This research characterizes the nature of fractures in Paleozoic and Mesozoic caprock seal analogs exposed in central and south-eastern Utah. The results of this research show evidence for fluid flow and mineralization in the subsurface as well as reactivation of fractures suggesting that the fractures act as a loci for fluid flow through time. The heterolithic nature of the caprock seals and meso-scale (cm to m) variability in fracture distributions and morphology highlight the strong link between the variation in material properties and the response to changing stress conditions. The variable connectivity of fractures and the changes in fracture density at the meso-scale plays a critical role in subsurface fluid flow. The presence or formation of new fractures can result in seal bypass systems, which can cause failure of hydrocarbon traps, CO2 geosequestration sites, waste and subsurface fluid repositories. An integrated approach of field, borehole geophysical, burial and stress history modeling, rock strength testing, and numerical modeling are used to understand the effects changing material properties, rock strength, and stress history have on sealing capacity. Simplified stress history models derived from burial history curves are combined with laboratory derived rock properties to understand the importance variations in rock properties and differential and effective mean stress have on the mechanical failure of fine-grained clastic sedimentary rocks. Burial history and rock strength data show that in units that experience similar burial depths and changing mechanical property exert a control on deformation type. Geomechanical models reveal changes in local strain magnitudes at locked mechanical interfaces, suggesting that elastic mismatch between layers results in differential strain distribution. Characterization of fracture patterns, rock strength variability and the modeled changes in subsurface strain distribution is especially important for understanding the response of low-­‐permeability rocks to changing stress in the subsurface, and is applicable to multiple geo-engineering scenarios such as exploitation of natural resources, waste disposal, and management of fluids in the subsurface. The analyses presented in this dissertation provide analog fracture data for fine-grained clastic rocks and a dataset for better understanding the importance of heterogeneity in low permeability rocks.

Cette étude s'inscrit dans le cadre de la modélisation distribuée à base physique des interactions entre processus de surface et de subsurface. Une nouvelle approche de modélisation, dite darcéenne multidomaine , est présentée. Les équations de Richards et de l'onde diffusive sont respectivement utilisées pour décrire le processus d'infiltration et de ruissellement. L'équation de l'onde diffusive est transformée en une équation de diffusion non linéaire similaire à l'équation de Richards. L'écoulement d'eau à la surface du sol est alors assimilé à un écoulement dans un milieu poreux aux propriétés particulières. Une couche de milieu poreux, appelée couche de ruissellement, est introduite dans le domaine de calcul. L'ensemble de la dynamique surface/subsurface est alors décrite dans un continuum darcéen par une seule équation de Darcy non linéaire avec des paramètres domaine-dépendants. Cela permet notamment d'imposer une continuité hydraulique entre l'eau de surface et l'eau de subsurface. Un modèle de transport permettant de s'attaquer à la problématique de la séparation d'hydrogramme est également implémenté. Le modèle développé est évalué à partir de cas tests classique de la littérature. Une analyse de sensibilité ainsi qu'une étude détaillée du ruissellement hortonien sont ensuite présentée. Enfin, l'expérience réalisée par l'IRD sur la parcelle de Thies au Sénégal est reproduite. Les résultats sont encourageants et laisse penser que l'approche de modélisation développée permet de reproduire correctement à petite échelle la dynamique fortement couplée des systèmes hydrologiques de type parcelle ou versants.

The sole purpose of every form of visual representation is to make something look believable. Even among abstract or conceptual representation, the purpose is to create something that within the defined visual language the audience will consider believable and accepted. In the field of computer generated representation there are numerous visual languages that have been developed throughout the years, attempting to solve different visualization or artistic problems. This thesis presents an alternative light transfer model for participating media focused on the intuitive control of the illumination data and the artistic value of the resulting image. The purpose is not focused on accurately modeling lights physical behavior and its interaction with the surfaces and elements. My thesis describes an artistic approach which aims to offer an organic and intuitive control of the glow and temperature of the effects of participating media and direct the value and hues through the surfaces. The system described in the thesis approximates light transfer through a given volume by calculating light contribution in the volume with discreet sampling and subsequently gathering these values to determine the diffuse scattering contribution for the volume. I will also discuss the assumptions made to allow such approximations, as well as how the intuitive control offered by the approach and these approximations allow new forms or representation and artistic direction.

