Recent advances in plant genetic engineering offer substantial benefits to farmers throughout the world. Genetic research has identified many exogenous genes that could considerably decrease production costs through transgene-mediated resistance to insect, viral, fungal and bacterial pathogens. Potato can be produced from true potato seed (TPS) through a sexual polyploidization step, known as 4x-2x hybridization. Little is known regarding the stability of transgenes through sexual polyploidization in potato, although studies have associated ploidy elevation with transgene silencing in plants such as Arabidopsis thaliana. In the present study, potato was transformed with two different transgenes, cry3Aa and PVYo cp, and transgene expression was analyzed through 4x-2x hybridization. Transgene introgression did not affect fertility or agronomic performance (tuber set, average tuber weight, total tuber yield) of the resulting 4x-2x hybrids; however, reduced seed germination was observed for several transgenic lines in an in vitro study. Ploidy elevation did not affect a highly expressed single copy cry3Aa transgene, simplex or duplex, transmitted through pollen to 4x-2x hybrids. By contrast, multiple copies of cry3Aa triggered significant transgene silencing in diploids and silencing was further pronounced upon pollen transmission to 4x-2x hybrids. Crosses between two, single insert plants demonstrated additional evidence that multiple cry3Aa transgenes resulted in reduced expression, as well as provided evidence for maternal effects on expression of the cry3Aa transgene. Finally, Cry3Aa expression levels of progeny derived from low expressing, multiple copy 4x-2x hybrids indicated that reduction of transgene number in progeny, through meiotic segregation, could increase Cry3Aa expression. The results suggest that 4x-2x hybridization using single copy, male parents can result in high expressing, transgenic 4x-2x hybrids while segregating for a low frequency of non-transgenic hybrids that create a "refuge" to inhibit development of resistance to transgenes in pest populations. / Ph. D.

There are numerous examples in the literature of time-dependent changes in the proper-ties of sands, or aging effects. Most of these aging effects are of increases in the cone penetration resistance. Time-dependent increases in penetration resistance have been measured in hydraulically placed fills and freshly densified deposits, with the largest in-creases following the use of ground modification techniques such as vibrocompaction, dynamic compaction, and blast densification. It is not known what causes these increases in penetration resistance to occur. The objective of this research was to gain an understanding of the possible mechanisms responsible for aging effects in sands. Current hypotheses to explain what causes aging effects in sands include increased interlocking of particles, internal stress arching, and precipitation of silica or carbonate minerals at the contacts between grains. To date, no unambiguous evidence has been presented to support these hypotheses. A laboratory testing program was developed to study the influence of different variables on the pres-ence and magnitude of aging effects. Three different sands were tested in rigid wall cells and buckets. Samples were aged under different effective stresses, densities, tempera-tures, and pore fluids. In every rigid wall cell, three independent measurements were made to monitor property changes during the aging process: small strain shear modulus using bender elements, electrical conductivity, and mini-cone penetration resistance. At the end of each test, detailed mineralogical tests were performed to assess changes in the chemistry of the samples and pore fluids. A total of 22 tests in rigid wall cells were per-formed with periods of aging ranging from 30 to 118 days. Mini-cone penetration resis-tances were measured in the buckets before and at various times during the aging process. Increases in the small strain shear modulus were measured with time. It was found that sand type and pore fluid composition greatly influenced the amount of increase in small strain shear modulus. Density was also found to influence the amount of increase in small strain shear modulus. Temperature was found to have little influence on the in-crease in small strain shear modulus with time. Changes in the chemistry of the samples were also measured with time. The dissolution and precipitation of minerals in solution was monitored with electrical conductivity measurements. In most of the tests, there was continual dissolution of minerals with time. Mineralogical studies and conductivity measurements indicated precipitation of carbonates and silica in two of the tests; however, scanning electron micrographs showed no visible evidence of precipitation. Despite the measured increases in small strain shear modulus and evidence of mineral precipitation, there were no increases in the mini-cone penetration resistance with time. This finding is significant and suggests that small-scale laboratory experiments do not capture the mechanism(s) that are responsible for time-dependent increases in penetration resistance in the field. / Ph. D.

