Electronic Structure Theory has led to a variety of developments and applications. In the Nooijen group the focus is on the development and use of Coupled Cluster based approaches. Coupled Cluster is a very strong and accurate approach to the quantum mechanical problem. The research results presented in the thesis testify to the Similarity Transformed Equation of Motion Coupled Cluster (STEOM-CC) for being a very accurate and yet computationally inexpensive approach for excited states. This study reveals new features about STEOM and provides promise regarding future improvement in the methodology. STEOM can be used as the first step in the construction of the Vibronic model, which is a strong tool to move to paradigms beyond the Born-Oppenheimer approximation. Spin-Orbit Coupling (SOC) is a very important ingredient required to study relativistic phenomena and its quantum mechanical implementation for many body systems is not straightforward. The most widely used SOC operator in Chemical Physics is the Breit-Pauli operator, which requires employing non-trivial approximations to the Dirac equation to adapt the theory to many body systems. The integration of electronic structure approaches, Vibronic Coupling, and SOC is essential to study the phenomenon of intersystem crossing (transition between spin states) in fine detail. In this thesis a computational benchmark of STEOM is discussed, while the frameworks of Vibronic Coupling and Spin-Orbit Coupling (SOC) are considered on a theoretical level.

Marine ecosystem-based management requires end to end models, which are models capable of representing the entire ecosystem including physical, chemical and biological processes, anthropogenic activities, and multiple species with different sizes, life histories and from different trophic levels. To adequately represent ecosystem dynamics in shallow coastal regions, end-to-end models may need to include macrobiota species (wild and aquacultured) and may have to allow feedbacks (i.e. two-way coupling) between macrobiota and planktonic ecosystem dynamics. This is because the biomass of macrobiota can locally exceed the biomass of plankton, thus influencing the distribution of planktonic ecosystem tracers and altering the overall food web structure. Here, I describe a hybrid (Eulerian/Individual-Based) ecosystem framework, implemented in the Regional Ocean Modeling System (ROMS), a state-of-the-art 3-D ocean circulation model. The framework was applied to a model of a synthetic embayment containing seagrass, rockweed and kelp beds, a wild oyster reef, a mussel ranch and a fish farm. I found that two-way coupling is essential to reproduce expected spatial patterns of all variables and to conserve mass in the system. I also developed a shellfish ecophysiology model (SHELL E) and compared its results against water samples collected over 5 years in Ship Harbour, a fjord with mussel aquaculture in Nova Scotia, Eastern Canada. Also, from a high-resolution bio-optical survey of the fjord, I found that mussels decrease phytoplankton biomass inside the farm, but also cause a bloom of phytoplankton outside the farm. Using ROMS/SHELL-E, I determined that the increase of phytoplankton around the farm is caused by the waste products of the farmed bivalves, which have a fertilization effect, enhancing phytoplankton production outside the farm during nutrient-limited and light-replete conditions (i.e. late spring to late fall in Ship Harbour). The main conclusion of this thesis is that—in shallow coastal regions—ecosystem models must represent bilateral interactions between macrobiota and physical-planktonic dynamics, in a spatially-explicit setting, to adequately represent mass flows and ecosystem dynamics. The hybrid end-to-end modelling system provides a computationally efficient framework for describing these interactions and, through careful comparisons against observations, can be a powerful tool to test hypotheses and generate insights into coastal ecosystems.

