The International Civil Aviation Organization (ICAO) proposed to introduce new operational strategies across the North Atlantic (NAT) airspace. This includes Minimum Navigation Performance Specifications (MNPS) airspace to increase the capacity and efficiency of the North Atlantic Organized Track System (NAT OTS). A numerical integration and simulation model called North Atlantic Simulation and Modeling (NATSAM) is developed to study the effects of these new strategies on NAT system performance. The model is capable of investigating the effects of implementing different operational policies and strategies proposed by ICAO such as Reduced Lateral Separation Minimum (RLatSM), NAT Region Data link mandate (DLM), Reduced Longitudinal Separation Minimum (RLongSM), cruise-climb profiles, variable Mach number profiles, step-climbs and other operational concepts to be studied by the ICAO. NATSAM models the individual flight performance using the Base of Aircraft Data (BADA) 3.9 model to calculate the flight profiles and fuel burn. The model employs simple heuristics to execute flight track assignment in the organized track system for each scenario. Detailed outputs and also aggregated outputs are provided by the model from which various key performance indicators (KPI) can be derived to assess the performance of the system. / Master of Science

In this thesis, I examine filtering based stabilization methods to design new regularized reduced order models (ROMs) for under-resolved simulations of unsteady, nonlinear, convection-dominated systems. The new ROMs proposed are variable delta filtering applied to the evolve-filter-relax ROM (V-EFR ROM), variable delta filtering applied to the Leray ROM, and approximate deconvolution Leray ROM (ADL-ROM). They are tested in the numerical setting of Burgers equation, a nonlinear, time dependent problem with one spatial dimension. Regularization is considered for the low viscosity, convection dominated setting. / Master of Science / Numerical solutions of partial differential equations may not be able to be efficiently computed in a way that fully captures the true behavior of the underlying model or differential equation, especially if significant changes in the solution to the differential equation occur over a very small spatial area. In this case, non-physical numerical artifacts may appear in the computed solution. We discuss methods of treating these calculations with a goal of improving the fidelity of numerical solutions with respect to the original model.

The work presented in this thesis attempts to provide an understanding of the physics behind the dynamic stall process by simulating the flow past pitching NACA-0012 airfoil at 100,000 and 1 million Reynolds number based on the chord length of the airfoil and at different reduced frequencies of 0.188 and 0.25 respectively in a three dimensional flow field. The mean angles of attack are 12 deg. and 15 deg. and the amplitudes of pitching are 6 deg. and 10 deg. respectively. The turbulence in the flow field is resolved using large eddy simulations with dynamic Smagorinsky model at the sub grid scale. The lift hysteresis plots of this simulation for both the configurations are compared with the corresponding experiments. The development of dynamic stall vortex, vortex shedding and reattachment as predicted by the present study are discussed in detail. There is a fairly good match between the predicted and experimentally measured lift coefficient during the upstroke for both cases. The net lift coefficient for the Re = 100,000 case during downstroke matches with the corresponding experimental data, the present study under-predicts the lift coefficient as compared to the experimental values at the start of downstroke and over-estimates for the remaining part of the downstroke. The trend of the lift coefficient hysteresis plot with the experimental data for the Re = 1 million case is also similar. This present simulations have shown that the downstroke phase of the pitching motion is strongly three dimensional and is highly complex, whereas the flow is practically two dimensional during the upstroke. / Master of Science

