Quantifying the effects of temperature and concentration on variable-density flow in numerical modeling of groundwater systems: Implications for predictive uncertainty and data collection

Groundwater systems of different densities are often mathematically modeled to understand and predict environmental behavior such as seawater intrusion or submarine groundwater discharge. Additional data collection may be justified if it will cost-effectively aid in reducing the uncertainty of a model's prediction. The collection of salinity, as well as, temperature data could aid in reducing predictive uncertainty in a variable-density model. However, before numerical models can be created, rigorous testing of the modeling code needs to be completed. This research documents the benchmark testing of a new modeling code, SEAWAT Version 4. The benchmark problems include various combinations of density-dependent flow resulting from variations in concentration and temperature. The verified code, SEAWAT, was then applied to two different hydrological analyses to explore the capacity of a variable-density model to guide data collection. ^ The first analysis tested a linear method to guide data collection by quantifying the contribution of different data types and locations toward reducing predictive uncertainty in a nonlinear variable-density flow and transport model. The relative contributions of temperature and concentration measurements, at different locations within a simulated carbonate platform, for predicting movement of the saltwater interface were assessed. Results from the method showed that concentration data had greater worth than temperature data in reducing predictive uncertainty in this case. Results also indicated that a linear method could be used to quantify data worth in a nonlinear model. ^ The second hydrological analysis utilized a model to identify the transient response of the salinity, temperature, age, and amount of submarine groundwater discharge to changes in tidal ocean stage, seasonal temperature variations, and different types of geology. The model was compared to multiple kinds of data to (1) calibrate and verify the model, and (2) explore the potential for the model to be used to guide the collection of data using techniques such as electromagnetic resistivity, thermal imagery, and seepage meters. Results indicated that the model can be used to give insight to submarine groundwater discharge and be used to guide data collection. ^

Lattice Boltzmann modeling of fluid flow and solute transport in karst aquifers

A novel modeling approach is applied to karst hydrology. Long-standing problems in karst hydrology and solute transport are addressed using Lattice Boltzmann methods (LBMs). These methods contrast with other modeling approaches that have been applied to karst hydrology. The motivation of this dissertation is to develop new computational models for solving ground water hydraulics and transport problems in karst aquifers, which are widespread around the globe. This research tests the viability of the LBM as a robust alternative numerical technique for solving large-scale hydrological problems. The LB models applied in this research are briefly reviewed and there is a discussion of implementation issues. The dissertation focuses on testing the LB models. The LBM is tested for two different types of inlet boundary conditions for solute transport in finite and effectively semi-infinite domains. The LBM solutions are verified against analytical solutions. Zero-diffusion transport and Taylor dispersion in slits are also simulated and compared against analytical solutions. These results demonstrate the LBM’s flexibility as a solute transport solver. The LBM is applied to simulate solute transport and fluid flow in porous media traversed by larger conduits. A LBM-based macroscopic flow solver (Darcy’s law-based) is linked with an anisotropic dispersion solver. Spatial breakthrough curves in one and two dimensions are fitted against the available analytical solutions. This provides a steady flow model with capabilities routinely found in ground water flow and transport models (e.g., the combination of MODFLOW and MT3D). However the new LBM-based model retains the ability to solve inertial flows that are characteristic of karst aquifer conduits. Transient flows in a confined aquifer are solved using two different LBM approaches. The analogy between Fick’s second law (diffusion equation) and the transient ground water flow equation is used to solve the transient head distribution. An altered-velocity flow solver with source/sink term is applied to simulate a drawdown curve. Hydraulic parameters like transmissivity and storage coefficient are linked with LB parameters. These capabilities complete the LBM’s effective treatment of the types of processes that are simulated by standard ground water models. The LB model is verified against field data for drawdown in a confined aquifer.

