As an intern with URS Corporation, I participated in several remediation and wastewater treatment projects during the year 2004. A groundwater remediation project was selected to present in this record of study for my Doctor of Engineering degree not only because I spent more time on it than any other project, but also because it represents the broadness and depth of a typical URS remediation project. In this report, findings from previous environmental investigations were summarized and used for computer modeling and remediation strategy evaluation. Computer models were used to simulate site conditions and assist in remedy design for the site. Current pump-and-treat systems were evaluated by the model under various scenarios. Recommendations were made for the pump-and-treat system to control the contaminant plume. Various remediation technologies were evaluated and compared for their applicability at the site. A combination of on-site remediation and downgradient plume control was chosen as the site remediation strategy. Treatability studies and additional modeling work are needed for the remediation system design and optimization.

This research evaluates and improves capabilities incorporated in the Water Rights Analysis Package (WRAP) modeling system for tracking salt loads, particularly for applications dealing with natural salt pollution problems that are prevalent in several major river basins in Texas and neighboring states. WRAP is the river/reservoir system simulation model incorporated in the Water Availability Modeling (WAM) System applied by agencies and consulting firms in Texas in planning and water right regulatory activities. A salinity simulation component of WRAP called WRAP-SALT was developed recently at Texas A&M University. WRAP-SALT was based on the premise of complete mixing within the monthly computational time step. However, salt concentrations actually have time variation throughout a reservoir. This thesis research investigates more realistic salinity routing methods. Historical gauged data provide a basis for calibration of routing parameters. The timing of the inflow load to determine outflow concentration is calculated by lag parameters with the monthly time steps. Complete mixing occurs during the lag months. Two options are incorporated into WRAP-SALT for setting the lag parameter. With the first option, the model-user sets a constant that is applied during every month of the simulation. This option requires calibration studies to determine the lag. With the alternative option, a variable lag is computed within the model in each month based on the concept of retention time, which is a representation of the time required for a monthly volume of water and its salt load to flow through a reservoir. When the lag is activated, the accuracy between observed and computed mean monthly salinity concentrations through the reservoir is generally improved. The basin-wide simulation was performed for the Brazos River Basin for conditions with and without salt control dams proposed by the Corps of Engineers. The proposed salt control impoundments improve water quality throughout the basin.

Traffic congestion is a serious problem in the United States and is likely to get worse. A number of strategies encompassing increasing supply and managing demand have been suggested to mitigate the problem of traffic congestion. These strategies seek to reduce travel time and/or make travel time more reliable. The use of managed lanes is one such strategy. Faced with successful implementation of a managed lane strategy, it is important to understand potential public perception of the managed lane as well as estimate the number of travelers willing to use managed lanes. Such an estimate would help estimate the toll rates for optimal usage of managed lanes by carpoolers and toll paying travelers. An online survey augmented by paper and laptop survey was conducted in Houston and Dallas to collect information about travelers’ travel behavior, socio-economic characteristics, managed lane perception, and potential use of managed lanes. A comparison of interest in using managed lanes revealed that in majority of cases there was no difference in interest in using managed lanes across user groups. Travel time reliability and ability to travel faster were indicated as top two reasons for interest in managed lanes. This was true for all travelers regardless of mode. Mode choice model using multinomial logit modeling were estimated for Houston and Dallas. Simulation studies were conducted using these mode choice models to estimate the percentage of Single Occupant Vehicle (SOV) travelers on managed lane (ML), High Occupancy Vehicle with two travelers (HOV2) on ML, High Occupancy Vehicle with three or more travelers (HOV3+) on ML, SOV travelers on general purpose lane (GPL), HOV2 travelers on GPL, and HOV3+ travelers on GPL. These scenarios compared the managed lane usage for different speeds on GPL (25 miles per hour, 30 miles per hour, and 35 miles per hour). For the case when general purpose lane speed is 25 miles per hour, an increase of $11.75 in SOV tolls ($18 from $6.25) decreases the modal share of SOV travelers on Houston ML from 23.3 percent to 16.9 percent. A similar increase in Dallas tolls decreases the modal share of SOV ML travelers from 22.0 percent to 16.3 percent.