Ethanol is used as fuel in neat form in some countries (Brazil and India) or blended with gasoline (Europe, Canada and the United States). The benefits of ethanol use include octane enhancement, a cleaner environment and a secure renewable energy supply. BTEX compounds (benzene, toluene, ethylbenzene, m-xylene, p-xylene and o-xylene) are aromatic hydrocarbons present in gasoline. The fate of these compounds in the environment is of great health concern due to their carcinogenic (benzene) and toxic properties, and due to their high solubility in water compared to the other gasoline hydrocarbons. Ethanol present in gasoline may affect BTEX degradation, in an event of a spill into the subsurface environment. To address the effects of ethanol on subsurface microorganisms, microbial activity and growth in the presence of ethanol (concentrations ranging 0 to 70% v/v) were assessed. Microcosms studies showed that ethanol at concentration ranging 0. 5 to3% (v/v) enhanced microbial activity and did not interfere inmicrobial growth at 10oC temperature, when another source of carbon was present (glucose). Ethanol at 0. 5% concentration enhanced microbial activity over water soluble gasoline components and R2A medium combined. Both microbialactivity and growth were not detected at ethanol concentrations equal and above 5%. Biodegradation study was conducted, in which subsurface material and ground water were exposed to BTEX and ethanol at 0. 5 and 1. 5% (v/v) concentration. The controls had BTEX alone and ethanol alone, sterile and nutrient-free. Total BTEX degradation was observed whenever ethanol was absent. Ethanol and BTEX were simultaneously degraded, however in microcosms containing 0. 5% ethanol, BTEX degradation was slowed, compared to microcosms without ethanol. Competition for inorganic nutrients was the major problem in slowed BTEX degradation in the presence of ethanol. In microcosms where 1. 5% ethanol was present, BTEX compounds and ethanol degradation were not observed.

Thermal stream loadings from both natural and anthropogenic sources have significant relevance with respect to ecosystem health and water resources management, particularly in the context of future climate change. In recent years, there has been an increase in field-based research directed towards characterizing thermal energy transport exchange processes that occur at the surface water/groundwater interface of streams. In spite of this effort, relatively little work has been performed to simulate these exchanges and elucidate their roles in mediating surface water temperatures and to simultaneously take into account all the pertinent hydrological, meteorological and surface/variably-saturated subsurface processes. To address this issue, HydroGeoSphere, a fully-integrated surface/subsurface flow and transport model, was enhanced to include fully-integrated thermal energy transport. HydroGeoSphere can simulate water flow, evapotranspiration, and advective-dispersive heat and solute transport over the 2D land surface and water flow and heat and solute transport in 3D subsurface variably-saturated conditions. In this work, the new thermal capabilities of HydroGeoSphere are tested and verified by comparing HydroGeoSphere simulation results to those from a previous subsurface thermal groundwater injection study, and also by simulating an example of atmospheric thermal energy exchange. A proof of concept simulation is also presented which illustrates the ability of HydroGeoSphere to simulate fully-integrated surface/subsurface thermal energy transport. High-resolution 3D numerical simulations of a well-characterized reach of the Pine River in Ontario, Canada are also presented to demonstrate steady-state thermal energy transport in an atmosphere-groundwater-surface water system. The HydroGeoSphere simulation successfully matched the spatial variations in the thermal patterns observed in the river bed, the surface water and the groundwater. Transient simulations of the high-resolution Pine River domain are also presented. Diurnal atmospheric conditions were incorporated to illustrate the importance of fluctuations in atmospheric parameters on the entire hydrologic regime. The diurnal atmospheric input fluxes were found to not only change the temperatures of the surface and subsurface throughout the cycle, but also the magnitude and direction of the transfer of thermal energy between the surface and subsurface. Precipitation events were also simulated for the Pine River domain using three different rainfall rates. The surface temperatures responded quickly to the rainfall events, whereas the subsurface temperatures were slower to respond in regions where infiltration was not significant. A thermal energy signal from the precipitation event was evident in the subsurface, and dissipated once the rainfall ceased. This indicates that temperature can potentially be used as a tracer for hydrograph separation. The potential of a thermal energy tracer for hydrograph separation was investigated using HydroGeoSphere simulations of the Borden rainfall-runoff experiment. These results matched both measured and previous simulation results using a bromide tracer. The hydrograph separation results from the thermal energy tracer were sensitive to temperature conditions in the subsurface, although this sensitivity reduced considerably when the precipitation event and subsurface temperatures were significantly different. The contribution of each atmospheric component to thermal energy transport was investigated using the Pine River and Borden examples. Each atmospheric component was individually neglected from the simulation of both sites to investigate their impact on thermal energy transport. The results show that longwave radiation dominates the atmospheric inputs for the Borden example, whereas shortwave radiation dominates in the Pine River example. This indicates that the atmospheric contributions to the thermal energy distribution are site-specific and cannot be generalized. In addition, these results indicate that the atmospheric contributions should not be ignored; measuring atmospheric data in the field is an important component in developing an accurate thermal energy transport model. The addition of thermal energy transport to HydroGeoSphere provides a valuable tool for investigating the impact of anthropogenic and non-anthropogenic changes to the atmospheric and hydrological thermal energy system. This computational framework can be used to provide quantitative guidance towards establishing the conditions needed to maintain a healthy ecosystem.

