According to the World Health Organization (WHO), Cardiovascular Disease (CVD) is the leading cause of death in the world. Biomechanics and fluid dynamics of blood flow play an important role in CVD mediation. Shear stress plays a major role in platelet-substrate interactions and thrombus formation and growth in blood flow, where under both pathological and physiological conditions platelet adhesion and accumulation occur. In this study, a three-dimensional dynamic model of platelet-rich thrombus growth in stenosed vessels using computational fluid dynamics (CFD) methods is introduced. Platelet adhesion, aggregation and activation kinetics are modeled by solving mass transport equations for blood components involved in thrombosis. The model was first verified under three different shear conditions and at two heparin levels. Three-dimensional simulations were then carried out to evaluate the performance of the model for severely damaged (stripped) aortas with mild and severe stenosis degrees. For these cases, linear shear-dependent functions were developed for platelet-surface and platelet-platelet adhesion rates. It was confirmed that the platelet adhesion rate is not only a function of Reynolds number (or wall shear rate) but also the stenosis severity of the vessel. General correlations for adhesion rates of platelets as functions of stenosis and Reynolds number were obtained based on these cases. The model was applied to different experimental systems and shown to agree well with measured platelet deposition. Then, the Arbitrary Lagrangian Eulerian (ALE) formulation was used to model dynamic growth by including geometry change in the simulation procedure. The wall boundaries were discretely moved based on the amount of platelet deposition that occurs on the vessel wall. To emulate the dynamic behavior of platelet adhesion kinetics during thrombus growth, the validated model for platelet adhesion, which calculates platelet-surface adhesion rates as a function of stenosis severity and Reynolds number, was applied to the model. The model successfully predicts the nonlinear growth of thrombi in the stenosed area. These simulations provide a useful guide to understand the effect of growing thrombus on platelet deposition rate, platelet activation kinetics and occurrence of thromboembolism (TE) in highly stenosed arteries. / Ph. D.

Tsunamis and storms are the most devastating coastal hazards that can cause great loss of life and infrastructure damage. To assess tsunami and storm hazard, the magnitude and frequency of each type of event are needed. However, major tsunamis and storms are very infrequent, especially tsunamis, and the only reliable record is the deposits they leave behind. Tsunami and storm deposits can be used to calculate the magnitudes of the respective event, and to contribute to the hazard frequency where there is no historical records. Therefore, for locations where both events could occur, it is crucial to differentiate between the two types of events. Existing studies on the similarities and differences between the two types of deposits all suffer from paucity of the number of events and field data, and a wide range of initial conditions, and thus an unequivocal set of distinguishing deposit characteristics has not been identified yet. In this study, we aim to tackle the problem with the MEso-SCAle Particle Transport model (MESCAPT) that combines the advantages of concentration-based Eulerian methods and particle-based method. The advantage of the former is efficiency and the latter is detailed sediment transport and deposit information. Instead of modeling individual particles, we assume that a group of sediment grains travel and deposit together, which is called a meso-scale particle. This allows simulation domains that are large enough for tsunami and storm wave propagation and inundation. The sediment transport model is coupled with a hydrodynamic model based on the shallow water equations. Simulation results of a case study show good agreements with field measurements of deposits left behind by the 2004 Indian Ocean Tsunami. Idealized tsunami and storm case studies demonstrate the model's capabilities of reproducing morphological changes, as well as microscopic grain-size trends. / Ph. D.

Underground coal mine ground control persists as a unique challenge in rock mass engineering. Fall of roof and rib continue to present a hazard to underground personnel. Stability of underground openings is a prerequisite for successful underground coal mine workings. An adaptation of a civil engineering design standard for analyzing the stability of underground excavations for mining geometries is given here. The ground response curve--developed over seventy years ago for assessing tunnel stability--has significant implications for the design of underground excavations, but has seen little use in complex mining applications. The interaction between the small scale (pillar stress-strain) and the large scale (ground response curve) is studied. Further analysis between these two length scales is conducted to estimate the stress on pillars in a room-and-pillar coal mine. These studies are performed in FLAC3D by implementing a two-scale, two-step approach. This two-scale approach allows for the interaction between the small, pillar scale and the large, panel scale to be studied in a computationally efficient manner. / Ph. D.