Tularemia is a one of the most complex zoonotic diseases. Francisella tularensis McCoy and Chapin, the causative agent of tularemia is considered endemic in Texas, but outbreaks are rare and there are few human cases each year. Tularemia is listed as a Category A biological weapon and air samples are taken daily in select major metropolitan areas, including Houston, to monitor for its presence. I determined the potential risk for tularemia introduction and spread in southeast Texas through field surveillance for the pathogen and its major arthropod vector in the region, Amblyomma americanum (L.); completion of a habitat capability map for A. americanum, based on landscape analysis of the study area; and potential movement and long-term establishment of tularemia through development of a spatially explicit, agent-based, simulation model. Field and laboratory investigations resulted in the identification of two samples positive for F. tularensis. A feral cat tested positive for Type B tularemia using a new aptamer-based assay, and one sample returned positive in Amblyomma maculatum by polymerase chain reaction. This work sheds light on a complex host-pathogen-vector interaction in the rural to urban interface and establishes a framework for future tularemia field work and pathogen modeling in the rural to urban interface.

Modeling of changing pressure, temperature, and density profiles in a wellbore as a function of time is crucial for design and analysis of pressure-transient tests (particularly when data are gathered above perforations), real-time management of annular-pressure buildup (ABP) and identifying potential flow-assurance issues. Other applications of this modeling approach include improving design of production tubulars and artificial-lift systems and gathering pressure data for continuous reservoir management. This work presents a transient wellbore model coupled with a semianalytic temperature model for computing wellbore-fluid-temperature profile in flowing and shut-in wells. The accuracy of the analytic heat-transfer calculations improved with a variable-formation temperature model and a newly developed numerical-differentiation scheme. Surrounding formation temperature is updated in every timestep up to a user specified distance to account for changes in heat-transfer rate between the hotter wellbore fluid and the cooler formation. Matrix operations are not required for energy calculations because of the semianalytic formulation. This efficient coupling with the semianalytic heat-transfer model increased the computational speed significantly. Either an analytic or a numeric reservoir model can be coupled with the transient wellbore model for rapid computations of pressure, temperature, and velocity. The wellbore simulator is used for modeling a multirate test from a deep offshore well. Thermal distortion and its effects on pressure data is studied using the calibrated model, resulting in development of correlations for optimum gauge location in both oil and gas wells. Finally, predictive capabilities of the wellbore model are tested on multiple onshore wells experiencing annular-pressure buildup problems. Modeling results compare quite well with the field data and also with the state-of-the-art commercial wellbore simulator.

Most paved roads in the United States are surfaced with asphalt. These asphalt pavements suffer from fatigue cracking and thermal cracking, aggravated by the oxidation and hardening of asphalt. This negative impact of asphalt oxidation on pavement performance has not been considered adequately in pavement design. Part of the reason is that the process of asphalt oxidation in pavement is not well understood. This work focused on understanding the asphalt oxidation kinetics and on developing pavement oxidation model that predicts asphalt oxidation and hardening in pavement under environmental conditions. A number of asphalts were studied in laboratory condition. Based on kinetics data, a fast-rate ? constant-rate asphalt oxidation kinetics model was developed to describe the early nonlinear fast-rate aging period and the later constant-rate period of asphalt oxidation. Furthermore, reaction kinetics parameters for the fast-rate and constant-rate reactions were empirically correlated, leading to a simplified model. And the experimental effort and time to obtain these kinetics parameters were significantly reduced. Furthermore, to investigate the mechanism of asphalt oxidation, two antioxidants were studied on their effectiveness. Asphalt oxidation was not significantly affected. It was found that evaluation of antioxidant effectiveness based on viscosity only is not reliable. The asphalt oxidation kinetics model was incorporated into the pavement oxidation model that predicts asphalt oxidation in pavement. The pavement oxidation model mimics the oxidation process of asphalt in real mixture at pavement temperatures. A new parameter, diffusion depth, defined the oxygen diffusion region in the mastic. A field calibration factor accounted for the factors not considered in the model such as the effect of small aggregate particles on oxygen diffusion. Carbonyl area and viscosity of binders recovered from field cores of three pavements in Texas were measured and were used for model calibration and validation. Results demonstrated that the proposed model estimates carbonyl growth over time in pavement, layer-by-layer, quite well. Finally, this work can be useful for incorporating asphalt oxidation into a pavement design method that can predict pavement performance with time and for making strategic decisions such as optimal time for maintenance treatments.