Riparian zones (RZ) are known to act as buffers, reducing the transfer of potentially harmful nutrients from agricultural fields to surface water bodies. However, many of the same processes in the subsurface that help to reduce this nutrient loading, may also be leading to greenhouse gas (GHG) production and emissions from these areas. Agricultural riparian zones in Southern Ontario are often characterized by a sloped topography, with the highest topographic position being closest to the field edge, decreasing towards an adjacent stream or other surface water body. This topographic variability, combined with lateral chemical inputs from both upland areas and the stream, is expected to cause variable hydrochemical environments throughout the RZ, which may therefore lead to variable N2O dynamics between upland, mid-riparian and lowland areas. The objectives of this study were to examine these spatial trends in N2O production and resulting emissions, as related to the hydrochemical environment in these three distinct zones. Objectives were achieved by instrumenting 6 sites across two transects running perpendicular from the agricultural field edge, towards the stream edge, analyzing for subsurface N2O, moisture and temperature, groundwater NO3, NH4, dissolved organic carbon (DOC), dissolved oxygen, and surface fluxes of N2O. Subsurface N2O concentrations and ground water nutrient concentrations displayed distinct spatial and temporal/seasonal trends in the three positions across the RZ, however N2O fluxes across the soil-atmosphere interface did not display strong or consistent spatial trends. There was a disconnect between the subsurface variables and the fluxes at the surface, in that N2O emissions did not reflect the N2O concentrations produced in the shallow soil profile (150 cm deep), nor were they significantly related to the geochemical environment at each position. The lack of visible spatial trends in N2O fluxes may have been due to an “oxic blanket” effect which may divide the surface from the subsurface soil profile. As N2O fluxes in this study (-0.28 to 1.3 nmol m-2 s-1) were within the range observed at other, similar study sites, the oxic blanket doesn’t appear to impede concentrations of N2O reaching the soil-atmosphere interface. This may suggest that the N2O released as a flux was being produced in the very shallow soil profile (0 – 5 cm), above the soil gas profile arrays installed at this site. Subsurface concentrations of N2O were fairly high at certain depths and times, which was not reflected in the fluxes. This may have resulted from nitrifier denitrification reducing N2O to N2 before it reached the surface, in aerobic zones above the water table. Another potential reason for the lack of connection between subsurface processes and surface emissions was the high heterogeneity observed across the RZ, which may have overshadowed potential differences between positions. Physical soil properties like porosity and bulk density across the RZ also potentially impacted the N2O movement through the soil profile, resulting in similar fluxes among positions, and over time. The missing connection between subsurface N2O concentrations, ground water nutrients, and the surface fluxes was not a hypothesized result, and requires further research and analysis for a better understanding of the production and consequent movement of N2O.

Ethanol is used as fuel in neat form in some countries (Brazil and India) or blended with gasoline (Europe, Canada and the United States). The benefits of ethanol use include octane enhancement, a cleaner environment and a secure renewable energy supply. BTEX compounds (benzene, toluene, ethylbenzene, m-xylene, p-xylene and o-xylene) are aromatic hydrocarbons present in gasoline. The fate of these compounds in the environment is of great health concern due to their carcinogenic (benzene) and toxic properties, and due to their high solubility in water compared to the other gasoline hydrocarbons. Ethanol present in gasoline may affect BTEX degradation, in an event of a spill into the subsurface environment. To address the effects of ethanol on subsurface microorganisms, microbial activity and growth in the presence of ethanol (concentrations ranging 0 to 70% v/v) were assessed. Microcosms studies showed that ethanol at concentration ranging 0. 5 to3% (v/v) enhanced microbial activity and did not interfere inmicrobial growth at 10oC temperature, when another source of carbon was present (glucose). Ethanol at 0. 5% concentration enhanced microbial activity over water soluble gasoline components and R2A medium combined. Both microbialactivity and growth were not detected at ethanol concentrations equal and above 5%. Biodegradation study was conducted, in which subsurface material and ground water were exposed to BTEX and ethanol at 0. 5 and 1. 5% (v/v) concentration. The controls had BTEX alone and ethanol alone, sterile and nutrient-free. Total BTEX degradation was observed whenever ethanol was absent. Ethanol and BTEX were simultaneously degraded, however in microcosms containing 0. 5% ethanol, BTEX degradation was slowed, compared to microcosms without ethanol. Competition for inorganic nutrients was the major problem in slowed BTEX degradation in the presence of ethanol. In microcosms where 1. 5% ethanol was present, BTEX compounds and ethanol degradation were not observed.

