure could be based on the geographic model, as they share several similar uncanny traits. The geometry of proteins can be modeled using the spatial types provided in a spatial database. In a similar way, special geometry queries used for geographical analysis can also be used to provide information for analysis on the structure of the proteins. This thesis will explore the mechanics of extracting structural information for a protein from a flat file (PDB), storing that information into a spatial data model based on a spatial data model, and making analysis using geometric operators provided by the spatial database. The database used is Oracle 9i. Most features are provided by the Oracle Spatial package. Queries using the ideas aforementioned will be demonstrated.

Dendritic or branching structures are commonly seen in natural phenomena such as lightning, cracking and vegetal growth. They are also often used for artistic or decorative purposes, ranging from ornamentation to decorative ceramics. Existing procedural methods for modeling these structures remain very limited in terms of control and flexibility. As a result, these objects tend to be modeled individually, which is a painstaking and costly process.<p>We present a new procedural method for modeling dendritic structures based on a path planning approach. Our method includes the implementation of a partial non-scalar distance metric that gives us effective and flexible control handles over the evolving dendritic structure. These control handles are demonstrated by guiding the growth of dendritic structures using input images, allowing us to create a form of stylistic dendritic halftoning and to embed hidden images in dendritic trees to create pareidolia effects. These applications demonstrate the vast diversity of structures that can easily be modeled by our process a flexibility that existing methods definitely lack. We also demonstrate the application of the partial non-scalar distance metric to the context of texture synthesis from example, and show how it holds promise for many other contexts.

Relational database systems have successfully solved many business data processing problems. The primary reason of this success is that the relational data model provides a simple, yet flexible view of data as tables. In studying VLSI/CAD data, we noticed that they are often represented in formats similar to relational tuples. Therefore, they can be stored easily in relational tables. However, it is generally agreed that conventional relational database systems are inefficient for VLSI/CAD applications, since such applications often access large amounts of data repetitively. In order to solve this problem, we designed and implemented a data mapping subsystem that converts VLSI/CAD data stored in relational tables into internal data structures so that they can be efficiently manipulated in C. By using our data mapping language, we could reduce the amount of code required by the data-structure construction parts of some real VLSI/ CAD tools to about 1/10 of that required by C implementation. Our data-structure builder consumes several times more CPU cycles. / Graduation date: 1991

In this dissertation, I examine the marking of focus and givenness in Nte?kepmxcin (Thompson River Salish). The focus is, roughly, the answer to a wh-question, and is highlighted by the primary sentential accent in stress languages like English. This has been formalized as the Stress-Focus Correspondence Principle. Given material is old information, and is de-accented in languages like English. Nte?kepmxcin is a stress language, but marks focus structurally. However, I argue that the structure has a prosodie motivation: the clause is restructured such that the focus is leftmost in the intonational phrase. It follows that Salish focus structures lack the special semantics that motivates the use of English structural focus (clefts). As a theoretical contribution, I show that the Stress-Focus Correspondence Principle does not account for focus marking in all stress languages, nor does the "distress-given" generalization account for the marking of given information. This is because focus surfaces leftmost, while the nuclear stress position is rightmost. Instead of "stress-focus", I propose that alignment with prosodie phrase edges is the universally common thread in focus marking. This mechanism enables listeners to rapidly recover the location of the focus, by identifying coarse-grained phonological categories (p-phrases and i-phrases). In Thompson River Salish, the focus is associated with the leftmost p-phrase in the matrix intonational phrase. The analysis unifies the marking of focus across languages by claiming that focus is always marked prosodically, by alignment to a prosodie category. The study combines syntactic analysis of focus utterances with their phonetic realization and semantic characteristics. As such, this dissertation is a story about the interfaces. This research is based on a corpus of conversational data as well as single sentence elicitations, all of which are original data collected during fieldwork. The second contribution of this dissertation is thus methodological: I have developed various fieldwork techniques for collecting both spontaneous and scripted conversational discourses. The empirical contribution that results is a collection of conversational discourses, to add to the single speaker traditional texts already recorded for Nte?kepmxcin.