Models are used widely within software engineering and have been studied from many perspectives. A perspective that has received little attention is the role of modeler intent in modeling. Knowing the intent of the modeler supports both model comprehension by providing the correct context for interpreting the model and model quality by clearly defining what information the model must contain. Furthermore, formal expressions of this intent allow automated support for this. Despite the value that the knowledge of modeler intent can provide, there are no adequate means in the current state of modeling practice for expressing this information. The focus of this thesis is to address this gap by providing mechanisms for expressing modeler intent both explicitly and formally. We approach this problem by recognizing the existence of a role level in modeling where the role each model plays defines what information it should contain and how this is related to the information in other models. The specification of these roles is what we refer to as the expression of modeler intent. We then present a framework that incorporates four aspects of modeler intent at the role level: the existential intent for a model that arises in response to the need for a set of information by stakeholders, the content criteria that express what information the model is intended to contain, model relationships that express how models are intended to constrain one another and the decomposition criteria that express the intent behind how a model is decomposed into a collection of models. A key contribution of this thesis is the specification of the macromodeling language as a new modeling language designed for the role level that supports the expression of all four aspects of modeler intent. We evaluate these techniques by applying them to two real-world modeling examples.

Over the past decade, the constraint-based approach to metabolic modeling has become an important tool for understanding and controlling biology. Unfortunately, the application of this novel approach to systems biology in biotechnology has been limited by three significant technical issues: existing metabolic modeling methods cannot completely model the overflow metabolism, cannot model the metabolism of microbial communities, and cannot design strains optimized for productivity and titer. Three computational methods – the Flux Balance Analysis with Membrane Economics (FBAME) method, the Dynamic Multi-species Metabolic Modeling (DyMMM) framework, and the Dynamic Strain Scanning Optimization (DySScO) strategy – have been developed to resolve these issues respectively. First, the FBAME method, which adopts the membrane occupancy limitation hypothesis, was used to explain and predict the phenomenon of overflow metabolism, an important metabolic phenomenon in industrial fermentation, in Escherichia coli. Then, the DyMMM framework was used to investigate the community metabolism during uranium bioremediation, and demonstrated that the simultaneous addition of acetate and Fe(III) may be a theoretically viable uranium bioremediation strategy. Lastly, the DySScO strategy, which combines the DyMMM framework with existing strain design algorithms, was used to design commodity-chemical producing E. coli optimized for a balanced product yield, titer, and volumetric productivity. These novel computational methods allow for broader applications of constraint-based metabolic models in biotechnology settings.

Metabolic channelling occurs when two enzymes that act on a common substrate pass that intermediate directly from one active site to the next without allowing it to diffuse into the surrounding aqueous medium. In this study, properties of channelling are investigated through the use of computational models and cell simulation tools. The effects of enzyme kinetics and thermodynamics on channelling are explored with the emphasis on validating the hypothesized roles of metabolic channelling in living cells. These simulations identify situations in which channelling can induce acceleration of reaction velocities and reduction in the free concentration of intermediate metabolites. Databases of biological information, including metabolic, thermodynamic, toxicity, inhibitory, gene fusion and physical protein interaction data are used to predict examples of potentially channelled enzyme pairs. The predictions are used both to support the hypothesized evolutionary motivations for channelling, and to propose potential enzyme interactions that may be worthy of future investigation.

This dissertation focuses on the development of a mechanics based soil-roller interaction model intended to determine the degree of compaction of the top soil layer. The model was calibrated with, and compared to, soils data obtained from field and laboratory tests. The model contained 2 soil layers, but can be expanded to include additional layers. This study concludes that the developed soil-roller interaction model is capable of accurately determining the degree of compaction of the upper soil layer through back calculation of the soil modulus values. The model was able to reach convergence between the calculated and measured values of roller drum deflection through a regression analysis of soil stiffness and damping characteristics. The final values of the stiffness and damping characteristics needed to achieve a 1 percent difference between the calculated and measured values of roller drum deflection fell within expected ranges for the type of material tested. Part of this study included a sensitivity analysis of the input characteristics. The results of the sensitivity analysis revealed that the output of the model was highly sensitive to the mass of the second soil layer and to the elastic and plastic stiffness characteristics within both soil layers, but relatively insensitive to the mass of the first soil layer. The lack of sensitivity to the mass of the first soil layer means that large changes in the layer mass, and by extension the density, will have little effect on the output of the model. This characteristic is a drawback for conventional, density based specifications. However, specifications based on installing fill to the designed values of stiffness or modulus could benefit from the model. Much of the initial difference between calculated and measured roller drum deflection was probably caused by the difficulty in determining accurate starting values for the soil stiffness, damping and mass model characteristics. Future research should focus on ways to determine accurate values of the required input characteristics.