Thermal stream loadings from both natural and anthropogenic sources have significant relevance with respect to ecosystem health and water resources management, particularly in the context of future climate change. In recent years, there has been an increase in field-based research directed towards characterizing thermal energy transport exchange processes that occur at the surface water/groundwater interface of streams. In spite of this effort, relatively little work has been performed to simulate these exchanges and elucidate their roles in mediating surface water temperatures and to simultaneously take into account all the pertinent hydrological, meteorological and surface/variably-saturated subsurface processes. To address this issue, HydroGeoSphere, a fully-integrated surface/subsurface flow and transport model, was enhanced to include fully-integrated thermal energy transport. HydroGeoSphere can simulate water flow, evapotranspiration, and advective-dispersive heat and solute transport over the 2D land surface and water flow and heat and solute transport in 3D subsurface variably-saturated conditions. In this work, the new thermal capabilities of HydroGeoSphere are tested and verified by comparing HydroGeoSphere simulation results to those from a previous subsurface thermal groundwater injection study, and also by simulating an example of atmospheric thermal energy exchange. A proof of concept simulation is also presented which illustrates the ability of HydroGeoSphere to simulate fully-integrated surface/subsurface thermal energy transport. High-resolution 3D numerical simulations of a well-characterized reach of the Pine River in Ontario, Canada are also presented to demonstrate steady-state thermal energy transport in an atmosphere-groundwater-surface water system. The HydroGeoSphere simulation successfully matched the spatial variations in the thermal patterns observed in the river bed, the surface water and the groundwater. Transient simulations of the high-resolution Pine River domain are also presented. Diurnal atmospheric conditions were incorporated to illustrate the importance of fluctuations in atmospheric parameters on the entire hydrologic regime. The diurnal atmospheric input fluxes were found to not only change the temperatures of the surface and subsurface throughout the cycle, but also the magnitude and direction of the transfer of thermal energy between the surface and subsurface. Precipitation events were also simulated for the Pine River domain using three different rainfall rates. The surface temperatures responded quickly to the rainfall events, whereas the subsurface temperatures were slower to respond in regions where infiltration was not significant. A thermal energy signal from the precipitation event was evident in the subsurface, and dissipated once the rainfall ceased. This indicates that temperature can potentially be used as a tracer for hydrograph separation. The potential of a thermal energy tracer for hydrograph separation was investigated using HydroGeoSphere simulations of the Borden rainfall-runoff experiment. These results matched both measured and previous simulation results using a bromide tracer. The hydrograph separation results from the thermal energy tracer were sensitive to temperature conditions in the subsurface, although this sensitivity reduced considerably when the precipitation event and subsurface temperatures were significantly different. The contribution of each atmospheric component to thermal energy transport was investigated using the Pine River and Borden examples. Each atmospheric component was individually neglected from the simulation of both sites to investigate their impact on thermal energy transport. The results show that longwave radiation dominates the atmospheric inputs for the Borden example, whereas shortwave radiation dominates in the Pine River example. This indicates that the atmospheric contributions to the thermal energy distribution are site-specific and cannot be generalized. In addition, these results indicate that the atmospheric contributions should not be ignored; measuring atmospheric data in the field is an important component in developing an accurate thermal energy transport model. The addition of thermal energy transport to HydroGeoSphere provides a valuable tool for investigating the impact of anthropogenic and non-anthropogenic changes to the atmospheric and hydrological thermal energy system. This computational framework can be used to provide quantitative guidance towards establishing the conditions needed to maintain a healthy ecosystem.

