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During the past few decades, Computational Fluid Dynamics (CFD) modelling hasbecome very popular in the coastal and offshore engineering community. Both Eulerianand Lagrangian methods have achieved great successes; typical examples are thegrid-based OpenFOAM® model and the meshless Smoothed Particle Hydrodynamics(SPH) method based model (e.g. SPHysics). While the former tends to be moreefficient and has advantages in enforcing incompressibility and boundary conditionsvia use of a grid, the latter is more suitable for handling large free-surface deformationsusing particles. In an attempt to combine the advantages of both methods, theParticle-In-Cell (PIC) method was devised through a combined use of particles andgrid. However, so far this hybrid method has not been very well exploited for use inthe coastal and offshore engineering field, where modelling complex wave-structureinteraction with computational efficiency still remains an important challenge. This thesis develops a novel "full particle" PIC based numerical model that solves theincompressible Newtonian Navier-Stokes equations for single-phase free-surface flowswith an emphasis on fluid-structure interaction. The use of the phrase "full particle"here indicates that all of the fluid properties, such as the mass and momentum,are assigned only to the particles, rather than being split between the particles andgrid as is the case in "classical" PIC. The novelty of the model lies in the fact thatthe particles are employed to solve the nonlinear advection term and track the fluidconguration (including the free surface), while the underlying grid is solely usedfor computational convenience for solving the non-advection terms. In addition, atailored Distributed Lagrange Multiplier method and a Cartesian cut cell based two-waystrong coupling algorithm are incorporated for fluid-structure interaction. Themodel is developed in both two and three spatial dimensions, and the 3D modelis parallelised using the Message Passing Interface (MPI) approach. The model isvalidated using benchmark tests in the coastal and offshore engineering field withsimulating nonlinear wave-structure interaction being the principal interest. It isshown that the present "full particle" PIC model is flexible, efficient (in terms ofCPU cost) and accurate when modelling complex free-surface flows and the violentinteraction of such flows with (surface-piercing) structures of arbitrary shape anddegree of freedom. With new innovations, the model has great potential to become ahigh quality numerical tool for use in coastal and offshore engineering applications.

Heavy transition metal (TM) compounds often display highly unusual physical properties due to strong spin-orbit coupling and spatially-extended \textit{d} orbitals. The latter promotes large intersite orbital hopping \textit{t}. In many cases, these enhanced \textit{t} values become comparable or even larger than Hund's coupling $J_H$. In this case, ``molecules in solids" could be a more appropriate picture when we have heavy-TM clusters, where some inter-site covalent bonds form due to the strong orbital overlap. Therefore, molecular orbital (MO) effects may become extremely important, although they have historically been ignored when studying heavy transition metal compounds. This thesis consists of three projects that were designed to study MO effects in heavy transition metal compounds with the 6H-perovskite structure.The first chapter of this thesis describes background material required to understand the original research presented later, while the second chapter describes the experimental techniques used in the research. In Chapter 3, we discovered the realization of the orbital-selective Mott state at the molecular level in \ch{Ba3LaRu2O9}, which appears to represent the first conclusive example of this phenomenon. Chapter 4 is based on my published work of \ch{Ba3CeRu2O9}, where we found a large zero-field slitting ~85 meV that is a consequence of molecular orbital formation within the Ru dimers of this material. We explored further by extending our study to the 5$d$ iridate \ch{Ba4LiIr3O12} in Chapter 5. This material adopts the same 6H-perovskite space group as the materials discussed in Chapters 3 and 4, and appears to be a rare example of a 5\textit{d}4 system exhibiting magnetic order. All these examples together suggest that MO effects cannot be ignored in heavy transition metal molecular magnets. Instead, they need to be treated on equal footing with intra-site effects to ensure an accurate description of the magnetism in these materials.

We rely on visual information to navigate through the natural environment. The extraction of visual features by the nervous system first arises in the retina. The retina sends processed visual information to cortical and sub-cortical brain regions through 20-40 types of retinal ganglion cells (RGCs), each encodes specific aspect of the visual scene. One of the most prominent visual processing in the retina is the computation of motion direction, implemented by retinal direction selective circuit. While our notions about retinal direction circuit have come from the usage of simple parametric stimuli, natural scenes are rarely homogeneous but full of competing signals. This thesis focuses on understanding the underlying mechanisms of noise resilience of retinal direction computation. In chapter 1, we review the recent understanding of the dynamic engagement of circuitry and synaptic mechanisms for robust retinal directional selectivity under various visual conditions. Chapter 2 described the protocol we developed for recording and functional imaging of retinal neurons under two-photon microscopy in the laboratory. In chapter 3, we used synapse-specific genetic manipulation to dissect the role of distinct sets of inhibitory motifs for motion processing. We found that the functional circuitries that process bright versus dark moving objects are not mirrored symmetric. Furthermore, Lateral inhibitory motifs in retinal direction selective circuit are only recruited in the noisy visual condition in On pathway. Based upon findings in chapter 3, chapter 4 further investigated the mechanistic implementation of noise resilience by lateral inhibition motif. We found that one particular form of lateral inhibition, the mutual inhibition of lateral inhibition, prevents use-dependent synaptic suppression triggered by competing signals, thus maintains the strength and fidelity of synaptic transmission in the circuitry. Since feature selectivity, including direction selectivity, relies on the veto of spiking activities to "null" stimuli. This silencing of neuronal spiking requires timely cancellation of excitation by inhibition. In chapter 5, we investigated how retinal direction selective circuit maintains the ~ms time-scale covariation of inhibition and excitation for robust direction selectivity.

