The purpose of this report is to cover the procedure of creating and explaining how to use a tool kit that allows the haptic Application Programming Interface (API) H3D from SenseGraphics to be used in conjunction with an advanced physics simulator from Meqon. Both haptic applications and physics engines have developed rapidly the last couple of years but they are rarely used together. If such a connection would be created it would be possible to interact with complex environments in a new way and a variety of haptic applications can be produced. The physics engine from Meqon has gained recognition for its abilities to produce realistic results due to efficient implementation of collision detection system, friction models and collision handling, among other things. H3D is a completely open source API that is based on standards such as OpenGL and X3D. H3D consists of a data base containing nodes, an XML parser to extract a scene graph from the data base and functionality to produce a graphic and haptic interface. The tool kit produced in this thesis is an extension to H3D. A fundamental function of the tool kit is to communicate with the Meqon system and still be a part of the H3D structure. The Meqon system has a modular structure where each module has its own abilities. Only the rigid body module is utilised by the tool kit, which however is the most important module. It is possible to define global settings of the engine and rigid body module, add rigid bodies with several elements and insert constraints on the motion of the rigid bodies into the engine. All of these operations are done from the X3D file format that H3D uses, thus letting all functionality of the H3D system available.

In the analyses of steel framed structures it is customary to assume the beam to column connections as either fully rigid which means that all moments are transferred from beam to column with negligible rotation or ideally pinned that resists negligible moment. This assumption is reasonable for some types of connections. However when considering steel connections such as bolted-bolted double web angle connections it can be seen that the behavior of these connections is in between the two extreme cases. Thus a third connection type, namely semi rigid or partially restrained connection, is introduced. However this type of connection exhibits such a nonlinear behavior that modeling this behavior necessities a substantial effort. Moreover to perform a performance based analyses the true behavior of these connections should be incorporated as part of the modeling effort. Several researches dealing with these two topics have been undertaken in literature. Despite these efforts, modeling of the moment rotation behavior of these connections still requires improvement especially under cyclic loading conditions. In addition to this, performing an analysis with existing elements incorporating semi-rigid connections as a spring attached to beam ends is not practical because of the fact that displacement based formulation increases meshing significantly which requires substantial computational power. In this study a hysteretic (quadra-linear) moment rotation model considering pinching, damage and possibility of residual moment capacity is developed. The behavior is calibrated via experimental data available in the literature. Furthermore a force based macro element considering spread inelastic behavior along the element is presented. With this element several connections located anywhere along the beam could be incorporated in the analysis with less degree of freedom with respect to displacement based elements. Moreover the macro element model can be used in conjunction with corotational formulation for the capture of nonlinear geometric effects.

Image registration is the process of aligning two images such that their mutual features overlap. This is of great importance in several medical applications. In 2008 a novel method for simultaneous T1, T2 and proton density quantification was suggested. The method is in the field of quantitative Magnetic Resonance Imaging or qMRI. In qMRI parameters are quantified by a pixel-to-pixel fit of the image intensity as a function of different MR scanner settings. The quantification depends on several volumes of different intensities to be aligned. If a patient moves during the data aquisition the datasets will not be aligned and the results are degraded due to this. Since the quantification takes several minutes there is a considerable risk of patient movements. In this master thesis three image registration methods are presented and a comparison in robustness and speed was made. The phase based algorithm was suited for this problem and limited to finding rigid motion. The other two registration algorithms, originating from the Statistical Parametrical Mapping, SPM, package, were used as references. The result shows that the pixel-to-pixel fit is greatly improved in the datasets with found motion. In the comparison between the different methods the phase based algorithm turned out to be both the fastest and the most robust method.

The primary study of this thesis is the experimental realization of the non-equilibrium dynamics of a quantum inverted pendulum as examined in the collective spin dynamics of a spin-1 Bose-Einstein condensate. In order to compare experimental results with the simulation past the low depletion limit, current simulation techniques needed to be extended to model atomic loss. These extensions show that traditional measurements of the system evolution (e.g. measuring the mean and standard deviation of the evolving quantity) were insufficient in capturing the quantum nature of the evolution. It became necessary to look at higher order moments and cumulants of the distributions in order to capture the quantum fluctuations. Extending the implications of the loss model further, it is possible that the system evolves in a way previously unpredicted. Spin-mixing from a hyperbolic fixed point in the phase space and low noise atom counting form the core of the experiment to measure the evolution of the distributions of the spin populations. The evolution of the system is also compared to its classical analogue, the momentum-shortened inverted pendulum. The other experimental study in this thesis is mapping the mean-field phase space. The mean-field phase space consists of different energy contours that are divided into both phase-winding trajectories and closed orbits. These two regions are divided by a separatrix whose orbit has infinite period. Coherent states can be created fairly accurately within the phase space and allowed to evolve freely. The nature of their subsequent evolution provides the shape of the phase space orbit at that initial condition. From this analysis a prediction of the nature of the entire phase space is possible.