Biomimetic modeling of the nitrogen-centered radical postulated to occur during the inhibition of ribonucleotide reductases by 2'-azido-2'-deoxynucleotides

Ribonucleotide reductases (RNR) are essential enzymes that catalyze the reduction of ribonucleotides to 2'-deoxyribonucleotides, which is a critical step that produces precursors for DNA replication and repair. The inactivation of RNR, logically, would discontinue producing the precursors of the DNA of viral or cancer cells, which then would consequently end the cycle of DNA replication. Among different compounds that were found to be inhibitors of RNR, 2'-azido-2'-deoxynucleotide diphosphates (N3NDPs) have been investigated in depth as potent inhibitors of RNR. Decades of investigation has suggested that the inactivation of RNR by N3NDPs is a result of the formation of a nitrogen-centered radical (N·) that is covalently attached to the nucleotide at C3' and cysteine molecule C225 [3'-C(R-S-N·-C-OH)]. Biomimetic simulation reactions for the generation of the nitrogen-centered radicals similar to the one observed during the inactivation of the RNR by azionuclotides was investigated. The study included several modes: (i) theoretical calculation that showed the feasibility of the ring closure reaction between thiyl radicals and azido group; (ii) synthesis of the model azido nucleosides with a linker attached to C3' or C5' having a thiol or vicinal dithiol functionality; (iii) generation of the thiyl radical under both physiological and radiolysis conditions whose role is important in the initiation on RNR cascades; and (iv) analysis of the nitrogen-centered radical species formed during interaction between the thiyl radical and azido group by electron paramagnetic resonance spectroscopy (EPR). Characterization of the aminyl radical species formed during one electron attachment to the azido group of 2'-azido-2'-deoxyuridine and its stereospecifically labelled 1'-, 2'-, 3'-, 4'- or 5,6-[2H 2]-analogues was also examined. This dissertation gave insight toward understanding the mechanism of the formation of the nitrogen-centered radical during the inactivation of RNRs by azidonucleotides as well as the mechanism of action of RNRs that might provide key information necessary for the development of the next generation of antiviral and anticancer drugs.

Development of methods for spatial modeling of sediments quality in Lake Okeechobee, Florida

The major objectives of this dissertation were to develop optimal spatial techniques to model the spatial-temporal changes of the lake sediments and their nutrients from 1988 to 2006, and evaluate the impacts of the hurricanes occurred during 1998–2006. Mud zone reduced about 10.5% from 1988 to 1998, and increased about 6.2% from 1998 to 2006. Mud areas, volumes and weight were calculated using validated Kriging models. From 1988 to 1998, mud thicknesses increased up to 26 cm in the central lake area. The mud area and volume decreased about 13.78% and 10.26%, respectively. From 1998 to 2006, mud depths declined by up to 41 cm in the central lake area, mud volume reduced about 27%. Mud weight increased up to 29.32% from 1988 to 1998, but reduced over 20% from 1998 to 2006. The reduction of mud sediments is likely due to re-suspension and redistribution by waves and currents produced by large storm events, particularly Hurricanes Frances and Jeanne in 2004 and Wilma in 2005. Regression, kriging, geographically weighted regression (GWR) and regression-kriging models have been calibrated and validated for the spatial analysis of the sediments TP and TN of the lake. GWR models provide the most accurate predictions for TP and TN based on model performance and error analysis. TP values declined from an average of 651 to 593 mg/kg from 1998 to 2006, especially in the lake’s western and southern regions. From 1988 to 1998, TP declined in the northern and southern areas, and increased in the central-western part of the lake. The TP weights increased about 37.99%–43.68% from 1988 to 1998 and decreased about 29.72%–34.42% from 1998 to 2006. From 1988 to 1998, TN decreased in most areas, especially in the northern and southern lake regions; western littoral zone had the biggest increase, up to 40,000 mg/kg. From 1998 to 2006, TN declined from an average of 9,363 to 8,926 mg/kg, especially in the central and southern regions. The biggest increases occurred in the northern lake and southern edge areas. TN weights increased about 15%–16.2% from 1988 to 1998, and decreased about 7%–11% from 1998 to 2006.