Rotordynamic instability problems in turbomachinery have become more important in recent years due to rotordynamic components with higher speeds and higher power densities. These features typically lead to increased instability risk in rotor dynamic components as fluids-structure interactions take place. In addition, critical damage of rotordynamic components can result from high level vibrations of supporting bearing system, where the reduced rotor speed can lead to system operating near the rotor critical speed. Therefore, increased accuracy in modeling of rotordynamic components is required to predict the potential instability issues in high performance rotordynamic design. The instability issue may potentially be eliminated in design stage by varying the characteristics of the unstable components. One such turbomachinery component is the annular pressure seal. The annular pressure seals are specifically designed to prevent the fluid leakage from high pressure stage to low pressure stage in turbomachinery. Typical annular pressure seals have two different flow regions, an annular jet-flow region between the rotor and stator, and cylindrical or circumferential indentions on the stator/rotor surface that serve as cavities where flow recirculation occurs. As the working fluid enters the cavities and recirculates, the kinetic energy is reduced, resulting in a reduction of leakage flow. The current challenge is to model with higher precision the interaction between the rotordynamic components and the working fluid. In this dissertation, this challenge was overcome by developing a hybrid Bulk Flow/CFD method to compute rotordynamic responses for the annular pressure seals. In addition, design of experiments studies were performed to relate the surface patterning with the resulting rotordynamic response for the annular pressure seals, in which several different geometry specifications were investigated. This study on annular pressure seal design generated regression models for rotordynamic coefficients that can be used as optimization guidelines. Research topics related to the annular pressure seals were presented in this dissertation as well. The reduced order model of both hole-pattern seals and labyrinth seals were investigated. The results showed that the flow field representing the flow dynamics in annular pressure seals can be expressed as a combination of first three proper orthogonal decomposition modes. In addition, supercritical state of carbon dioxide (sCO2) process fluid was examined as the working fluid in a preliminary study to better understand the effects on annular pressure seals. The results showed that the performance and stability in the annular pressure seals using sCO2 as process fluid can both be improved. / Doctor of Philosophy / This dissertation focused on understanding the correlations between surface patterning and rotordynamic responses in the annular pressure seals. The annular pressure seals are a specific type of rotordynamic component that was designed to prevent the fluid leakage from high pressure stage to low pressure stage in turbomachinery. As the working fluid enters the cavities and recirculates, the kinetic energy is reduced, resulting in a reduction of leakage flow through the annular pressure seals. Rotordynamic instability becomes an issue that may be related to the annular pressure seals in some cases. In recent years, rotordynamic components with higher rotor speeds and higher power densities are commonly used in industrial applications. These features could lead to increased instability risk in rotor-bearing systems as fluids-structure interactions take place. Therefore, high precision modeling of the rotodynamic components is required to predict the instability issues in high performance rotordynamic design. The instability issue may potentially be eliminated in design stage by varying the characteristics of the potentially unstable components. In this study, the surface patterning and rotordynamic responses were investigated for several different annular pressure seal models with a hybrid Bulk Flow/Computational Fluid Dynamics method. This dissertation provides for the first time regression models for rotordynamic coefficients that can be used as optimization guidelines. Research topics related to the annular pressure seals were presented in this dissertation as well. The reduced order model of both hole-pattern seals and labyrinth seals were investigated. The results showed that the flow field representing the flow dynamics in annular pressure seals can be expressed as a combination of first three proper orthogonal decomposition modes. In addition, supercritical state of carbon dioxide (sCO2) process fluid was examined to better understand the effects of working fluid on annular pressure seals. The results showed that the performance and stability in the annular pressure seals using sCO2 as process fluid can both be improved.

