As human activity along coastlines increase, degradation and destruction of coastal marine ecosystems around the globe will increase at an alarming rate. In an effort to mitigate degradation and destruction of coastal marine ecosystems, artificial reefs have been used in restoration and enhancement projects. As artificial reefs are the main method of restoring diversity to a degraded area, it is important to know the mechanisms that drive marine community assembly and diversity on those reefs. Understanding community assembly patterns of foundational species, in particular, may provide insight to community assembly patterns at higher trophic levels. Subtidal macroalgae are commonly seen as foundational species in marine environments and both deterministic and stochastic processes play a role in their assembly. Environmental gradients, which are deterministic processes, play a significant role in structuring subtidal macroalgae communities. Depth, which is negatively correlated with light, is the main driver structuring subtidal macroalgal communities, however, other gradients such as water flow, and distance to a propagule source also impact their assembly. This study sought to determine which environmental gradients play a prominent role in subtidal macroalgal community assembly. To study subtidal macroalgal community assembly, 92 artificial reef units called Reef Balls were deployed east of the Ogden Point Breakwater in Victoria, BC in June 2009. Two years passed to allow for macroalgal growth and early successional processes to occur prior to sampling the communities on thirty Reef Balls via underwater collection in July 2011. Algae were sorted by genus and dry weight was measured. To determine effects of environmental gradients on community assembly light, depth, water flow, distance to the nearest Reef Ball and distance to the breakwater were measured at each Reef Ball. A redundancy analysis revealed that depth was the most significant environmental gradient shaping algae communities and had the greatest effect on upper canopy algae. Spatial plots reveal a depth and coastline zonation of algae genera comprising the canopy. While depth was found to significantly structure algae genera found in the canopy, there was a high degree of unexplained variation in the model. This suggests that unmeasured variables such as colonization and priority effects may be driving algal community structure in the lower canopy. Differences in community structure between upper and lower canopy reveal that multiple mechanisms are responsible for shaping subtidal algal communities. Further study is required to determine the importance of stochastic colonization events and priority effects. / Graduate / 0329 / vmucciar@uvic.ca

An experimental program is designed to study the salient features of separated and reattached flows in pressure gradients generated in asymmetric diverging and converging channels. The channels comprised a straight flat floor and a curved roof that was preceded and followed by straight parallel walls. Reference measurements were also made in a parallel-wall channel to facilitate the interpretation of the pressure gradient flows. A transverse square rib located at the start of convergence/divergence was used to create separation inside the channels. In order to simplify the interpretation of the relatively complex separated and reattached flows in the asymmetric converging and diverging channels, measurements were made in the plain converging and diverging channel without the rib on the channel wall. All the measurements were obtained using a high resolution particle image velocimetry technique. The experiments without the ribs were conducted in the diverging channel at Reynolds number based on half channel depth (Reh) of 27050 and 12450 and in the converging channel at Reh = 19280. For each of these three test conditions, a high resolution particle image velocimetry technique (PIV) was used to conduct detailed velocity measurements in the upstream parallel section, within the converging and diverging section, and downstream of the converging and diverging sections. From these measurements, the boundary layer parameters and profiles of the mean velocities, turbulent quantities as well as terms in the transport equations for turbulent kinetic energy and Reynolds stresses were obtained to document the effects of pressure gradient on the flow. In the adverse pressure gradient case, the turbulent quantities were enhanced more significantly in the lower boundary layer than the upper boundary layer. On the other hand, favorable pressure gradient attenuated the turbulence levels and the effect was found to be similar on both the upper and the lower boundary layers. For the separated and reattached flows in the converging, diverging and parallel-wall channels at Reh = 19440, 12420 and 15350, respectively. The Reynolds number based on the approach velocity and rib height was Rek  2700. From these measurements, profiles of the mean velocities, turbulent quantities and the various terms in the transport equations for turbulent kinetic energy and Reynolds stresses were also obtained. The flow dynamics in the upper boundary layer in the separated region and the early stages of flow redevelopment were observed to be insensitive to the pressure gradients. In the lower boundary layer, however, the flow dynamics were entirely dominated by the separated shear layer in the separated region as well as the early region of flow redevelopment. The effects of the separated shear layer diminished in the redevelopment region so that the dynamics of the flow were dictated by the pressure gradients. The proper orthogonal decomposition (POD) was applied to educe the dominant large scale structures in the separated and reattached flows. These dominant scales were used to document structural differences between the canonical upstream flow and the flow field within the separated and redeveloping region. The contributions of these dominant structures to the dynamics of the Reynolds normal and shear stresses are also presented and discussed. It was observed that the POD recovers Reynolds shear stress more efficiently than the turbulent kinetic energy. The reconstruction reveals that large scales contribute more to the Reynolds shear stress than the turbulent kinetic energy.

