Nonlinear microscopy has become an indispensable tool in the study of biological systems. It includes many nonlinear contrast mechanisms, each sensitive to different biological structures. However, interpretation of the images generated in nonlinear microscopy is a complex matter due to factors such as the structural complexity of the sample, phase relationships between the excitation beam and the detected signal and the nonlinear interactions in the focal volume of the microscope. This thesis contains a new theoretical and numerical framework that describes the focusing of an excitation beam in a nonlinear microscope, the nonlinear optical interactions with the material in the focal volume, and the resulting nonlinear optical signal in the far field. The framework is the first to include reflection and refraction of the excitation beam and nonlinear signals by an arbitrary number of interfaces in the focal volume, which is especially significant for the interpretation of third harmonic generation (THG). It also uses the chirp-z transform to speed up calculations by orders of magnitude compared to numerical integration techniques. The framework is used to investigate second harmonic generation (SHG) by collagen. Focusing effects alter polarization-dependent SHG measurements of collagen properties compared to the plane wave approximation, and this is verified experimentally. Furthermore, a technique of imaging the far field SHG radiation from collagen fibres is proposed, which can be used to extract the orientation of collagen fibres unambiguously. The framework is then applied to analyze the influence of interfaces on THG. Reflection effects at interfaces significantly affect THG, which leads to the development of a new super-resolution THG imaging technique based on backward-propagating THG. This super-resolution technique is experimentally demonstrated by imaging surface profiles with tens of nanometers resolution, which is the first time that such resolution is obtained in coherent nonlinear microscopy. Therefore, this imaging technique shows promise to become an important tool in high-resolution imaging of (biological) samples. The theoretical and numerical framework provides a foundation for future research on the origin of nonlinear microscopy signals. The new imaging techniques based on this framework have great potential in quantifying fibrillar structures and interfaces in biological samples.

The structural performance of Rounded Dovetail Connections (RDC) has been studied experimentally and numerically to provide information needed for connection structural design. RDC are mainly used to transfer vertical shear forces, but test results show that they can carry considerable load in tension and bending. Geometric parameters, such as dovetail flange angle and dovetail height are shown to significantly effect affect the structural performance of RDC. Results show that it is impractical to determine a set of empirical equations to describe the structural performance of RDC based on basic wood material properties. RDC manufactured and tested with low and constant moisture content outperformed those evaluated under other climatic conditions, and test results demonstrate that RDC should be produced at low machine speed and with minimal a gap between the connecting members. RDC in laminated strand lumber have higher capacity and fail under larger deformations compared to RDC in western hemlock. A three-dimensional finite element method model is presented and validated with experimental tests. Good agreement is achieved between the load deformation response predicted by the model and the experimentally observed load deformation response. Therefore the model is deemed suitable for estimating the stresses needed to develop failure criteria. A failure criterion for the analysis of RDC is presented taking into account size effect in the strength of wood. Based on the experimental and numerical studies, a design equation for RDC is presented that provides the engineering community with a new design tool. Finally, self tapping screws as reinforcement have been studied and are shown to significantly improve the structural performance of RDC under vertical shear loading.

This thesis reports a detailed investigation into the use of the Shear Strength Reduction (SSR) method to determine factor of safety values in discontinuum models using the Universal Distinct Element Code. The SSR method depends on the definition of failure within the model and two different criteria were compared: the numerical unbalanced force definition and a more qualitative displacement-monitoring based method. A parametric study was first undertaken, using a simple homogeneous rock slope, with three different joint networks representing common kinematic states. Lessons learned from this study were then applied to a more complex case history used for validation of the SSR method. The discontinuum models allow for the failure surface to propagate based on constitutive models that better idealize the rockmass than simpler methods such as limit equilibrium (e.g. either method of slices or wedge solutions) and even numerical continuum models (e.g. finite difference, finite element). Joints are explicitly modelled and can exert a range of influences on the SSR result. Simple elasto-plastic models are used for both the intact rock and joint properties. Strain-softening models are also discussed with respect to the SSR method. The results presented highlight several important relationships to consider related to both numerical procedures and numerical input parameters. The case history was modelled similar to how a typical forward analysis would be undertaken: i.e. simple models with complexities added incrementally. The results for this case generally depict a rotational failure mode with a reduced factor of safety due to the presence of joints within the rockmass when compared to a traditional limit equilibrium analysis. Some models with large persistence of steeply dipping joints were able to capture the actual failure surface. Softening models were employed in order to mimic the generation and propagation of joints through the rockmass in a continuum; however, only discontinuum models using explicitly defined joints in the model were able to capture the correct failure surface.