In insects, ecdysis is an important feature of growth and development and is tightly controlled by a variety of neuropeptides. In holometabolous insects, crustacean cardioactive peptide (CCAP) is one of many factors that regulate ecdysis behaviours; however, not much is known about the control of ecdysis in hemimetabolous insects. In this thesis, the CCAP-signaling pathway is shown to be essential for successful ecdysis in the hemimetabolous insect, Rhodnius prolixus. The cDNA sequence of the CCAP gene has been cloned from the R. prolixus central nervous system (CNS) and the functional role of CCAP as a neuromodulator/neurotransmitter demonstrated. Specifically, the expression of RhoprCCAP in CNS neurons producing extensive CCAP-like immunoreactive processes within the neuropile indicates that CCAP plays central roles in coordination of other neurons. RhoprCCAP also acts as a neurohomone/neuromodulator released peripherally to coordinate many tissues. Thus, CCAP-like immunoreactive processes are found in neurohemal sites and also on peripheral tissues. The RhoprCCAP receptor (RhoprCCAPR) has been cloned and shown to be a G-protein coupled receptor (GPCR). RhoprCCAPR expression is observed in the CNS and certain peripheral tissues of R. prolixus. Also, CCAP stimulates hindgut contractions and increases the heartbeat rate in a dose-dependent manner. The involvement of CCAP in R. prolixus ecdysis has been investigated. Up-regulation of the RhoprCCAP transcript in the CNS and the RhoprCCAP receptor (RhoprCCAPR) transcript in the CNS and specific peripheral tissues was observed immediately prior to ecdysis. Also, decreasing staining intensity of CCAP-like immunoreactivity in neurons immediately following ecdysis indicates the release of CCAP during ecdysis. The critical importance of the CCAP-signalling pathway was further demonstrated by knockdown of the RhoprCCAP and RhoprCCAPR transcripts utilizing double stranded RNA interference. Insects with these transcripts knocked down have high mortality (up to 84%), typically at the expected time of ecdysis, or have ecdysis extremely delayed. Taken together, this thesis demonstrates that RhoprCCAP plays a crucial role in regulating ecdysis behaviours in R. prolixus, and clearly shows the conserved nature of the CCAP-signaling pathway in ecdysis for both holometabolous and hemimetabolous insects.

A growing demand for more detailed modeling of subsurface physics as ever more challenging reservoirs - often unconventional, with significant geomechanical particularities - become production targets has moti-vated research in coupled flow and geomechanics. Reservoir rock deforms to given stress conditions, so the simplified approach of using a scalar value of the rock compressibility factor in the fluid mass balance equation to describe the geomechanical system response cannot correctly estimate multi-dimensional rock deformation. A coupled flow and geomechanics model considers flow physics and rock physics simultaneously by cou-pling different types of partial differential equations through primary variables. A number of coupled flow and geomechanics simulators have been developed and applied to describe fluid flow in deformable po-rous media but the majority of these coupled flow and geomechanics simulators have limited capabilities in modeling multiphase flow and geomechanical deformation in a heterogeneous and fractured reservoir. In addition, most simulators do not have the capability to simulate both coarse and fine scale multiphysics. In this study I developed a new, fully implicit multiphysics simulator (TAM-CFGM: Texas A&M Coupled Flow and Geomechanics simulator) that can be applied to simulate a 2D or 3D multiphase flow and rock deformation in a heterogeneous and/or fractured reservoir system. I derived a mixed finite element formu-lation that satisfies local mass conservation and provides a more accurate estimation of the velocity solu-tion in the fluid flow equations. I used a continuous Galerkin formulation to solve the geomechanics equa-tion. These formulations allowed me to use unstructured meshes, a full-tensor permeability, and elastic stiffness. I proposed a numerical upscaling of the permeability and of the elastic stiffness tensors to gener-ate a coarse-scale description of the fine-scale grid in the model, and I implemented the methodology in the simulator. I applied the code I developed to the simulation of the problem of multiphase flow in a fractured tight gas system. As a result, I observed unique phenomena (not reported before) that could not have been deter-mined without coupling. I demonstrated the importance and advantages of using unstructured meshes to effectively and realistically model a reservoir. In particular, high resolution discrete fracture models al-lowed me to obtain more detailed physics that could not be resolved with a structured grid. I performed numerical upscaling of a very heterogeneous geologic model and observed that the coarse-scale numerical solution matched the fine scale reference solution well. As a result, I believed I developed a method that can capture important physics of the fine-scale model with a reasonable computation cost.