The problem of shape control of composite laminated smart structures with piezoelectric patches placed at optimal location is considered in this thesis. Laminated plate structures with piezoelectric patches for shape control applications are modeled using a shear deformable plate formulation by including the piezoelectric layers into the plate substrate. A composite plate finite element model is also developed for composite plates with self-sensing actuators. Non-linear hysteresis models for piezoelectric materials are presented and discussed. Numerical simulation of composite plate structures with piezoelectric actuators is conducted and presented. The optimization problem of finding the optimal location of actuators using a linear quadratic control algorithm is done and the results are discussed. Static shape control strategies are also discussed.

When dealing with massive data sets, standard algorithms may easily ``run out of memory''. In this thesis, we design efficient algorithms in space-conscious models. In particular, in-place algorithms, multi-pass algorithms, read-only algorithms, and stream-sort algorithms are studied, and the focus is on fundamental geometric problems, such as 2D convex hulls, 3D convex hulls, Voronoi diagrams and nearest neighbor queries, Klee's measure problem, and low-dimensional linear programming. In-place algorithms only use O(1) extra space besides the input array. We present a data structure for 2D nearest neighbor queries and algorithms for Klee's measure problem in this model. Algorithms in the multi-pass model only make read-only sequential access to the input, and use sublinear working space and small (usually a constant) number of passes on the input. We present algorithms and lower bounds for many problems, including low-dimensional linear programming and convex hulls, in this model. Algorithms in the read-only model only make read-only random access to the input array, and use sublinear working space. We present algorithms for Klee's measure problem and 2D convex hulls in this model. Algorithms in the stream-sort model use sorting as a primitive operation. Each pass can either sort the data or make sequential access to the data. As in the multi-pass model, these algorithms can only use sublinear working space and a small (usually a constant) number of passes on the data. We present algorithms for constructing convex hulls and polygon triangulation in this model.

Oil and gas exploration and production activities in deep and ultra deep waters in hostile environments necessitates the need to develop innovative riser systems capable of ensuring transfer of fluids from the seabed to a floating vessel and vice versa, with little or no issues with respect to influences of environmental loads and vessel motions.The design of the riser system must focus on different types of loading and load effects than for traditional water-depth. A variety of different riser concepts are proposed, both with respect to geometric shape and selection of materials.In the last few years, steel catenary risers have been a preferred riser solution for deep-water field developments due to its simple engineering concept, cost effective, flexibility in using different host platform and flexibility in geographical and environmental conditions. In this report, a case study considering a steel catenary riser operating in 1000 m water depth was conducted. The riser was subjected to extreme environmental conditions and static and dynamic response analyses were performed by the computer program RIFLEX.Last, parametric study is carried out to investigate the effects of parameter variation based on some parameters like current profiles, mesh density, wall thickness and so on. These parameters have significant effect on the structural response, especially in the touch down region.