Seafloor hydrothermal systems have been intensively studied for the past few decades; however, the location of recharge zones and details of fluid circulation patterns are still largely uncertain. To better understand the effects of anhydrite precipitation on hydrothermal flow paths, we conduct 2-D numerical simulations of hydrothermal circulation at a mid-ocean ridge using a NaCl-H2O numerical code. The simulations focus on East Pacific Rise hydrothermal system at 950N due to availability of key observational data to constrain the models. Seismicity data that is available suggests that fluid flow is primarily along axis and that recharge is focused into a small zone near a 4th order discontinuity in the ridge axis. Simulations are carried out in an open-top square box 1500 m on a side maintained at a surface pressure of 25 MPa, and nominal seawater temperature of 10 C. The sides of the box are assumed to be impermeable and insulated. A constant temperature distribution is maintained along the bottom of the box consisting of a 1000 m long central-heated region maintained at 450 C to represent the axial magma chamber and ensure P-T conditions for phase separation; a linearly decreasing temperature profile from 450 to 300 C is maintained along the 250 m long segments adjacent to the heated region to delineate the recharge zone. We constructed a homogeneous model with a uniform cell size of 25 m with a permeability of 10-13 m2 and a similar model with a 200 m thick layer 2A region with a permeability of 10-12 m2. For the homogeneous model the simulations were run for 100 years to approximate steady state conditions and the model with layer 2A was run for 50 years. Assuming that anhydrite precipitation resulted from the decrease in solubility with increasing temperature as downwelling fluid gets heated, the rate of porosity decrease and sealing time was calculated at 50 and 100 years. The results showed that sealing occurred most rapidly at the bottom of the recharge areas near the base of the high-temperature plumes, where complete sealing occurred after ~55-625 years for an initial porosity of 0.1. The simulations also suggested that sealing would occur more slowly at the margins of the ascending plumes, with times ranging between ~ 80 and 5000 years. The sealing times in the deep recharge zone determined in these simulations are considerably greater than estimated from 1D analytical calculations, suggesting that with a 2D model, focused recharge at the EPR 950N site may occur, at least on a decadal time scale. More detailed analyses are needed to determine whether such focused recharge can be maintained for longer times. / Master of Science

The relatively rapid stream capture of the New River basin by the Roanoke River basin provides a unique example of topographic change within a tectonically inactive environment. A previous investigation of abandoned river deposits has shown the capture of ~225 km2 of New River basin area, which has caused approximately 250 m of incision by the Roanoke River (Prince et al., 2011). Difference in base level elevations between the lower Roanoke to the higher New River could be the source of potential energy driving rapid incision (Prince et al., 2011). Significant incongruities in base level elevations at the boundaries of an aquifer can steepen the gradient and shift the groundwater divide further toward the higher elevation boundary (Yechieli et al., 2009). If a steep groundwater gradient and expanded groundwater basin exists beneath the Roanoke River tributaries, this would suggest a groundwater control on incision and capture. In this investigation we incorporate average total head, measured from 18 domestic wells, and constant-head river boundary conditions into numerical models to calculate water levels and gradients between the rivers. We also utilized thermal patterns and particle tracking of spring locations to better understand flow paths in the region. Our results show the groundwater divide is shifted toward the higher elevation boundary, indicating that the groundwater basin is captured prior to surface capture. Flow pathways utilized by groundwater capture can be either diffuse or conduits, however further work should be done to better understand travel times and flow depths. / Master of Science

The response of an aggregate pier foundation system during seismic loading was investigated. The factors and phenomena governing the performance of the aggregate pier and the improved ground were identified and clarified. The key factors affecting the performance of the aggregate pier include soil density, stiffness modulus, and drainage capacity. The improved ground is influenced by soil stratification, soil properties, pore pressure dissipation, and earthquake time history. Comprehensive numerical modeling using FLAC were performed. The focus of the study in this research was divided into three parts: the studies of the ground acceleration, the excess pore water pressure ratio and the shear stress in soil matrix generated during seismic loading. Two earthquake time histories scaled to different peak acceleration were used in the numerical modeling: the 1989 Loma Prieta earthquake (pga = 0.45g) and the 1988 Saguenay earthquake (pga = 0.05g). The main results of the simulation showed the following effects of aggregate pier on liquefiable soil deposits: 1) The aggregate pier amplifies the peak horizontal acceleration on the ground surface (amax), 2) The aggregate pier reduces the liquefaction potential up to depth where it is installed, 3) Pore pressures are generally lower for soils reinforced with aggregate pier than unreinforced soils except for very strong earthquake, 4) The maximum shear stresses in soil are much smaller for reinforced soils than unreinforced soils. The excess pore water pressure ratio and the shear stress in the soil matrix calculated by FLAC were generally lower than those predicted by available procedures. / Master of Science