As human activity along coastlines increase, degradation and destruction of coastal marine ecosystems around the globe will increase at an alarming rate. In an effort to mitigate degradation and destruction of coastal marine ecosystems, artificial reefs have been used in restoration and enhancement projects. As artificial reefs are the main method of restoring diversity to a degraded area, it is important to know the mechanisms that drive marine community assembly and diversity on those reefs. Understanding community assembly patterns of foundational species, in particular, may provide insight to community assembly patterns at higher trophic levels. Subtidal macroalgae are commonly seen as foundational species in marine environments and both deterministic and stochastic processes play a role in their assembly. Environmental gradients, which are deterministic processes, play a significant role in structuring subtidal macroalgae communities. Depth, which is negatively correlated with light, is the main driver structuring subtidal macroalgal communities, however, other gradients such as water flow, and distance to a propagule source also impact their assembly. This study sought to determine which environmental gradients play a prominent role in subtidal macroalgal community assembly. To study subtidal macroalgal community assembly, 92 artificial reef units called Reef Balls were deployed east of the Ogden Point Breakwater in Victoria, BC in June 2009. Two years passed to allow for macroalgal growth and early successional processes to occur prior to sampling the communities on thirty Reef Balls via underwater collection in July 2011. Algae were sorted by genus and dry weight was measured. To determine effects of environmental gradients on community assembly light, depth, water flow, distance to the nearest Reef Ball and distance to the breakwater were measured at each Reef Ball. A redundancy analysis revealed that depth was the most significant environmental gradient shaping algae communities and had the greatest effect on upper canopy algae. Spatial plots reveal a depth and coastline zonation of algae genera comprising the canopy. While depth was found to significantly structure algae genera found in the canopy, there was a high degree of unexplained variation in the model. This suggests that unmeasured variables such as colonization and priority effects may be driving algal community structure in the lower canopy. Differences in community structure between upper and lower canopy reveal that multiple mechanisms are responsible for shaping subtidal algal communities. Further study is required to determine the importance of stochastic colonization events and priority effects. / Graduate / 0329 / vmucciar@uvic.ca

Thermochemical Nanolithography (TCNL) is a scanning probe microscope (SPM) based lithographic technique modified with a semi-conducting cantilever. This cantilever is capable of locally heating a surface and with a well-engineered substrate, this spatially confined heating induces chemical or physical transformation. While previous works focused primarily on proof of principle and binary studies, there is limited research on controlling and understanding the underlying mechanisms governing the technique. In this thesis, a chemical kinetics model is employed to explain the driving mechanisms and to control the technique. The first part focuses on studying surface reactions. By coupling a thermally activated organic polymer with fluorescence microscopy, the chemical kinetics model is not only verified but also applied to control the surface reactions. The work is then expanded to include 3D effects, and some preliminary results are introduced. Finally, applications are discussed.

No description available.

The Kim and Chan experiment in 2004 gave the first experimental evidence of a possible supersolid state. Even though the origin of this state is not clear yet, several experimental and theoretical investigations suggest defects are responsible for this curious phase. We have used heat pulses and thermal quenching to study pressure gradients and annealing mechanisms in solid 4He crystals. Large pressure gradients exist in crystals grown at constant volume. These can be enhanced by phase transitions, thermal quenching or by partial melting. Annealing reduces defect densities and hence pressure gradients in crystals. Our measurements show that the pressure at different points in a crystal can behave differently, even if there is little change in the crystals average pressure. We measured the activation energy that is associated with the annealing process.