This paper presents modifications to two widely used numerical groundwater flow models in an effort to improve upon the interaction between a well of finite length and conductivity with the surrounding formation. The first objective is to discard the common assumptions about flux- or head-based boundary conditions along the well screen by coupling pipe flow hydraulics and groundwater flow. The second objective is to avoid restricting the wellbore hydraulics to a single flow regime. Five flow regimes (laminar through rough-turbulent), based on Reynolds number and pipe roughness, are considered. The modifications are integrated into the highly versatile, well-documented and well-tested models HydroGeoSphere (finite-element/finite-difference) and USGS MODFLOW (finite-difference). Verification of the algorithm and code and is performed by comparing results to: 1) the idealized, analytical Theis solution; 2) the original, unmodified code; and 3) the results of a third party numerical solution that also accounts for variable frictional wellbore losses. Results highlight the inadequacy of either a uniform flux or a uniform head assumption along the wellbore. The solution also tends to produce much steeper hydraulic gradients in those portions of the aquifer nearest the pump intake than have previously been predicted. Systems most affected by in-well hydraulic losses include those for which well screen is long, pumping rate is large, pipe diameter is small, pipe roughness is large (either through design or aging) and aquifer conductivity is high. Improved modeling of the non-linear hydraulic conditions within the well screen can particularly influence the interpretation of wellbore flowmeter and tracer tests, leading to more precise knowledge of the variation of local aquifer hydraulic conductivity along well screens. Aquifer drawdown curves, solute transport and inflow velocities will also be influenced, which can impact capture zones and remediation costs. Given that the solution is incorporated within the HydroGeoSphere and MODFLOW models, it presents the additional advantage over existing approaches of offering a wide range of modeling capabilities, such as three-dimensional flow, arbitrary well inclination and surface-subsurface flow integration. / Thesis (Master, Civil Engineering) -- Queen's University, 2008-01-04 17:27:50.629

Facile procedures based on hyphenated ion-exchange chromatography (IEC) and inductively coupled plasma mass spectrometry (ICP-MS) were developed to determine conditional stability constants, speciate chromium species and investigate the reduction of Cr(VI). 1. Improvements were made to a method previously developed to determine the conditional stability constant, Kf’, and chelation number, n, using IEC-ICP-MS. This method allowed the accurate determination of the conditional stability constant of a simple system. However, the corresponding chelation number was significantly different to the expected value because the principal assumption, i.e. that the ligand was in excess, was not realized in the experimentation. Furthermore, it neglected complexes other than that formed with EDTA4-. By taking into account these factors, accurate Kf’ and n were obtained for Co-EDTA and Zn-EDTA systems. 2. A simple method was developed for chromium speciation analysis at sub-µg L-1 level in potable water by IEC-ICP-MS. Cr(VI) and Cr(III) were separated on IonPac® AG-7 guard column within 7.5 minutes using gradient elution with 0.1 M ammonium nitrate and 0.8 M nitric acid. H2 collision/reaction interface gas eliminated chlorine-based and carbon-based polyatomic interferences on Cr detection. Water samples were analyzed directly, without any pretreatment. The accuracy of the method was verified through accurate analysis of riverine water certified reference material. Limits of detection of 0.02 and 0.04 µg L-1 for Cr(VI) and Cr(III), respectively, were obtained. 3. This speciation analysis method was then used for kinetics studies of Cr(VI) reduction in acidified riverine water. Water was spiked with Cr(VI), with or without Cr(III), and evolution of each Cr species with time was monitored by speciation analysis, showing that the reduction of Cr(VI) was a pseudo first order reaction. By plotting the logarithm of the peak area ratio of the instant Cr(VI) concentration over that of the original spiking versus time, the reaction rate constant was obtained as the slope. The reduction rate increased with decreasing pH and increasing temperature. The activation energy of the reaction at pH 1.3 was calculated using an Arrhenius plot. This method offers the advantages of small sample consumption, minimal sample manipulation, and easy data interpretation. / Thesis (Ph.D, Chemistry) -- Queen's University, 2010-09-30 08:05:27.342

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