To add damping to structures, viscoelastic materials (VEM) are added to structures. In order to enhance the damping effect of the VEM, a constraining layer is attached, creating a passive constrained layer damping treatment (PCLD). When this constraining layer is an active element, the treatment is called active constrained layer damping (ACLD). Recently, the investigation of ACLD treatments has shown it to be an effective method of vibration suppression. In this work, two new hybrid configurations are introduced by separating the passive and active elements. In the first variation, the active and passive element are constrained to the same side of the beam. The other variation allows one of the treatments to be placed on the opposite side of the beam. A comparison will be made with pure active, PCLD, ACLD and a variation which places the active element underneath PCLD. Energy methods and Lagrange's equation are used to obtain equations of motion, which are discretized using assumed modes method. The frequency dependent damping is modeled using the Golla-Hughes-McTavish (GHM) method and the system is analyzed in the time domain. GHM increases the size of the original system by adding fictitious dissipation coordinates that account for the frequency dependent damping. An internally balanced model reduction method is used to reduce the equations of motion to their original size. A linear quadratic regulator and output feedback are used to actively control vibration. The length and placement of treatment is optimized using different criteria. It is shown that placing the active element on the opposite side of the passive element is capable of vibration suppression with lower control effort and more inherent damping. If the opposite surface is not available for treatment, a suitable alternative places the PZT underneath the PCLD. LQR provides the best control, since it assumes all states are available for feedback. Usually only select states are available and output feedback is used. It is shown that output feedback, while not as effective as full state feedback, is still able to damp vibration. / Ph. D.

In homogenous materials the life of a component is controlled by damage associated with a single crack while that of non-homogenous materials is the result of a distributed damage state. The life prediction of composite materials is thus carried out using damage mechanics two common approaches of which are, macro- and micro-mechanical modeling. The former assumes homogeneity at the lamina level while the latter evaluates failure processes at the fiber-matrix level. In the first part of this study the remaining strength life prediction methodology MRLife, modified for ceramic composites (CCLife), is integrated into the finite element package CSTEM. to create an integrated design tool for ceramic matrix composites. Using this tool, a case study is carried out to predict the life of a notched Nicalon™/Silicon Carbide 2-D woven laminated composite coupon with a temperature distribution subject to fatigue loading. Global failure of the notched plate is predicted based on a Whitney-Nuismer type average strength criterion. In the second part of this study, simulation of events occurring at the fiber-matrix level are used to develop micro-mechanical models for the time-dependent behavior of fiber-reinforced composites due to shear creep of the fiber-matrix interface and slow crack growth in the fibers. At first, simulations of the time-dependent failure of the composite are performed using a modified Monte-Carlo fast-fracture model the results of which are then used to validate the analytical models developed for the two mechanisms. Finally, an analytical model for the time-dependent failure of a composite due to the combined effects of the two mechanism, shear creep and slow crack growth is presented. The potential for including the time-dependent failure model into CCLife is evaluated by comparing these results with those form CCLife results under the same conditions. / Ph. D.