The presence of man-made levees along the Lower Mississippi River (MR) has significantly reduced the River sediment input to the wetlands and much of the River's sediment is now lost to the Gulf of Mexico. The sediment load in the River has also been decreased by dams and river revetments along the Upper MR. Freshwater and sediment diversions are possible options to help combat land loss. Numerical modeling of hydrodynamics and sediment transport of the MR is a useful tool to evaluate restoration projects and to improve our understanding of the resulting River response. The emphasis of this study is on the fate of sand in the river and the distributaries. A 3-D unsteady flow mobile-bed model (ECOMSED; HydroQual 2002) of the Lower MR reach between Belle Chasse (RM 76) and downstream of Main Pass (RM 3) was calibrated using field sediment data from 2008 – 2010 (Nittrouer et al. 2008; Allison, 2010). The model was used to simulate River currents, diversion sand capture efficiency, erosional and depositional patterns with and without diversions over a short period of time (weeks). The introduction of new diversions at different locations, e.g., Myrtle Grove (RM 59) and Belair (RM 65), with different geometries and with different outflows was studied. A 1-D unsteady flow mobile-bed model (CHARIMA; Holly et al. 1990) was used to model the same Lower MR reach. This model was used for longer term simulations (months). The simulated diversions varied from 28 m3/s (1, 000 cfs) to 5, 700 m3/s (200, 000 cfs) for river flows up to 35, 000 m3/s (1.2x106 cfs). The model showed that the smaller diversions had little impact on the downstream sand transport. However, the larger diversions had the following effects: 1) reduction in the slope of the hydraulic grade line downstream of the diversion; 2) reduction in the available energy for transport of sand along distributary channels; 3) reduced sand transport capacity in the main channel downstream of the diversion; 4) increased shoaling downstream of the diversion; and 5) a tendency for erosion and possible head-cutting upstream of the diversion.

This thesis focuses on solutions of reactive transport problems in porous media. The principle mechanisms of flow and reactive mass transport in porous media are investigated. Global implicit approach (GIA), where transport and reaction are fully coupled, and sequential noniterative approach (SNIA) are implemented into the software OpenGeoSys (OGS6) to couple chemical reaction and mass transport. The reduction scheme proposed by Kräutle is used in GIA to reduce the number of coupled nonlinear differential equations. The reduction scheme takes linear combinations within mobile species and immobile species and effectively separates the reaction-independent linear differential equations from coupled nonlinear ones (i.e. reducing the number of primary variables in the nonlinear system). A chemical solver is implemented using semi-smooth Newton iteration which employs complementarity condition to solve for equilibrium mineral reactions. The results of three benchmarks are used for code verification. Based on the solutions of these benchmarks, it is shown that GIA with the reduction scheme is faster (ca. 6.7 times) than SNIA in simulating homogeneous equilibrium reactions and (ca. 24 times) in simulating kinetic reaction. In simulating heterogeneous equilibrium mineral reactions, SNIA outperforms GIA with the reduction scheme by 4.7 times. / Diese Arbeit konzentriert sich auf die numerische Berechnung reaktiver Transportprobleme in porösen Medien. Es werden prinzipielle Mechanismen von Fluidströmung und reaktive Stofftransport in porösen Medien untersucht. Um chemische Reaktionen und Stofftransport zu koppeln, wurden die Ansätze Global Implicit Approach (GIA) sowie Sequential Non-Iterative Approach (SNIA) in die Software OpenGeoSys (OGS6) implementiert. Das von Kräutle vorgeschlagene Reduzierungsschema wird in GIA verwendet, um die Anzahl der gekoppelten nichtlinearen Differentialgleichungen zu reduzieren. Das Reduzierungsschema verwendet Linearkombinationen von mobilen und immobile Spezies und trennt die reaktionsunabhngigen linearen Differentialgleichungen von den gekoppelten nichtlinearen Gleichungen (dh Verringerung der Anzahl der Primärvariablen des nicht-linearen Gleichungssystems). Um die Gleichgewichtsreaktionen der Mineralien zu berechnen, wurde ein chemischer Gleichungslaser auf Basis von ”semi-smooth Newton-Iterations” implementiert. Ergebnisse von drei Benchmarks wurden zur Code-Verifikation verwendet. Diese Ergebnisse zeigen, dass die Simulation homogener Equilibriumreaktionen mit GIA 6,7 mal schneller und bei kinetischen Reaktionen 24 mal schneller als SNIA sind. Bei Simulationen heterogener Equilibriumreaktionen ist SNIA 4,7 mal schneller als der GIA Ansatz.

