This study developed an integrated biogeochemical and hydrological modelling system by incorporating the latest versions of the nitrogen coupled Canadian Land Surface Scheme-Canadian Terrestrial Ecosystem Model (CLASS-CTEM) into the Modelisation Environmentale Communautaire (MEC) Surface and Hydrology system (MESH), hereafter referred to as MESH-CTEM. The newly developed MESH-CTEM modelling system allows simulations of energy, water, carbon and nitrogen fluxes and their feedbacks on vegetation growth and exploration of impacts of future climatic changes on catchment-scale processes. Performance of the MESH-CTEM system was tested at the Big Creek watershed within Norfolk county, Ontario, Canada, which is a 573 km2 crop-dominated catchment with areas of broadleaf and needleleaf forests, using observed eddy covariance flux, meteorological and hydrological datasets from October 2004 to December 2017 at a grid resolution of 0.02o latitude × 0.02o longitude. MESH-CTEM showed a significant increase in the simulated streamflow as compared to MESH running with only CLASS, excluding dynamic vegetation growth and carbon fluxes, resulting in an overall increase in the accuracy of streamflow with Nash-Sutcliffe Efficiency (NSE) indices of 0.38 and 0.12 respectively. Significant improvements were also seen for each Plant Functional Type (PFT) within the catchment with respect to energy fluxes, evaporation and soil water regimes. Many of these improvements in simulated fluxes were due in part by changes in the canopy conductance formulation, more realistic soil heat and water processes due to the introduction of fine soil layers, inter-grid transfers of water and other spatial components and vegetation cover feedbacks on energy, water and carbon exchanges by using dynamic vegetation growth processes. Simulated averaged gross ecosystem productivity, ecosystem respiration, latent heat flux and sensible heat flux for the entire catchment were respectively 660 g C m−2 yr−1, 640 g C m−2 yr−1, 32.5 W m-2 and 27.1 W m-2. Application and use of MESH-CTEM will help to study the impact of climate change and extreme events on energy, water and carbon fluxes and associated feedbacks at the catchment scale. Additionally, this will help bridge a major gap in hydrologic modelling studies through integration of biogeochemical processes. / Thesis / Master of Science (MSc)

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Adaptivity in both space and time has become the norm for solving problems modeled by partial differential equations. The size of the discretized problem makes uniformly refined grids computationally prohibitive. Adaptive refinement of meshes and time steps allows to capture the phenomena of interest while keeping the cost of a simulation tractable on the current hardware. Many fields in science and engineering require the solution of inverse problems where parameters for a given model are estimated based on available measurement information. In contrast to forward (regular) simulations, inverse problems have not extensively benefited from the adaptive solver technology. Previous research in inverse problems has focused mainly on the continuous approach to calculate sensitivities, and has typically employed fixed time and space meshes in the solution process. Inverse problem solvers that make exclusive use of uniform or static meshes avoid complications such as the differentiation of mesh motion equations, or inconsistencies in the sensitivity equations between subdomains with different refinement levels. However, this comes at the cost of low computational efficiency. More efficient computations are possible through judicious use of adaptive mesh refinement, adaptive time steps, and the discrete adjoint method. This dissertation develops a complete framework for fully discrete adjoint sensitivity analysis and inverse problem solutions, in the context of time dependent, adaptive mesh, and adaptive step models. The discrete framework addresses all the necessary ingredients of a state–of–the–art adaptive inverse solution algorithm: adaptive mesh and time step refinement, solution grid transfer operators, a priori and a posteriori error analysis and estimation, and discrete adjoints for sensitivity analysis of flux–limited numerical algorithms. / Ph. D.

Computational fluid dynamics (CFD) has proven to be an invaluable tool for both engineering design and analysis. As the performance of engineering devices become more reliant upon the accuracy of CFD simulations, it is necessary to not only quantify and but also to reduce the numerical error present in a solution. Discretization error is often the primary source of numerical error. Discretization error is introduced locally into the solution by truncation error. Truncation error represents the higher order terms in an infinite series which are truncated during the discretization of the continuous governing equations of a model. Discretization error can be reduced through uniform grid refinement but is often impractical for typical engineering problems. Grid adaptation provides an efficient means for improving solution accuracy without the exponential increase in computational time associated with uniform grid refinement. Solution accuracy can be improved through local grid refinement, often referred to as h-adaptation, or by node relocation in the computational domain, often referred to as r-adaptation. The goal of this work is to examine the effectiveness of several r-adaptation techniques for reducing discretization error. A framework for geometry preservation is presented, and truncation error is used to drive adaptation. Sample problems include both subsonic and supersonic inviscid flows. Discretization error reductions of up to an order of magnitude are achieved on adapted grids. / Master of Science