TRANSIMS (Transportation Analysis Simulation System) is part of a multi-track Travel Model Improvement Program sponsored by the U. S. Department of Transportation (DOT), and the Environmental Protection Agency (EPA). The main objective of this thesis is to enhance and implement a principal module in TRANSIMS, called the Route Planner Module. The purpose of the Route Planner Module is to find time-dependent label-constrained shortest paths for transportation activities performed by travelers in the system. There are several variations of shortest path problems and algorithms that vary by application, contexts, complexity, required data, and computer implementation techniques. In general, these variants require some combination of the following inputs: a network consisting of nodes and links, and a travel time function on each link, which could be a time-independent or a time-dependent function, where the time-dependent functions account for time-of-day delays resulting from actual travel conditions such as peak-hour congestion. The problem then seeks a shortest path between one or more origin-destination pairs. A new variant, introduced in the context of TRANSIMS and which is the focus of the present study, also specifies labels for each arc denoting particular modes of travel, along with strings of admissible labels that delineate the permissible travel mode sequences that could be adopted by the user in traveling from the origin to the destination of the trip. The technique adopted by TRANSIMS to identify a suitable travel route for any user is a variant of Dijkstra's procedure for finding shortest paths, which is suitably modified to accommodate time-dependent travel times and label sequence constraints. The underlying problem is referred to as a Time-Dependent Label-Constrained Shortest Path Problem. The main objective of this research is to improve upon this procedure and study its implementation in order to develop a more effective scheme for determining time-dependent label-constrained shortest paths as a practical routing tool in multimodal transportation networks. Specifically, we enhance the following features of this procedure: (a) We recommend a method to work implicitly with a certain composition graph G* that combines the transportation network with the admissible label-sequence graph. This graph G* captures all possible paths for a given single trip starting from the origin node and ending at the destination node, while conforming with the admissible mode string. (b) We use more modern partitioned shortest path algorithmic schemes to implement the time-dependent label-constrained procedure. (c) We introduce the notion of curtailing search based on various indicators of progress and projected travel times to complete the trip. Finally, computer programs in C++ are written to implement the proposed overall algorithm, and are applied to solve some real multimodal transportation network problems. The indicators used to evaluate the performance of the algorithm include (i) time taken for computation on the real network, (ii) quality of solution obtained, (iii) ease of implementation, and (iv) extensibility of the algorithm for solving other variants of the shortest path problem. The results exhibit that the proposed algorithm, even without the approximate curtailing of the search process, exhibits good performance in finding optimal routes for real multimodal transportation networks. Although the various heuristic curtailments result in only approximate solutions, typically, they run much faster than the exact algorithm for the intuitive reason that the shortest path tree developed grows more pointedly in the direction of the destination. Among the different strategies implemented, our results suggest that the scheme based on the geometric structure of the underlying network, using either a constant predictive term, or multiplying this term with a suitable exponential decay function, yields an attractive candidate for heuristically curtailing the search. / Master of Science

Use of a magnetic compass has been demonstrated in all major classes of vertebrates as well as several classes of invertebrates, and is proposed to involve a photo-induced radical pair mechanism (RPM). My dissertation research consisted of characterizing a magnetic compass in a model species, Drosophila melanogaster. Preliminary experiments were carried out with adult flies, however, due to the behavioral complexity of adult responses a new behavioral assay of magnetic compass orientation was developed using larval Drosophila that elicits a robust magnetic compass response in a trained magnetic direction. This manuscript describes experiments that were conducted showing that larval magnetic compass orientation: 1) demonstrates a complex 3-dimensional pattern of response consistent with a RPM; 2) is consistent with a receptor mechanism that utilizes short- and long-wavelength antagonistic photopigments, proposed to explain wavelength dependent effects in vertebrates (e.g. amphibians and birds); and 3) produces axially symmetrical patterns of response with respect to the geomagnetic field. Additionally, tests of adult Drosophila under low and high intensities of monochromatic long wavelength light revealed a similar behavioral response to varying intensities of monochromatic light as previously reported in migratory birds (E. rubecula). These findings indicate that the magnetic compass of larval Drosophila shares a common functional architecture and similar biophysical mechanism with that of at least some vertebrates (e.g. amphibians and possibly birds), suggesting that the magnetic compass of modern vertebrates may have evolved once in a common ancestor of these three lineages over 450 million years ago. Furthermore, findings indicating a spontaneous preference for magnetic directions in D. melanogaster larvae suggest that a light-dependent magnetoreception mechanism is more widespread in insects than was previously suspected. The development of a behavioral assay to study the light-dependent magnetic compass in an organism with a simple nervous system, a limited behavioral repertoire, and with the possibility of using the full power of modern molecular and genetic techniques holds considerable promise to increase our understanding of the biophysical mechanism(s) and neurophysiological structures underlying magnetic orientation in terrestrial animals. / Ph. D.

The fact that traffic congestion upstream of a bottleneck causes a reduction in the discharge flow rate through the bottleneck has been well documented in several empirical studies. However, what has been missing is an understanding of the causes of these empirically observed flow reductions. An identification of these causes is important in order to develop various mitigation schemes through the use of emerging technology. The concept of capacity drop can be introduced at time-independent bottlenecks (e.g. freeways) as well as time-dependent bottlenecks (e.g. signalized intersections). While to the author's knowledge no one has attempted to link these phenomena, the research presented in this thesis serves as a first step in doing so. The research uses the INTEGRATION simulation software, after demonstrating its validity against empirical data, to simulate time-independent and time-dependent bottlenecks in an attempt to characterize and understand the contributing factors to these flow reductions. Initially, the INTEGRATION simulation software is validated by comparing its results to empirically observed traffic stream behavior. This thesis demonstrates that the discharge flow rate is reduced at stationary bottlenecks at the onset of congestion. These reductions at stationary bottlenecks are not recovered as the traffic stream propagates downstream. Furthermore, these reductions are not impacted by the level of vehicle acceleration. Alternatively, the drop in the discharge flow rate caused by time-dependent bottleneck is recoverable and is dependent on the level of acceleration. The difference in behavior is attributed to the fact that in the case of a stationary bottleneck the delay in vehicle headways exceeds the losses caused by vehicle accelerations and thus is not recoverable. In the case of vehicles discharging from a backward recovery wave the dominant factor is the delay caused by vehicle acceleration and this can be recuperated as the traffic stream travels downstream. / Master of Science