In this paper I give a thorough account of the history of the open question argument. I have provide Moore’s original impetus for it and its traditional formulation. I then examine the Cornell Realists’ objection to that original formulation and showed that their objection does indeed show the open question argument to be incorrect in its conclusions. Having presented the history of the open question argument and having assessed the most challenging objections to it, I turn to Andrew Altman’s powerful reconstruction of the open question argument in order to see how well, if at all, it sidesteps the objections leveled against the classical formulation. I then argue that while Altman does present the most coherent defense of the open question argument available, I conclude that insofar as he has rested upon a commitment to Carnap's philosophy of language over a Fregean semantic and an untenable rendering of post-Kripkean philosophy of language as it concerns rigid designation, we must reject his reformulation. Given that rigid designation itself undermines Altman’s position, I conclude that the open question is still in need of a defense before it can regain its position as a major player in the discipline of ethics.

The following report contains an evaluation of the use of mathematical simulation programs at the company Isaberg Rapid AB. The work includes booth FE and motion simulations where the results are compared with real life test data. The goal of the report is to evaluate the accuracy of simulations which can be performed by engineers as a part of the design process. By using mathematical simulation tools it is possible to find a good design solution early in the development phase and thereby shorten lead time and reduce costs.

The purpose of this study is to develop an approach that considers fire as a load in the design of structures. Recent studies of the full-scale fire tests in Cardington, UK and the World Trade Centre collapse have shown that the behaviour of steel structures in fire when assembled into a frame differs from that measured or predicted by fire testing of individual structural elements, revealing the importance of accounting for realistic fire loads in the design of structures and the potential inadequacy of fire testing individual elements as employed by current building codes. Yet, there has been limited basic research and development to allow consideration of fire as a load in the analysis and design of structures. In response to this much needed work, this thesis develops an approach to include fire as a load in the analysis of a 2-bay by 2-storey structure when a semi-rigid connection is exposed to thermal loads typical of those that might be encountered during a real fire. The structural fire analysis is principally based on incorporating moment-rotation-temperature data for the connection, as found in archival literature, into a structural analysis software package developed at the University of Waterloo. The software employs a modified Displacement Method for analyzing structures, which involves the computation of stiffness reduction factors that represent the deterioration of strength of the structural elements as they are subjected to various loads. By modifying the moment-rotation-temperature data for a semi-rigid connection into a form recognized by the software, a fire load is simulated by incrementally elevating the temperature of the affected steel connection. In this way, a fragility analysis of the entire structure under fire load is conducted. A series of example calculations are presented for cases in which the semi-rigid connection is exposed to increasing temperatures of 20°C, 200°C, 400°C and 600°C. The analysis showed that as the connection is heated, it is weakened, and the steel structure undergoes a redistribution of moments from the heated connection to other non-heated elements within the framework, which is essentially a form of fire-resistance of the assembled structure that unassembled members in isolation do not have. The study also demonstrated that the experimental moment-rotation-temperature data reported in archival literature can be incorporated into the structural analysis, and that additional force-deformation data obtained from further experimental work or through finite-element analyses would allow the study to be extended to analyze the effects of fire loading on other structural elements of an assembled framework. To demonstrate the link between the predicted structural response at different temperatures and the development of a compartment fire, a fire modelling analysis is also performed.

Conformational selection is the idea that proteins traverse positions on the conformational space represented by their potential energy landscape, and in particular positions considered as local energy minima. Conformational selection a useful concept in ligand binding studies and in exploring the behavior of protein structures within that energy landscape. Often, research that explores protein function requires the generation of conformational ensembles, or collections of protein conformations from a single structure. We describe a method of conformational ensemble generation that uses joint-constrained rigid-body dynamics (an approach that allows for explicit consideration of rigidity) and the elastic network model (providing structurally derived directional guides for the rigid-body model). We test our model on a selection of unbound proteins and examine the structural validity of the resulting ensembles, as well as the ability of such an approach to generate conformations with structural overlaps close to the ligand-bound versions of the proteins.