Structure-based modeling of head -related transfer functions towards interactive customization of binaural sound systems

One of the most popular techniques for creating spatialized virtual sounds is based on the use of Head-Related Transfer Functions (HRTFs). HRTFs are signal processing models that represent the modifications undergone by the acoustic signal as it travels from a sound source to each of the listener's eardrums. These modifications are due to the interaction of the acoustic waves with the listener's torso, shoulders, head and pinnae, or outer ears. As such, HRTFs are somewhat different for each listener. For a listener to perceive synthesized 3-D sound cues correctly, the synthesized cues must be similar to the listener's own HRTFs. ^ One can measure individual HRTFs using specialized recording systems, however, these systems are prohibitively expensive and restrict the portability of the 3-D sound system. HRTF-based systems also face several computational challenges. This dissertation presents an alternative method for the synthesis of binaural spatialized sounds. The sound entering the pinna undergoes several reflective, diffractive and resonant phenomena, which determine the HRTF. Using signal processing tools, such as Prony's signal modeling method, an appropriate set of time delays and a resonant frequency were used to approximate the measured Head-Related Impulse Responses (HRIRs). Statistical analysis was used to find out empirical equations describing how the reflections and resonances are determined by the shape and size of the pinna features obtained from 3D images of 15 experimental subjects modeled in the project. These equations were used to yield “Model HRTFs” that can create elevation effects. ^ Listening tests conducted on 10 subjects show that these model HRTFs are 5% more effective than generic HRTFs when it comes to localizing sounds in the frontal plane. The number of reversals (perception of sound source above the horizontal plane when actually it is below the plane and vice versa) was also reduced by 5.7%, showing the perceptual effectiveness of this approach. The model is simple, yet versatile because it relies on easy to measure parameters to create an individualized HRTF. This low-order parameterized model also reduces the computational and storage demands, while maintaining a sufficient number of perceptually relevant spectral cues. ^

Physics-based modeling of power system components for the evaluation of low-frequency radiated electromagnetic fields

The low-frequency electromagnetic compatibility (EMC) is an increasingly important aspect in the design of practical systems to ensure the functional safety and reliability of complex products. The opportunities for using numerical techniques to predict and analyze system's EMC are therefore of considerable interest in many industries. As the first phase of study, a proper model, including all the details of the component, was required. Therefore, the advances in EMC modeling were studied with classifying analytical and numerical models. The selected model was finite element (FE) modeling, coupled with the distributed network method, to generate the model of the converter's components and obtain the frequency behavioral model of the converter. The method has the ability to reveal the behavior of parasitic elements and higher resonances, which have critical impacts in studying EMI problems. For the EMC and signature studies of the machine drives, the equivalent source modeling was studied. Considering the details of the multi-machine environment, including actual models, some innovation in equivalent source modeling was performed to decrease the simulation time dramatically. Several models were designed in this study and the voltage current cube model and wire model have the best result. The GA-based PSO method is used as the optimization process. Superposition and suppression of the fields in coupling the components were also studied and verified. The simulation time of the equivalent model is 80-100 times lower than the detailed model. All tests were verified experimentally. As the application of EMC and signature study, the fault diagnosis and condition monitoring of an induction motor drive was developed using radiated fields. In addition to experimental tests, the 3DFE analysis was coupled with circuit-based software to implement the incipient fault cases. The identification was implemented using ANN for seventy various faulty cases. The simulation results were verified experimentally. Finally, the identification of the types of power components were implemented. The results show that it is possible to identify the type of components, as well as the faulty components, by comparing the amplitudes of their stray field harmonics. The identification using the stray fields is nondestructive and can be used for the setups that cannot go offline and be dismantled

Lattice boltzmann modeling of fluid flow to determine the permeability of a karst specimen

A limestone sample was scanned using computed tomography (CT) and the hydraulic conductivity of the 3D reconstructed sample was determined using Lattice- Boltzmann methods (LBM) at varying scales. Due to the shape and size of the original sample, it was challenging to obtain a consistent rectilinear test sample. Through visual inspection however, 91 mm and 76 mm samples were digitally cut from the original. The samples had porosities of 58% and 64% and produced hydraulic conductivity values of K= 13.5 m/s and K=34.5 m/s, respectively. Both of these samples were re-sampled to 1/8 and 1/64 of their original size to produce new virtual samples at lower resolutions of 0.542 mm/lu and 1.084 mm/lu, while still representing the same physical dimensions. The hydraulic conductivity tended to increase slightly as the resolution became coarser. In order to determine an REV, the 91 mm sample was also sub-sampled into blocks that were 1/8 and 1/64 the size of the original. The results were consistent with analytical expectations such as those produced by the Kozeny-Carman equation. A definitive REV size was not reached, however, indicating the need for a larger sample. The methods described here demonstrate the ability of LBM to test rock structures and sizes not normally attainable.