Abstract: The intimate association between bitumen components and clay minerals is an important feature of oil sands fine solids. These organically-modified clay minerals cause serious problems in Canadian oil sands production: hindering bitumen extraction, stabilizing water-in-bitumen emulsions, fouling upgrading equipment, and contributing to the formation of indefinitely-stable mature fine tailings suspensions. In the present work, the irreversible adsorption of asphaltenes from toluene solutions onto kaolinite was studied as a model system for the unextractable adsorption of bitumen components on clay mineral. Native clay minerals obtained from Athabasca bitumen froth, with and without a hydrothermal treatment (at 300–420°C), were examined by several techniques including quantitative nanomechanical mapping atomic force microscopy (QNM-AFM) and X-ray photoelectron spectroscopy (XPS). The effect of the hydrothermal treatment on the organically-modified clay minerals and the consequent changes in their emulsification and filtration behaviors were investigated. The adsorption of asphaltenes on kaolinite was confirmed to be a largely irreversible process, based on the observation that circa 80% of asphaltenes remained adsorbed on kaolinite even after thorough toluene washing. The irreversibility of asphaltene adsorption is consistent with the presence of unextractable organic matter by toluene in oil sands fine solids reported in the literature. Thermal dehydroxylation enhanced the adsorption capacity of kaolinite for asphaltenes. The XPS-determined percent surface coverage was 18% and 41% on the untreated and dehydroxylated kaolinite, respectively, corresponding to a maximum adsorption density of 3 and 7 mg/m2. The incomplete surface coverage even at the highest adsorption density indicated the patchy characteristics of adsorbed asphaltenes on both kaolinite substrates. Analogously, patches of organic matter were also observed on the native clay minerals in oil sands, as indicated by the inhomogeneous spatial distribution of adhesion force on the surfaces of platy particles (determined by QNM-AFM). The surface coverage and mean domain thickness of the organic coating on the clay basal faces were estimated to be 17±6% and 1.4 nm, respectively. In addition to this patchy organic coating, there were organic materials trapped in the oil-mineral aggregates. These trapped organics were found to be softer (more deformable) than the asphaltene fraction of oil sands bitumen. Hydrothermal treatment at 390°C increased the surface carbon concentration of the fine solids in bitumen froth from 36 to 47 atom% (determined by XPS), but reduced their total organic carbon content from 15 to 10 wt% (determined by bulk elemental analysis). The hydrothermally-treated fine solids became more uniformly hydrophobic and more active in stabilizing emulsions. The volume of the produced emulsions was found to increase linearly and monotonically with the proportion of a specific sub-fraction of the fine solid particles with a critical surface tension of 27–30 mN/m (determined by the film flotation method), likely because of their intermediate hydrophobicity and thus relatively stronger emulsifying capacity. The filterability of the bitumen froth fine solids was enhanced after the hydrothermal treatment, as shown by both room-temperature filtration and in-situ hot filtration (at ~200°C) tests. Based on this observation, a conceptual bitumen froth cleaning approach is proposed, which combines the hydrothermal treatment of bitumen froth, water separation by venting, and solids removal by in-situ hot filtration. The small-scale laboratory tests using 500-mL Parr reactors and 0.5-μm pore size stainless steel filters showed that this procedure was able to reduce the fine solids content from 8 wt% in the original bitumen froth to 0.08 wt% in the bitumen product.

Abstract: In this work, a general dynamic model was proposed to simulate the dynamic motion of microtubules driven by dynein motors, which is of importance to the design of potential nano-bio machines composed of dynein motors and microtubules. The model was developed based on Newton's law of motion. By incorporating a DPD technique, the general model was applied to simulate the unidirectional motion of microtubule. The functions of dyneins and their coordination with each other, which plays an important role in the motion of microtubules, were studied. By taking into account the bending energy of microtubules, we extended the general model to study possible mechanisms responsible for the microtubule-microtubule and microtubule-wall interactions, which are essential to the design of optimal track patterns for potential nanomachine systems. This study helps to evaluate the influence of bending and rotation on microtubule joining processes, involving bumping force, bending moment and torque generation. Finally, a phenomenal modeling study based on the Monte Carlo method, was conducted to investigate the self-organization of microtubules driven by dynein motors and identify out key parameters that control the self-organized movement of microtubules, giving crucial information for nano device design. This modeling study helps to clarify several important issues regarding the interaction between dynein motors and microtubules as a power transfer medium, which provides important information for the development of potential nanobio-machines using dynein as a biological motor.