This work focuses on the simulation of fluids as they transition between a solid and a liquid state, and as they interact with rigid bodies in a realistic fashion. There is an underlying theme to my work that I did not recognize until I examined my body of research as a whole. The equations of motion that are generally considered appropriate only for liquids or gas can also be used to model solids. Without adding extra constraints, one can model a solid simply as a fluid with a high viscosity. Admittedly, this representation will only get you so far, but this simple representation can create some very nice animations of objects that start as solids, and then melt into liquid over time. Another way to represent solids with the fluid equations is to add extra constraints to the equations. I use this representation in the parts of this work that focus on the two-way coupling of liquids with rigid bodies. The coupling affects both how the liquid moves the rigid bodies, and how the rigid bodies in turn affect the motion of the fluid. There are three components that are needed to allow solids and fluids to interact: a rigid body solver, a fluid solver, and a mechanism for the coupling of the two solvers. The fluid solver used in this work was presented in [8]. This Melting and Flowing solver is a fast and stable system for animating materials that melt, flow, and solidify. Examples of realworld materials that exhibit these phenomena include melting candles, lava flow, the hardening of cement, icicle formation, and limestone deposition. Key to this fluid solver is the idea that we can plausibly simulate such phenomena by simply varying the viscosity inside a standard fluid solver, treating solid and nearly-solid materials as very high viscosity fluids. The computational method modifies the Marker-And-Cell algorithm [99] in order to rapidly simulate fluids with variable and arbitrarily high viscosity. The modifications allow the viscosity of the material to change in space and time according to variation in temperature, water content, or any other spatial variable. This in turn allows different locations in the same continuous material to exhibit states ranging from the absolute rigidity or slight bending of hardened wax to the splashing and sloshing of water. The coupling that ties together the rigid body and fluid solvers was presented in [7], and is known as the Rigid Fluid method. It is a technique for animating the interplay between rigid bodies and viscous incompressible fluid with free surfaces. Distributed Lagrange multipliers are used to ensure two-way coupling that generates realistic motion for both the solid objects and the fluid as they interact with one another. The rigid fluid method is so named because the simulator treats the rigid objects as if they were made of fluid. The rigidity of such an object is maintained by identifying the region of the velocity field that is inside the object and constraining those velocities to be rigid body motion. The rigid fluid method is straightforward to implement, incurs very little computational overhead, and can be added as a bridge between current fluid simulators and rigid body solvers. Many solid objects of different densities (e.g., wood or lead) can be combined in the same animation. The rigid body solver used in this work is the impulse based solver, with shock propagation introduced by Guendelman et al. in [36]. The rigid body solver allows for collisions ranging from completely elastic, where an object can bounce around forever without loss of energy, to completely inelastic where all energy is spent in the collision. Static and dynamic frictional forces are also incorporated. The details of this rigid body solver will not be discussed, but the small changes needed to couple this solver to interact with fluid will be. When simulating fluids, the fluid-air interface (free surface) is an important part of the simulation. In [8], the free surface is modelled by a set of marker particles, and after running a simulation we create detailed polygonal models of the fluid by splatting particles into a volumetric grid and then render these models using ray tracing with sub-surface scattering. In [7], I model the free surface with a particle level set technique [14]. The surface is then rendered by first extracting a triangulated surface from the level set and then ray tracing that surface with the Persistence of Vision Raytracer (http://povray.org).

Many bridges are damaged by collisions from over-height vehicles resulting in significant impact to the transportation network. To reduce the likelihood of impact from over-height vehicles, steel pedestals have been used as a cost-effective, efficient means to increase bridge clearance heights. However, these steel pedestals installed on more than 50 bridges in Georgia have been designed with no consideration of seismic loads and may behave in a similar fashion to high-type steel bearings. Past earthquakes have revealed the susceptibility of high-type bearings to damage, resulting in the collapse of several bridges. Although Georgia is located in a low-to-moderate region of seismicity, earthquake design loads for steel pedestals should not be ignored. In this study, the potential vulnerabilities of steel pedestals having limited strength and deformation capacity and lack of adequate connection details for anchor bolts is assessed experimentally and analytically. Full-scale reversed cyclic quasi-static experimental tests are conducted on a 40' bridge specimen rehabilitated with 19" and 33" steel pedestals to determine the modes of deformation and mechanisms that can lead to modes of failure. The inelastic force-deformation hysteretic behavior of the steel pedestals obtained from experimental test results is used to calibrate an analytical bridge model developed in OpenSees. The analytical bridge model is idealized based on a multi-span continuous bridge in Georgia that has been rehabilitated with steel pedestals. The analytical bridge model is subjected to a suite of ground motions to evaluate the performance of the steel pedestals and the overall bridge system. Recommendations are made to the Georgia Department of Transportation (GDOT) for the design and construction of steel pedestals. The results of this research are useful for Georgia and other states in low-to-moderate seismic zones considering the use of steel pedestals to elevate bridges and therefore reduce the likelihood of over-height vehicle collisions.