Riparian zones (RZ) are known to act as buffers, reducing the transfer of potentially harmful nutrients from agricultural fields to surface water bodies. However, many of the same processes in the subsurface that help to reduce this nutrient loading, may also be leading to greenhouse gas (GHG) production and emissions from these areas. Agricultural riparian zones in Southern Ontario are often characterized by a sloped topography, with the highest topographic position being closest to the field edge, decreasing towards an adjacent stream or other surface water body. This topographic variability, combined with lateral chemical inputs from both upland areas and the stream, is expected to cause variable hydrochemical environments throughout the RZ, which may therefore lead to variable N2O dynamics between upland, mid-riparian and lowland areas. The objectives of this study were to examine these spatial trends in N2O production and resulting emissions, as related to the hydrochemical environment in these three distinct zones. Objectives were achieved by instrumenting 6 sites across two transects running perpendicular from the agricultural field edge, towards the stream edge, analyzing for subsurface N2O, moisture and temperature, groundwater NO3, NH4, dissolved organic carbon (DOC), dissolved oxygen, and surface fluxes of N2O. Subsurface N2O concentrations and ground water nutrient concentrations displayed distinct spatial and temporal/seasonal trends in the three positions across the RZ, however N2O fluxes across the soil-atmosphere interface did not display strong or consistent spatial trends. There was a disconnect between the subsurface variables and the fluxes at the surface, in that N2O emissions did not reflect the N2O concentrations produced in the shallow soil profile (150 cm deep), nor were they significantly related to the geochemical environment at each position. The lack of visible spatial trends in N2O fluxes may have been due to an “oxic blanket” effect which may divide the surface from the subsurface soil profile. As N2O fluxes in this study (-0.28 to 1.3 nmol m-2 s-1) were within the range observed at other, similar study sites, the oxic blanket doesn’t appear to impede concentrations of N2O reaching the soil-atmosphere interface. This may suggest that the N2O released as a flux was being produced in the very shallow soil profile (0 – 5 cm), above the soil gas profile arrays installed at this site. Subsurface concentrations of N2O were fairly high at certain depths and times, which was not reflected in the fluxes. This may have resulted from nitrifier denitrification reducing N2O to N2 before it reached the surface, in aerobic zones above the water table. Another potential reason for the lack of connection between subsurface processes and surface emissions was the high heterogeneity observed across the RZ, which may have overshadowed potential differences between positions. Physical soil properties like porosity and bulk density across the RZ also potentially impacted the N2O movement through the soil profile, resulting in similar fluxes among positions, and over time. The missing connection between subsurface N2O concentrations, ground water nutrients, and the surface fluxes was not a hypothesized result, and requires further research and analysis for a better understanding of the production and consequent movement of N2O.

Estuarine wetlands and salt marshes are fundamentally driven by variations in freshwater inflow. In semi-arid salt marshes, such as the Nueces River Delta, TX, the stochastic nature of freshwater inflow events exposes resident organisms to a wide range of environmental conditions. In this study, we investigate (1) the relative importance of environmental variables on porewater salinity and (2) determination of freshwater inflow needs based on the response of emergent plants to salinity variations. Porewater salinity variations were tracked on a continuous basis with deployed conductivity sensors and on a synoptic basis with soil water extracts. We found that spatial patterns of porewater salinity were characterized by a high degree of variability in creekbank areas (23.8 ± 7.68) relative to interior marsh areas (44.2 ± 3.4). Our observations were used to test a simple model capable of predicting porewater salinities based on environmental variables. Both empirical measurements and model simulations indicated that semiannual tides play a critical role in controlling porewater flushing from precipitation and freshwater inflow events. Estimation of freshwater inflow needs for the Nueces Delta proceeded in two steps. First, we examined the response of three common emergent plants species (Borrichia frutescens, Spartina alterniflora, and Salicornia virginica) to variations in salinity. The abundance of one species in particular (S. alterniflora) was tightly coupled to salinity variations whereby salinities exceeding 25 ± 5 resulted in dramatic declines in coverage. Next, the relationship between freshwater inflow and porewater salinity was examined with respect to the salinity “tolerance” of S. alterniflora. Estimated inflow needs based on maintenance of substantial (> 20%) S. alterniflora coverage was comparable to both previous inflow needs estimates and mean annual inflows observed over the course of the study. The results of this study suggest that S. alterniflora abundance provides a reliable indicator of overall estuarine hydrological condition in the Nueces Delta. / text