Lattice Boltzmann Modeling of Fluid Flow and Solute Transport in Karst Aquifers

A novel modeling approach is applied to karst hydrology. Long-standing problems in karst hydrology and solute transport are addressed using Lattice Boltzmann methods (LBMs). These methods contrast with other modeling approaches that have been applied to karst hydrology. The motivation of this dissertation is to develop new computational models for solving ground water hydraulics and transport problems in karst aquifers, which are widespread around the globe. This research tests the viability of the LBM as a robust alternative numerical technique for solving large-scale hydrological problems. The LB models applied in this research are briefly reviewed and there is a discussion of implementation issues. The dissertation focuses on testing the LB models. The LBM is tested for two different types of inlet boundary conditions for solute transport in finite and effectively semi-infinite domains. The LBM solutions are verified against analytical solutions. Zero-diffusion transport and Taylor dispersion in slits are also simulated and compared against analytical solutions. These results demonstrate the LBM’s flexibility as a solute transport solver. The LBM is applied to simulate solute transport and fluid flow in porous media traversed by larger conduits. A LBM-based macroscopic flow solver (Darcy’s law-based) is linked with an anisotropic dispersion solver. Spatial breakthrough curves in one and two dimensions are fitted against the available analytical solutions. This provides a steady flow model with capabilities routinely found in ground water flow and transport models (e.g., the combination of MODFLOW and MT3D). However the new LBM-based model retains the ability to solve inertial flows that are characteristic of karst aquifer conduits. Transient flows in a confined aquifer are solved using two different LBM approaches. The analogy between Fick’s second law (diffusion equation) and the transient ground water flow equation is used to solve the transient head distribution. An altered-velocity flow solver with source/sink term is applied to simulate a drawdown curve. Hydraulic parameters like transmissivity and storage coefficient are linked with LB parameters. These capabilities complete the LBM’s effective treatment of the types of processes that are simulated by standard ground water models. The LB model is verified against field data for drawdown in a confined aquifer.

Characterization and modeling of multi-conductor transmission line using Finite-difference Time-Domain method

A two-dimensional, 2D, finite-difference time-domain (FDTD) method is used to analyze two different models of multi-conductor transmission lines (MTL). The first model is a two-conductor MTL and the second is a threeconductor MTL. Apart from the MTL's, a three-dimensional, 3D, FDTD method is used to analyze a three-patch microstrip parasitic array. While the MTL analysis is entirely in time-domain, the microstrip parasitic array is a study of scattering parameter Sn in the frequency-domain. The results clearly indicate that FDTD is an efficient and accurate tool to model and analyze multiconductor transmission line as well as microstrip antennas and arrays.

Dynamic fault tree analysis with PEWMA modeling of event rates and Bayesian updating of material balance parameters using MCMC

This research explores Bayesian updating as a tool for estimating parameters probabilistically by dynamic analysis of data sequences. Two distinct Bayesian updating methodologies are assessed. The first approach focuses on Bayesian updating of failure rates for primary events in fault trees. A Poisson Exponentially Moving Average (PEWMA) model is implemnented to carry out Bayesian updating of failure rates for individual primary events in the fault tree. To provide a basis for testing of the PEWMA model, a fault tree is developed based on the Texas City Refinery incident which occurred in 2005. A qualitative fault tree analysis is then carried out to obtain a logical expression for the top event. A dynamic Fault Tree analysis is carried out by evaluating the top event probability at each Bayesian updating step by Monte Carlo sampling from posterior failure rate distributions. It is demonstrated that PEWMA modeling is advantageous over conventional conjugate Poisson-Gamma updating techniques when failure data is collected over long time spans. The second approach focuses on Bayesian updating of parameters in non-linear forward models. Specifically, the technique is applied to the hydrocarbon material balance equation. In order to test the accuracy of the implemented Bayesian updating models, a synthetic data set is developed using the Eclipse reservoir simulator. Both structured grid and MCMC sampling based solution techniques are implemented and are shown to model the synthetic data set with good accuracy. Furthermore, a graphical analysis shows that the implemented MCMC model displays good convergence properties. A case study demonstrates that Likelihood variance affects the rate at which the posterior assimilates information from the measured data sequence. Error in the measured data significantly affects the accuracy of the posterior parameter distributions. Increasing the likelihood variance mitigates random measurement errors, but casuses the overall variance of the posterior to increase. Bayesian updating is shown to be advantageous over deterministic regression techniques as it allows for incorporation of prior belief and full modeling uncertainty over the parameter ranges. As such, the Bayesian approach to estimation of parameters in the material balance equation shows utility for incorporation into reservoir engineering workflows.