Nonlinear microscopy has become an indispensable tool in the study of biological systems. It includes many nonlinear contrast mechanisms, each sensitive to different biological structures. However, interpretation of the images generated in nonlinear microscopy is a complex matter due to factors such as the structural complexity of the sample, phase relationships between the excitation beam and the detected signal and the nonlinear interactions in the focal volume of the microscope. This thesis contains a new theoretical and numerical framework that describes the focusing of an excitation beam in a nonlinear microscope, the nonlinear optical interactions with the material in the focal volume, and the resulting nonlinear optical signal in the far field. The framework is the first to include reflection and refraction of the excitation beam and nonlinear signals by an arbitrary number of interfaces in the focal volume, which is especially significant for the interpretation of third harmonic generation (THG). It also uses the chirp-z transform to speed up calculations by orders of magnitude compared to numerical integration techniques. The framework is used to investigate second harmonic generation (SHG) by collagen. Focusing effects alter polarization-dependent SHG measurements of collagen properties compared to the plane wave approximation, and this is verified experimentally. Furthermore, a technique of imaging the far field SHG radiation from collagen fibres is proposed, which can be used to extract the orientation of collagen fibres unambiguously. The framework is then applied to analyze the influence of interfaces on THG. Reflection effects at interfaces significantly affect THG, which leads to the development of a new super-resolution THG imaging technique based on backward-propagating THG. This super-resolution technique is experimentally demonstrated by imaging surface profiles with tens of nanometers resolution, which is the first time that such resolution is obtained in coherent nonlinear microscopy. Therefore, this imaging technique shows promise to become an important tool in high-resolution imaging of (biological) samples. The theoretical and numerical framework provides a foundation for future research on the origin of nonlinear microscopy signals. The new imaging techniques based on this framework have great potential in quantifying fibrillar structures and interfaces in biological samples.

Contractors and tunnelling engineers consistently seek to identify techniques and equipment to improve the efficiency and lower the cost of tunnelling projects. Based on the recent successes of rock slope characterization with laser scanning techniques, the author proposes 3D laser scanning (LiDAR) as a new tool for geotechnical assessment in drill and blast tunnels. It has been demonstrated that practical deployment of a phase-based LiDAR system at the face of an active tunnel heading is possible with a simple tripod setup. With data collection requiring only 5 minutes at the tunnel face, it was shown that this technique could be integrated into geotechnical evaluation without interruption of the excavation cycle. Following the successful scanning at two active tunnelling projects and two completed unlined tunnels, the research explored the applications of the data. With detailed geometric data of the heading as it advanced, the author identified applications of interest to the contractor/on-site engineer as well as the geotechnical engineer or geologist responsible for rockmass characterization. Operational applications included the extraction of information about tunnel geometry and installed support, while geomechanical information provided important elements of rockmass characterization. Building on the success of retrieving joint network information, the research investigated the potential for LiDAR-derived structural databases to be the basis for highly-representative 3D discrete element models. These representative models were found to be useful for back-analysis or as predictive tools for future tunnel design. The primary implications of the thesis are that a) LiDAR data collection at the face of a drill and blast tunnel operation is practical and potentially has great value, b) data extraction is possible for a wide range of applications, and c) that discontinuum stability analysis becomes a much more powerful tool with the integration of LiDAR data. The cumulative result of the work presented is a proposed workflow for integrating LiDAR into tunneling operations. / Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2010-09-22 19:38:49.401

