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Across the United States, high tunnels are used as a means of season extension and control over climatic variability in fruit and vegetable production. However, high tunnel systems are an intensive form of agricultural production which may compromise soil and crop quality over time. This study examined the effects of the varying environmental conditions, created in two types of tunnel system, movable and stationary, on the flow of nitrogen from amendment to plant and impact on crop and soil quality parameters. The way nutrients cycled through these systems was different and the nutrient treatments had no consistent effects on soil nutrient parameters, although some microbial groups were affected by the nature of the nutrient amendment. No exposure to rainfall resulted in an accumulation of leachable NO3 in the stationary tunnels. Spinach yields were superior to those in a previous study at the same site however, leaf NO3 levels consistently exceeded EU maximum limits for fresh-sap leaf NO3. We cannot conclude from our data if there was a compromise of crop or soil quality in the high tunnel production systems and further investigation is necessary as high tunnels gain in popularity and make a larger footprint on the agricultural landscape.

Finding wide tunnels in protein structures is an important problem in Structural Bioinformatics with applications in various areas such as drug design. Several algorithms have been proposed for finding wide tunnels in a fixed protein conformation. However, to the best of our knowledge, none of the existing work have considered widening the tunnel, i.e., finding a wider tunnel in an alternative conformation of the given structure. In this thesis we initiate this line of research by proposing a tunnel-widening algorithm which aims to make the tunnel wider by a slight local change in the structure of the protein. Given a fixed conformation of a protein with a point located inside it, we first describe an algorithm to identify the widest tunnel from that point to the outside environment of the protein. Then we try to make the tunnel wider by considering various alternative conformations of the protein. We only consider conformations whose energies are not much higher than the energy of the initial conformation. Among these alternative conformations we select the one with the widest tunnel. However, the alternative conformation with the widest tunnel might not be accessible from the initial structure. Thus, in the next step we develop three algorithms for finding a feasible transition pathway from the initial structure to the alternative conformation, i.e., a sequence of intermediate conformations between the initial structure and the alternative conformation such that the energy values of all these intermediate conformations are close to the energy of the initial structure. We evaluate our tunnel-finding and tunnel-widening algorithms on various proteins. Our experiments show that in most cases we can make the tunnel wider in an alternative conformation. However, there are cases in which we find a wider tunnel in an alternative conformation, but the energy value of the alternative conformation is much higher than the energy of the initial structure. We also implemented our three pathway-finding algorithms and tested them on various instances. Our experiments show that although in most cases we can find a feasible transition pathway, there are cases in which the alternative conformation has energy close to the initial structure, but our algorithms cannot find any feasible pathway from the initial structure to the alternative conformation. Furthermore, there is a trade-off between the running time and accuracy of the three pathway-finding algorithms.

The design of supersonic flow paths for scramjet engines and high Mach number shock tunnel nozzles is complicated by high temperature flow effects and multidimensional inviscid/ viscous flow interactions. Due to these complications, design in the past has been enabled by making flow modelling simplifications that detract from the accuracy of the flow analysis. A relatively new approach to designing aerodynamic bodies, which automates design and does not require as many simplifying assumptions to be effective, is the coupling of a computational flow solver to an optimization algorithm. In this study, a new three-dimensional space-marching computational flow solver is developed and coupled to a gradient-search optimization algorithm. This new design tool is then used for the design optimization of an axisymmetric scramjet flow path and two high Mach number shock tunnel nozzles. The flow solver used in the design tool is an explicit, upwind, space-marching, finite-volume solver for integrating the three-dimensional parabolized Navier-Stokes equations. It is developed with an emphasis on simplicity and efficiency. Cross-stream fluxes are calculated using Toro's efficient upwind, linearized, approximate Riemann solver in flow regions of slowly varying data, and an Osher type solver in the remainder of the flow. Vigneron's technique of splitting the streamwise pressure gradient in subsonic regions is used to stabilise the flux calculations. A three-dimensional implementation of an algebraic turbulence model, a finite-rate chemistry model and a thermodynamic equilibrium model are also implemented within the solver. A range of test cases is performed to (1) validate and verify the phenomenological models implemented within the solver, thereby ensuring the simulation results used for design are credible, and (2) demonstrate the speed of the solver. The first application of the new computational design tool is the design of a scramjet flow path, which is optimized for maximum axial thrust at a flight Mach number of 12. The optimization of a scramjet flow path has been examined previously, however, this study differs to others published in that the flow is modelled using a turbulence model and a finite-rate chemical reaction model which add to the fidelity of the simulations. The external shape of the scramjet vehicle is constrained early on in the design process, therefore, the design of the scramjet is restricted to the internal flow path. Because of this constraint, and the large internal surface area of the combustor and the high skin friction iv within the combustor, the net calculated force exerted on the scramjet for both the initial and optimized design is a drag force. The drag force of the initial design, however, is reduced by 60% through optimization. The second application of the design tool is the wall contour of an axisymmetric Mach 7 shock tunnel nozzle, which is computationally optimized for minimum test core flow variation to a level of +/- 0.019 degrees for the flow angularity and +/- 0.26% for the Pitot pressure. The design is verified by constructing a nozzle with the optimized wall contour and conducting experimental Pitot surveys of the nozzle exit flow. The measured standard deviation in core flow Pitot pressure is 1.6%. However, because there is a large amount of experimental noise, it is expected that the actual core flow uniformity may be better than indicated by the raw experimental data. The last application of the computational design tool is a contoured Mach 7 square cross-section shock tunnel nozzle. This is a three-dimensional optimization problem that demonstrates the versatility of the design tool, since the effort required to implement the optimization algorithm is independent of the complexity of the flow-field and flow solver. Optimization results show that the variation in the test core flow properties could only be reduced to a Mach number variation of +/- 7% and flow angle variation of +/- 1.2 degrees ,for a short nozzle suitable for a shock tunnel. The magnitudes of the optimized nozzle exit flow deviations for the short nozzle and two other longer nozzles indicate that generating uniform flow becomes increasingly difficult as the length of square cross-section nozzles is reduced. Overall, the current research shows that coupling a flow solver to an optimization algorithm is an effective and insightful way of designing scramjets and shock tunnel nozzles.

Thesis (M. App. Sc.)--Carleton University, 2004. / Includes bibliographical references (p. 131-139). Also available in electronic format on the Internet.

Thesis (M. App. Sc.)--Carleton University, 2004. / Includes bibliographical references (p. 97-98). Also available in electronic format on the Internet.

Thesis (Ph. D.)--Carleton University, 2005. / Includes bibliographical references (p. 259-270). Also available in electronic format on the Internet.

Thesis (M.App.Sc.) - Carleton University, 2005. / Includes bibliographical references (p. 75-76). Also available in electronic format on the Internet.

Thesis (M.S.)--Mississippi State University. Department of Aerospace Engineering. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--California Institute of Technology, 1995. / "UMI number: 9539115"--P. [i]. Includes bibliographical references. Available on microfilm and online via the World Wide Web.