This study focused on an invasive riparian reed grass, Arundo donax L., a clonal plant of the family Poaceae that is widely distributed in North America. Water availability, including water taken up from the roots locally or transported from the neighboring ramets, may affect the performance of A. donax in riparian zones. The first objective was to find out how moisture gradients affected the performance of A. donax in riparian zones. I measured leaf photosynthetic rate, leaf δ13C ratio, and plant growth-related parameters across two summer growing seasons at four transects perpendicular to the water course on the Rio Grande in South Texas. The second objective was to find out whether physiological integration existed in A. donax and how resource sharing, if any, affected plant growth. A rhizome severing experiment was conducted on five paired plots to compare growth-related parameters between plots with rhizomes severed and intact at 3, 7, and 11 weeks after treatment. Heavy water (δ 2H ~1800‰) was applied on three 1-m2 area over 3 successive days and rhizome samples were collected beyond the watering zone after 5, 24, and 48 hours of last watering. At short-term scales, A. donax performance was adversely affected by both drought and inundated conditions; over longer time scales, plant performance decreased as water availability declined in general, but biomass and stem density were similar across moisture gradients. I also found evidence of physiological integration in A. donax. Water was transported through interconnected rhizomes at least 3.5 m; transport distances averaged 1.67 m. Rhizome severing stimulated higher ramet production initially but over longer periods produced shorter thinner stems with lower flood tolerance. However, after 11 weeks of re-growth, plot-level biomass was similar between plots with severed and intact rhizomes. These results suggest that performance of A. donax is affected by water availability in riparian zones; however, clonal plant plasticity, water use efficiency, and clonal integration ameliorate impacts of water stress on the performance of A. donax. Such traits enhance its resource use, which could potentially increase competitive ability rate of establishment, and extent of this invasive species in heterogeneous riparian environments.

We present a novel method for building 3D models from a user sketch. Given a 2D sketch as input, the approach aligns and deforms a chosen 3D template model to match the sketch. This is guided by a set of user-specified correspondences and an algorithm that deforms the 3D model to match the sketched profile. Our primary contribution is related to fitting the 3D deformable geometry to the 2D user sketch. We demonstrate our technique on several examples.

The effect of redistribution of artificial stock waters from a boredrain to pipes and troughs on the vegetation and soil resources was investigated from December 1994 to October 1998 in a sheep paddock in the semi-arid mulga woodlands of south west Queensland, eastern Australia. The study examined 1) the effect of changing water distribution on the distribution of understorey biomass, sheep, cattle and macropods at the paddock scale; 2) patterns in herbivores, vegetation and soil out from the boredrain and change through time following water redistribution; 3) patterns in herbivores, vegetation and soil out from the new troughs and change through time following water redistribution; and 4) the relative effects of native versus domestic stock on piosphere development out from a trough. Landscape zone and season were major drivers of vegetation and soil dynamics and patterns in this mulga landsystem. At the paddock scale, biomass and woody cover patterns were consistent with historical grazing gradients out from the boredrain, semipermanent waters and previous and current fencelines. There was a high degree of temporal variability in herbivore distribution patterns, not just related to changing water distribution. The native herbivores which presumably have evolved in this system were more likely to be correlated with forage resources than water at the scale of this study. This is in contrast to sheep whose spatial selection of feeding sites was partly influenced by non alimentary factors such as distance to waters, winds and fences, but largely unexplained. While sheep distribution was no longer correlated with distance from the boredrain following piping at the paddock scale, there was no evidence that 1) herbivores were focusing grazing activities around new troughs and 2) that vegetation patterns have changed following water redistribution. The boredrain had distinct gradients in vegetation and soil surface condition associated with it that persisted following rainfall and the lightening and then removal of domestic stock. Gradients in functional plant composition, diversity indices, grass cover and soil stability, revealed zones of reduced production potential parallel to the drain. Following closure of the drain herbivore activity rapidly declined, but there was little evidence of rehabilitation during three years of above average rainfall. Reassessment of the site at 5 yearly intervals over a period in excess of 20 years would better tell the story of change post-drain. Current data suggests the drain induced gradient will continue to persist for many years, providing a ‘ghost of waters past’ In the first two and a half years following changeover from the boredrain to point waters, there was little change to the natural landscape patterns in soil and vegetation out from the southern troughs. Patterns in soil and vegetation around troughs initially reflected patterns of geomorphic zone and tree and shrub distribution. While there was an increase in stocking intensity immediately around the new troughs, there was little evidence of a vegetation and soil response to this increased stocking activity. However increased soil erosion and restricted shrub recruitment close to the troughs perhaps signal the beginnings of change out from the new troughs through time. Comparison between prevailing total grazing pressure, kangaroo only grazing and no large herbivore grazing, found that removal of stock had the effect of dramatically increasing the rate of woody cover change over the period of the study. In contrast the proportion of unpalatable plants increased most at the highest stocking rate with both domestic and native herbivores present. Soil surface condition and plant species also responded to exclosure from domestic stock, indicating that resting paddocks has the potential to improve soil and vegetation condition providing macropod densities are at similar levels to when stock are present. Given that the rehabilitation of degraded areas adjacent to boredrains is unlikely at least in the short term, and that little change has occurred out from new troughs, it is likely that there will be little net change in degraded land as a result of piping bores in mulga landscapes with the level of water availability of this study. Factors likely to influence piosphere development and ecological and management implications for the Boredrain Replacement Program are identified.