The temperature and moisture content of biomass feedstocks both play a critical role in minimizing storage and transportation costs, achieving effective bioconversion, and developing relevant postharvest quality models. Hence, this study characterizes the heat and mass transfer occurring within baled switchgrass through the development of a mathematical model describing the relevant thermal and physical properties of this specific substrate. This mathematical model accounts for the effect of internal heat generation and temperature-induced free convection within the material in order to improve prediction accuracy. Inclusion of these terms is considered novel in terms of similar biomass models. Two disparate length scales, characterizing both the overall bale structure (global domain) and the individual stems (local domain), are considered with different physical processes occurring on each scale. Material and fluid properties were based on the results of hydraulic conductivity experiments, moisture measurements and thermal analyses that were performed using the constant head method, TDR-based sensors and dual thermal probes, respectively. The unique contributions made by each of these components are also discussed in terms of their particular application within various storage and bioconversion operations. Model validation was performed with rectangular bales of switchgrass (102 x 46 x 36 cm3) stored in an environmental chamber with and without partial insulation to control directional heat transfer. Bale temperatures generally exhibited the same trend as ambient air; although initial periods of microbial growth and heat generation were observed. Moisture content uniformly declined during storage, thereby contributing to minimal heat generation in the latter phases of storage. The mathematical model agreed closely with experimental data for low moisture content levels in terms of describing the temperature and moisture distribution within the material. The inclusion of internal heat generation was found to be necessary for improving the prediction accuracy of the model; particularly in the initial stage of storage. However, the effects of natural convection exhibited minimal contribution to the heat transfer as conduction was observed as the predominate mechanism occurring throughout storage. The results of this study and the newly developed model are expected to enable the maintenance of baled biomass quality during storage and/or high-solids bioconversion.

A silicon interposer platform with microfluidic cooling is proposed for high-performance computing systems. The key components and technologies for the proposed platform, including electrical and fluidic microbumps, microfluidic vias and heat sinks, and simultaneous flip-chip bonding of the electrical and fluidic microbumps, are developed and demonstrated. Fine-pitch electrical microbumps of 25 µm diameter and 50 µm pitch, fluidic vias of 100 µm diameter, and annular-shaped fluidic microbumps of 150 µm inner diameter and 210 µm outer diameter were fabricated and bonded. Electrical and fluidic tests were conducted to verify the bonding results. Moreover, the thermal and signaling benefits of the proposed platform were evaluated based on thermal measurements and simulations, and signaling simulations. Compared to the conventional air cooling, significant reductions in system temperature and thermal coupling are achieved with the proposed platform. Moreover, the signaling performance is improved due to the reduced temperature, especially for long interconnects on the silicon interposer. A numerical power distribution network (PDN) simulator is developed based on distributed circuit models for on-die power/ground grids, package- and board- level power/ground planes, and the finite difference method. The simulator enables power supply noise simulation, including IR-drop and simultaneous switching noise, for a full chip with multiple blocks of different power, decoupling capacitor, and power/ground pad densities. The distributed circuit model is further extended to include TSVs to enable simulations for 3D PDN. The integration of package- and board- level power/ground planes enables co-simulation of die-package-board PDN and exploration of new PDN configurations.