Complex deformation processes observed in massive slow-moving, active, landslides are contributed to by topography, non-uniform shear surfaces, heterogeneous rockmass and shear zone strength characteristics, composite failure mechanisms and hydrogeology. This thesis provides a systematic means to account for geology, geomorphology and geomechanics when interpreting slope deformation processes. Significant contributions to the field of landslide geomechanics have been made by analyzing how spatially discriminated slope deformations are influenced by spatial variation of geological and geotechnical factors and temporal changes in piezometric levels. The Downie and Beauregard landslides are massive instabilities that have extensive histories of slope monitoring and observational assessment, and where detailed site investigations have been completed. A methodology has been developed for the interpretation of 3-dimensional shear zone geometries using spatial prediction algorithms complemented by sound engineering judgment. The applicability of this process to other spatial data, such as displacement or piezometric records and measurements of material properties is demonstrated. Composite landslide deformations have been analyzed for both Downie and Beauregard to characterize global slope behaviour and identify localized events. Furthermore, a new interpretation of landslide morphological regions at Downie is provided. The research presented in this thesis demonstrates the importance and value of 3-dimensional numerical modelling. A rigorous procedure to numerically simulate large landslides has been developed. This sophisticated method accounts for complex geometries, heterogeneous shear zone strength parameters, internal shears, interaction between discrete landslide zones and piezometric fluctuations. This advance in state-of-the-art landslide modelling provides an important tool for investigating dynamic landslide systems. Based on Downie and Beauregard field data numerical models have been calibrated to reproduce observed slope behaviour. The calibration process has provided insight on key factors controlling massive slope mechanics. Calibrated models are used to investigate how trigger scenarios may accelerate deformations at Downie and the effectiveness of a proposed slope drainage system at Beauregard. The ability to reproduce observed behaviour and forward test hypothesized changes to boundary conditions has valuable application in landslide hazard management. The capacity of decision makers to interpret large amounts of data, respond to rapid changes in a system and understand complex slope dynamics has been enhanced. / Thesis (Ph.D, Geological Sciences & Geological Engineering) -- Queen's University, 2010-09-24 14:13:43.605

A numerical model (BioClog) is developed to examine changes in key municipal solid waste (MSW) leachate characteristics and the porosity of porous media (clogging) as the leachate passes through the drainage layer of a leachate collection system (LCS). The model considers multiple-species reactive leachate transport through porous media. It simulates biofilm growth and loss, deposition of suspended particles, and precipitation of minerals on the surface of porous media. It is used to examine the long-term performance of both the granular porous media and nonwoven geotextiles in LCSs. Modelling of laboratory mesocosm cells filled with gravel usually used in landfills and permeated by landfill leachate shows encouraging agreement between the observed and measured effluent chemical oxygen demand (COD) and calcium concentrations as well as the gravel porosity within the saturated drainage layers. Studies of early generation LCSs involving finger (French) drain systems show that the finger drains are not effective at controlling leachate mounding within the landfill and the calculated leachate mound thicknesses agree well with observed field data. A numerical examination of the recent generation of LCSs, comprised of the granular drainage blanket and perforated drainage pipes, shows that an increase in grain size increases the service life and that increasing the spacing between collection pipes (i.e., the drainage path) decreases the service life of LCSs. Filter-separator layers between the waste and granular drainage layers are shown to increase the service life of LCSs. The modelling results indicate that the calculated clog mass within the saturated drainage layer is dominated by the inorganic material and the calculated service life of LCSs is dependent on the leachate strength examined. Finally, a new practical model for estimating the service life of LCSs is developed and calibrated against the data from the BioClog model. The simplified model could be used by the practicing engineers for estimating the service life and optimizing the design of LCSs in MSW landfills. / Thesis (Ph.D, Civil Engineering) -- Queen's University, 2012-04-26 14:03:22.666