Overset, or Chimera, meshes are used to discretize the governing equations within a computational domain using multiple meshes that overlap in an arbitrary manner. The overset meshing technique is most applicable to problems dealing with multiple or moving bodies. Deep water simulations were carried out using both single and overset grid techniques for the evaluation of the overset grid application. These simulations were carried out using the commercial CFD code STAR-CCM+ by CD-adapco. The geometry simulated is that of a SES model (T-Craft) tested at the Naval Surface Warfare Center Carderock Division. The craft is simulated with two degrees of freedom, allowing movement in heave and pitch in response to displacement of the free surface. Agreement between the single and overset grid techniques was deemed reasonable to extend to future shallow water cases. However, due to longer run times of the overset mesh, the traditional or single mesh technique should be employed whenever applicable. In order to extend existing full craft CFD simulations of a surface effect ship (SES) into shallow water and maneuvering cases, an overset mesh is needed. Simulations of the SES were performed and monitored at various depth Froude numbers resulting in subcritical, critical, and supercritical flow regimes. Resistance, pitch response, and free surface response of the SES were compared between the shallow water simulations. The SES produced wider wakes, perpendicular to the craft, at simulations closer to the critical flow regime. Critical flow occurs at a depth Froude number between 0.9 and 0.95. Progression of shallow water effects through the three flow regimes agrees well with shallow water theory. / Master of Science

Visualization of large amounts of simulation data is important for the understanding of most physical phenomena. The limited capabilities of desktop machines make them unsuitable for handling excessive amounts of simulation data. The present day high speed networks have made it possible to remotely visualize the data being generated by a supercomputer in real time. In order for such a system to be reliable, a robust communication protocol and an efficient compression mechanism are needed. This work presents a remote visualization system that addresses these issues, and emphasizes the design and implementation of the application level network protocol. A control theory based adaptive rate control algorithm is presented for UDP streams that maximizes the effective throughout experienced by the stream while minimizing the packet loss. The algorithm is shown to make the system responsive to changing network conditions. This makes the system deployable over any network, including the Internet. / Master of Science

Yes / Polypropylene mesh for pelvic floor surgery is associated with serious complications ( e.g. erosion). A biodegradable tissue engineered mesh composed of a polylactic acid (PLA) scaffold seeded with autologous cells is a promising alternative. However, thus far elastin content (important for elastic recoil) in this tissue has been low. We aimed to increase elastin expression and test the resultant tensile properties.

Shifting Surfaces is an MFA thesis exhibition comprised of screenprints and sculptures. The written thesis contains documentation of the exhibition and a selection of related works, focusing on the progression of research and artmaking which led to the development of a new visual language. Shifting Surfaces employs emergent phenomena and abstraction to evoke the enmeshed relationship between bodies, ecology, and technology. / Master of Fine Arts / Shifting Surfaces is an MFA thesis exhibition comprised of screenprints and sculptures. The written thesis contains documentation of the exhibition and a selection of related works, focusing on the progression of research and artmaking which led to the development of a new visual language. Shifting Surfaces employs emergent phenomena and abstraction to evoke the enmeshed relationship between bodies, ecology, and technology.

Information retrieval is widely used for retrieving relevant information among a variety of data, such as text documents, images, audio and videos. Since the first medical batch retrieval system was developed in mid 1960s, significant research efforts have focused on applying information retrieval to medical data. However, despite the vast developments in medical information retrieval and accompanying technologies, the actual promise of this area remains unfulfilled due to properties of medical data and the huge volume of medical literature. Specifically, the recall and precision of the selected dataset from the TREC clinical decision support track are low. The overriding objective of this thesis is to improve the performance of information retrieval techniques applied to biomedical text documents. We have focused on improving recall and precision among the top retrieved results. To that end, we have removed redundant words, and then expanded queries by adding MeSH terms in TREC CDS topics. We have also used other external data sources and domain knowledge to implement the expansion. In addition, we have also considered using the doc2vec model to optimize retrieval. Finally, we have applied learning to rank which sorts documents based on relevance and put relevant documents in front of irrelevant documents, so as to return the relevant retrieved data on the top. We have discovered that queries, expanded with external data sources and domain knowledge, perform better than applying the TREC topic information directly. / Master of Science / Information retrieval is widely used for retrieving relevant information among a variety of data. Since the first medical batch retrieval system was developed in mid 1960s, significant research efforts have focused on applying information retrieval to medical data. However the actual promise of this area remains unfulfilled due to certain properties of medical data and the sheer volume of medical literature. The overriding objective of this thesis is to improve the performance of information retrieval techniques applied to biomedical text documents. This thesis presents several ways to implement query expansion in order to make more efficient retrieval. Then this thesis discusses some approaches to put documents relevant to the queries at the top.

Navigation mesh is a form of representation of a virtual environment, which allows effective navigation of intelligent virtual agents. This thesis deals with the development of a navigation mesh for the intelligent virtual agents in the environment of the computer game Unreal Tournament 2004. Before the development of the navigation mesh, the navigation graph was the only available representation of the environment that the agents could use for navigation. The navigation graph however provides only limited information about the environment. With the use of the navigation mesh the agents are able to navigate in the environment faster and over shorter paths. Creation of the navigation mesh from the environment's geometry extracted from Unreal Tournament 2004 map files is a part of the thesis. Finally, a new navigation module for Pogamut 3 - a platform that allows creation and controlling of intelligent virtual agents, is implemented. The new navigation module consists of the navigation mesh and a set of navigation algorithms Powered by TCPDF (www.tcpdf.org)