Centrifuge modeling of oblique pipe-soil interaction in dense and loose sand

Due to relative ground movement, buried pipelines experience geotechnical loads. The imposed geotechnical loads may initiate pipeline deformations that affect system serviceability and integrity. Engineering guidelines (e.g., ALA, 2005; Honegger and Nyman, 2001) provide the technical framework to develop idealized structural models to analyze pipe‒soil interaction events and assess pipe mechanical response. The soil behavior is modeled using discrete springs that represent the geotechnical loads per unit pipe length developed during the interaction event. Soil forces are defined along three orthogonal directions (i.e., axial, lateral and vertical) to analyze the response of pipelines. Nonlinear load-displacement relationships of soil defined by a spring, is independent of neighboring spring elements. However, recent experimental and numerical studies demonstrate significant coupling effects during oblique (i.e., not along one of the orthogonal axes) pipe‒soil interaction events. In the present study, physical modeling using a geotechnical centrifuge was conducted to improve the current understanding of soil load coupling effects of buried pipes in loose and dense sand. A section of pipeline, at shallow burial depth, was translated through the soil at different oblique angles in the axial-lateral plane. The force exerted by the soil on pipe is critically examined to assess the significance of load coupling effects and establish a yield envelope. The displacements required to soil yield force are also examined to assess potential coupling in mobilization distance. A set of laboratory tests were conducted on the sand used for centrifuge modeling to find the stress-strain behavior of sand, which was used to examine the possible mechanisms of centrifuge model test. The yield envelope, deformation patterns, and interpreted failure mechanisms obtained from centrifuge modeling are compared with other physical modeling and numerical simulations available in the literature.

Biomechanical modeling of parotid glands morphing in head & neck radiation therapy treatments

Durante i trattamenti radioterapici dei pazienti oncologici testa-collo, le ghiandole parotidee (PGs) possono essere indebitamente irradiate a seguito di modificazioni volumetriche-spaziali inter/intra-frazione causate da fattori quali il dimagrimento, l’esposizione a radiazioni ionizzanti ed il morphing anatomico degli organi coinvolti nelle aree d’irraggiamento. Il presente lavoro svolto presso la struttura di Fisica Medica e di Radioterapia Oncologica dell’A.O.U di Modena, quale parte del progetto di ricerca del Ministero della Salute (MoH2010, GR-2010-2318757) “ Dose warping methods for IGRT and Adaptive RT: dose accumulation based on organ motion and anatomical variations of the patients during radiation therapy treatments ”, sviluppa un modello biomeccanico in grado di rappresentare il processo di deformazione delle PGs, considerandone la geometria, le proprietà elastiche e l'evoluzione durante il ciclo terapeutico. Il modello di deformazione d’organo è stato realizzato attraverso l’utilizzo di un software agli elementi finiti (FEM). Molteplici superfici mesh, rappresentanti la geometria e l’evoluzione delle parotidi durante le sedute di trattamento, sono state create a partire dai contorni dell’organo definiti dal medico radioterapista sull’immagine tomografica di pianificazione e generati automaticamente sulle immagini di setup e re-positioning giornaliere mediante algoritmi di registrazione rigida/deformabile. I constraints anatomici e il campo di forze del modello sono stati definiti sulla base di ipotesi semplificative considerando l’alterazione strutturale (perdita di cellule acinari) e le barriere anatomiche dovute a strutture circostanti. L’analisi delle mesh ha consentito di studiare la dinamica della deformazione e di individuare le regioni maggiormente soggette a cambiamento. Le previsioni di morphing prodotte dal modello proposto potrebbero essere integrate in un treatment planning system per metodiche di Adaptive Radiation Therapy.

Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model