La compréhension du transfert des polluants et leurs mobilités dans les sols permet une meilleure approche des risques environnementaux. Elle nécessite une bonne caractérisation du substrat recevant le polluant, la connaissance de l’état de spéciation du polluant et des mécanismes de rétention mis en place : sorption, précipitation, complexation. Les mécanismes de transfert de l’arsenic (As) et du chrome (Cr) sur un substrat naturel sont étudiés dans le cadre de cette thèse. Le substrat, issu de la formation géologique de Gault, est composé majoritairement de quartz, mica et d’argile (Illite, Smectite, Kaolinite) avec la présence d’oxyde de fer sous forme de goethite. La méthodologie expérimentale repose sur une gamme de tests variée de type batch de sorption/désorption, DGT (Diffusif Gradient in Thin film), extractions séquentielles, colonnes. Un modèle géochimique de complexation de surface (MCS) est également mis en place pour approfondir la compréhension de la sorption d’As et du Cr. Les résultats montrent une rétention importante d’As (V) via des mécanismes de sorptions spécifiques sur les argiles et les oxydes de fer du substrat ainsi qu’une forte sensibilité de la sorption à la présence de phosphates dans le milieu. La sorption de Cr (VI) sur le substrat est faible. La rétention de Cr est donc soumise au processus de réduction de Cr (VI) en Cr (III), Cr (III) étant thermodynamiquement stable sous forme précipité dans une large gamme de pH-Eh. L’utilisation du MCS comme outil prédictif nécessite la levée de certains freins, liés aux systèmes complexes, mais permet de confirmer les hypothèses émissent à partir des résultats expérimentaux. / The understanding of the transfer of pollutants from solution to soil and their mobility improve environmental risks assessment. A detailed substrate characterization, good knowledge of speciation state and mechanisms of retention (sorption, precipitation, complexation) is necessary. Transfer mechanisms of arsenic (As) and chromium (Cr) on a natural substrate are studied in this thesis. The substrate,extracted from the Gault geological formation, is mainly composed of quartz, mica and clay (illite, smectite, kaolinite) and we noted a little part of iron oxide as goethite. The experimental methodology is based on a wide range of test: sorption and desorption batch, DGT (diffusive gradient in Thin Film), sequential extractions, columns. A geochemical model surface complexation (MSC) is constructed to access of the speciation of As and Cr on aqueous and solid phase. The results show a significant retention of As (V) on clay and goethite with specific sorption and a high sensitivity of As sorption in presence of phosphate. Sorption of Cr (VI) on the substrate is low. Retention of Cr depends on the reduction process of Cr (VI) to Cr (III), whose precipitates are thermodynamically stables on a wide range of pH-Eh. Use of MSC as a predictive tool requires further investigation but MCS can confirms the assumptions from experimental results.