The Amethyst hydro project was proposed on the West Coast of New Zealand as an answer to the increasing demand for power in the area. A previous hydro project in the area was deemed unviable to reopen so the current project was proposed. The scheme involves diverting water from the Amethyst Ravine down through penstocks in a 1040m tunnel and out to a powerhouse on the floodplain of the Wanganui River. The tunnel section of the scheme is the focus of this thesis. It has been excavated using drill and blast methods and is horseshoe shaped, with 3.5x3.5m dimensions. The tunnel was excavated into Haast Schist through its whole alignment, although the portal section was driven into debris flow material. The tunnel alignment and outflow portal is approximately 2km Southeast of the Alpine Fault, the right lateral thrusting surface expression of a tectonically complex and major plate boundary. The Amethyst Ravine at the intake portal is fault controlled, and this continuing regional tectonic regime has had an impact on the engineering strength of the rockmass through the orientation of defects. The rock is highly metamorphosed (gneissic in places) and is cut through with a number of large shears. Scanline mapping of the tunnel was completed along with re-logging of some core and data collection of all records kept during tunneling. Structural analysis was undertaken, along with looking at groundwater flow data over the length of the tunnel, in order to break the tunnel up into domains of similar rock characteristics and investigate the rockmass strength of the tunnel from first principles. A structural model, hydrological model and rockmass model were assembled, each showing the change in characteristics over the length of the tunnel. The data was then modeled using the 3DEC numerical modelling software. It was found that the shear zones form major structural controls on the rockmass, and schistosity changes drastically to either side of these zones. Schistosity in general steepens in dip up the tunnel and dip direction becomes increasingly parallel to the tunnel alignment. Water is linked to shear position, and a few major incursions of water (up to 205 l/s) can be linked to large (1.6m thick) shear zones. Modeling illustrated that the tunnel is most likely to deform through the invert, with movement also capable of occurring in the right rib above the springline and to a lesser extent in the left rib below the springline. This is due to the angle of schistosity and the interaction of joints, which act as cut off planes. The original support classes for tunnel construction were based on Barton’s Q-system, but due to complicated interactions between shears, foliations and joint sets, the designed support classes have been inadequate in places, leading to increased cost due to the use of supplementary support. Modeling has shown that the halos of bolts are insufficient due to the >1m spacing, which fails to support blocks which can be smaller than this in places due to the close spacing of the schistosity. It is recommended that a more broad support type be used in place of discreet solutions such as rock bolts, in order to most efficiently optimize the support classes and most effectively support the rock mass.

Shippagan Gully is a highly dynamic tidal inlet located on the Gulf of St-Lawrence near Le Goulet, New Brunswick. This tidal inlet is highly unusual due to the fact that the inlet has two open boundaries with phase lagged tidal cycles that drives flow through the inlet. Over the past few decades, the shipping activities through the inlet have been threatened due to the narrowing of the navigation channel caused by deposited sediment on the east side of the channel. Many engineering projects have been undertaken at Shippagan Gully in order to try and mitigate the deposition problem. However, these attempts have either been unsuccessful or the engineered structures have deteriorated over the years. This study uses the CMS-Flow and CMS-Wave numerical models to provide guidance concerning the response of the inlet to various potential interventions aimed at improving navigation safety.

The goal of this thesis is to improve our understanding of the Greenland ice sheet (GrIS) and how it responds to climate change. This was achieved using ice core records to infer elevation changes of the GrIS during the Holocene (11.7 ka BP to Present). The inferred elevation changes show the response of the ice sheet interior to the Holocene Thermal Maximum (HTM; 9-5 ka BP) when temperatures across Greenland were warmer than present. These ice-core derived thinning curves act as a new set of key constraints on the deglacial history of the GrIS. Furthermore, a calibration was conducted on a three-dimensional thermomechanical ice sheet, glacial isostatic adjustment, and relative sea-level model of GrIS evolution during the most recent deglaciation (21 ka BP to present). The model was data-constrained to a variety of proxy records from paleoclimate archives and present-day observations of ice thickness and extent.