Due to the substantial increase in oil and gas activities in Polar areas the demand for ice strengthen vessel has increased greatly. This increase in demand has highlighted the importance of designing ice strengthened ship structures that are more producible and maintain adequate safety and integrity. In order to encounter these new challenges, the international association of classification societies (IACS) has developed unified regulations for the designing of ice strengthened ship. In addition to these requirements, most of the classification societies have their regulation for design of polar ships. Stiffened plates are the basic structural building blocks of ships. So, the study mainly explores the plastic response of stiffened plate subject to lateral ice loads. The Non Linear Finite Element Method (NLFEM) is extensively used to study the plastic behavior of stiffened plates. The Abaqus non linear finite element program is used in this study.The aims of the study are to investigate the validity of the limit state equation employed in the IACS new Unified Requirements for Polar Ships [6], investigate the membrane effect at large deformation, determine the ALS design load, and assess limit loads when fracture in plating likely to take place. The study also focuses on the warping effect of unsymmetrical sections and the effect of end brackets on the lateral load carrying capacity of the stiffener. The effect of mid-span tripping bracket on the load deflection behavior of L and T stiffeners is also studied. In particular, the study focuses on the behavior of inclined T and L stiffener. As ships move forward by crushing ice, sides of ships&#146; bow come across with ice initially. To design ice strengthen vessel, it&#146;s very important to understand the behavior of ships&#146; side structure subjected to ice loads. So, this study extensively focuses on the non-linear finite element analysis of ships&#146; side structure subjected to ice loads. Normally, ship design rules are based on the behavior of single frame subjected to loads. It&#146;s reasonable to consider frames singly under the uniform loading but in case of ice loading which is non uniform, the behavior of the structure obtained from single frame based design does not accurately represent the true behavior of the structure. The load-deflection characteristic of frames in isolation, frames as part of a &#189;+1+&#189; frames and frames as part of a grillage subjected to unsymmetrical loading is studied. As, stiffeners in the side structure of ships&#146; bow are not normally perpendicular with shell plate, the lateral capacity of frames as part of a &#189;+1+&#189; frames and as part of a grillage is obtained for inclined stiffener.The analyses in this study cover the full range of stiffener behavior from elastic, through yield, through the formation of initial mechanisms, through large deformations. The parameters considered for the analyses are: &#149;frame profile: Angle, Tee&#149;frame span&#149;load length: patch (transverse), uniform (longitudinal)&#149;web thickness&#149;end brackets: with, without&#149;Angle of inclination of stiffener web with the plate flange&#149;Tripping bracket at mid span

Fatigue is an important character for the flexible pipes as they are always exposed to dynamic loading. For nonbonded flexible pipes, fatigue and stress analysis can be performed based on different assumptions of slip behaviour. Different slip assumptions used in estimating the slip stress always play a determinative role in the prediction of fatigue damage. Thus, this thesis will focus on the study of the slip behaviour between tensile armour layers of nonbonded flexible pipes. The results can be used to support the basic assumptions for further fatigue analysis. The main object of this thesis is to summarize the existing analytical methods for stress and slip analysis of nonbonded flexible pipe armouring layers and to verify that the improved finite element models can give adequate description of the flexible pipe slip behaviour.In previous version of BFLEX, the transverse slip effect for nonbonded flexible pipes has been neglected. In this thesis, transverse slip regime has been activated in the updated BFLEX by developing a new type of beam element hshear353 and a new type of contact element hcont453. Finite element models use these two elements have been made and several case studies have been carried out.For axisymmetric loading, two analytical solutions, one obtained from the equations by Witz&amp;Tan[13], one from S&#230;vik[2] have been compared with the result from numerical simulation. It has been found that S&#230;vik&#146;s solution matches better with the BFLEX solution comparing to Witz&amp;Tan&#146;s solution. For flexible pipes exposed to bending, influences on slip behaviour from several pipe parameters, namely friction coefficient, axial strain and global pipe curvature, have been investigated. The numerical results are also compared with analytical solutions obtained from S&#230;vik[2]. It has been found that the numerical solutions can give excellent agreement with analytical solutions. It is further concluded that the outer tensile armour layer do not influence much on the inner layer slip behaviour.In addition, the cyclic bending effects on nonbonded flexible pipes have been investigated. It has been found that the tendon behaves differently from case to case. The inner and outer layers behave differently. Only a few cases have been studied for this problem due to time limitation. The overall conclusion is that the developed BFLEX model is capable of describing the stresses and local displacements of flexible pipe for simple cases. The developed numerical model can further be used in the study of fatigue in flexible risers. However, more studies on influence from multi-tensile layers and cyclic bending are needed in the future.

The problem of shape control of composite laminated smart structures with piezoelectric patches placed at optimal location is considered in this thesis. Laminated plate structures with piezoelectric patches for shape control applications are modeled using a shear deformable plate formulation by including the piezoelectric layers into the plate substrate. A composite plate finite element model is also developed for composite plates with self-sensing actuators. Non-linear hysteresis models for piezoelectric materials are presented and discussed. Numerical simulation of composite plate structures with piezoelectric actuators is conducted and presented. The optimization problem of finding the optimal location of actuators using a linear quadratic control algorithm is done and the results are discussed. Static shape control strategies are also discussed.