Time-dependent queueing models are important since most of real-life problems are time-dependent. We develop a numerical approximation algorithm for the mean, variance and higher-order moments of the number of entities in the system at time t for the Ph(t)/Ph(t)/s/c queueing model. This model can be thought as a reparameterization to the G(t)/GI(t)/s. Our approach is to partition the state space into known and identifiable structures, such as the M(t)/M(t)/s/c or M(t)/M(t)/1 queueing models. We then use the Polya-Eggenberger distribution to approximate certain unknown probabilities via a two-moment matching algorithm. We describe the necessary steps to validate the approximation and measure the accuracy of the model. / Master of Science

In somatic cells, checkpoint pathways trigger cell cycle arrest in response to unreplicated or damaged DNA by inhibiting the activity of cyclin-dependent kinases (Cdks). In the Xenopus laevis embryo, checkpoints are not operational until the midblastula transition (MBT). Studies in cell-free egg extracts indicate that a threshold concentration of nuclei, which approximates the MBT concentration, is required to elicit a checkpoint. The checkpoint response to unreplicated DNA in the extract prevents transition into mitosis by inhibiting Cdk1/cyclin B, causing an increase in the minimum amount of cyclin B necessary to enter mitosis, termed the cyclin threshold. Once the threshold of cyclin is maintained or exceeded, the system will proceed into mitosis after a lag time. We have investigated the relationship between nuclear concentration and cell cycle regulation in the extract. By precisely regulating the concentration of cyclin B and nuclear content in extract samples, we have found 1) the concentration of nuclei affects cyclin B thresholds and lag time of entry into mitosis, 2) elevated cyclin thresholds caused by DNA replication blocks are further increased by increasing the concentration of nuclei, and 3) double-stranded DNA breaks in the extract system do not affect cyclin thresholds or lag time of entry into mitosis within the range of nuclear concentrations that can be efficiently replicated. This data provides evidence of the importance of the nucleocytoplasmic ratio in normal cell cycle progression and its importance for checkpoint acquisition during early Xenopus laevis development. / Master of Science

Accurate camber prediction in prestressed concrete bridge beams is important to all parties involved in bridge design and construction. Many current prestress loss prediction methods, necessary for proper camber calculation, were developed many years ago and are predicated on assumptions that may no longer be valid as higher strength concrete, wider beam spacing, and longer span lengths become more commonplace. This throws into question which models are appropriate for use in camber calculation by the bridge engineers and contractors of today. Twenty-seven high-strength concrete modified 79 in. Bulb Tee beams with a design compressive strength of 9,000 psi were periodically measured to determine camber growth. Most available models for concrete creep and shrinkage were used to calculate creep and shrinkage strain. The modulus of elasticity equation of each model was used to predict modulus of elasticity of the studied mix. The Shams and Kahn compressive strength and modulus of elasticity equations were modified in order to approximate measured modulus of elasticity. The creep, shrinkage, and modulus of elasticity equations were used as inputs to an incremental time step method. The time-dependent change in beam curvature calculated by the time step method was used to calculate theoretical camber using the Moment-Area method. Predicted camber, using inputs from each considered model, was then compared with measured camber to determine the most accurate camber prediction models. Season of casting was also examined to determine what, if any, affect ambient temperature has on camber growth. For the studied beams, the Shams and Kahn Model for creep, shrinkage, and modulus of elasticity, used as inputs for an incremental time step analysis, were found to most accurately predict camber values. Lower concrete compressive strength was observed for test cylinders from beams cast in summer versus beams cast in winter. Differences in beam deflection based on season of casting showed mixed results. / Master of Science