Most staple food crops were domesticated thousands of years ago through independent processes across different regions of the world. Studies of the history of such crops have been essential to our understanding of plant domestication as a process that started with the collection of wild material and continued with subsequent propagation, cultivation, and selection under human care. Domestication often involves a complex genetic structure with contributions from multiple founder populations, interspecific hybridization, chromosomal introgressions, and polyploidization events that occurred hundreds to thousands of years earlier. Such intricate origins complicate the systematic study of the sources of phenotypic variation. The analysis of recently domesticated, non-traditional, non-model species, such as Sinningia speciosa (Gesneriaceae), can expand the knowledge that we have on phenotypic variation under domestication, and help us to comprehend modern patterns of plant domestication and to broaden our understanding of the general trends. S. speciosa is commonly known as the 'florist's gloxinia', and it has been cultivated for 200 years as an ornamental houseplant. In our genomic study of S. speciosa, we examined an extensive diversity panel consisting of 115 individuals that included different species in the genus, wild representatives, and cultivated accessions, as well as 150 individuals from an F2 segregating population. Our analyses revealed that all of the domesticated varieties are derived from a single founder population that originated in or near the city of Rio de Janeiro in Brazil. We identified two loci associated with domesticated traits (flower symmetry and color) and did not detect any major hybridization or polyploidization events that could have contributed to the rapid increase in phenotypic diversity. Our findings, in conjunction with other features such as a small, low-complexity genome, ease of cultivation, and rapid generation time, makes this species an attractive model for the study of genomic variation under domestication. Basic research on non-model organisms with low economic importance is uncommon but necessary to understand the world from a broader perspective. In such cases, reduced representation approaches like Genotyping-by-Sequencing (GBS) are efficient low-cost alternatives to whole genome resequencing. However, most of these technologies are subject to patent protection, licensing processes, and fees that constrain genomic research for small non-profit research organizations. We have designed a protocol to construct reduced representation libraries from genomic DNA. Our approach, called Targeted Amplification of Scattered Sites (TASS), deviates from the traditional digestion-ligation-amplification process that is the subject of intellectual property that protects most current methods. Instead, TASS relies on 1) targeting and duplicating scattered regions in the genome by annealing and expanding long tail primers with short annealing sites, and 2) amplifying these regions using primers that are complementary to the added overhangs. At the moment GBS is more consistent and delivers more variants than TASS. However, we have established a foundation on which further optimization can produce an accessible, easy to implement, high-throughput genotyping approach. / Doctor of Philosophy / Most staple food crops were domesticated thousands of years ago through unrelated processes that were initiated across different regions of the world. Studies of the history of such crops have been essential to our understanding of plant domestication, a process that started with the collection of wild material and continued with subsequent propagation and cultivation under human care. Plant domestication has often involved a complex combination of ancestral lineages that encompass multiple populations, crosses with other species, and large DNA reorganizations that occurred hundreds to thousands of years earlier. Such intricate origins make the systematic study of plant domestication very challenging. The analysis of recently domesticated plants such as the 'florist's gloxinia' (Sinningia speciosa), can help us to better understand some of the changes that have occurred during domestication, as well as to comprehend modern patterns of plant domestication and to broaden our understanding of general trends. Florist's gloxinias are ornamental plants that have been cultivated during the last 200 years. In this study we examined 115 specimens, including wild and cultivated types of florist's gloxinias, as well as closely related species in Sinningia. We also constructed and evaluated an artificial population of 150 individuals from the cross of a wild and a cultivated form. Our analyses revealed that all of the domesticated varieties are descendants from a single wild population that originated in or near the city of Rio de Janeiro in Brazil. We also identified two regions of DNA that are responsible for the changes in flower shape and color, and crosses with other species did not introduce such alterations. Our findings, in conjunction with other features such as its small nuclear DNA content, the ease of cultivation indoors, and a rapid generation time, makes the florists' gloxinia an attractive crop to the study the effects of plant domestication. Research on organisms with low economic importance is uncommon but necessary to understand the world from a broader perspective. In such cases, analyzing the entire genetic information that is stored as DNA may be cost-prohibitive. Instead, approaches that sample small portions of DNA from each individual can be utilized. Most of these technologies are currently patented and subject to licensing processes and fees that limit their implementation by small non-profit research organizations. In this study we designed a protocol to sample small portions of DNA, similarly to existing techniques. However, our approach, called Targeted Amplification of Scattered Sites (TASS), employs a sampling process that deviates from the traditional patented procedure that is used in most current methods. At present, TASS is not as consistent and delivers less information than traditional approaches. However, we have established a foundation on which further optimization can produce an accessible and easy to implement technique.

We investigate the effect of spatial filtering on the recently proposed data-driven correction reduced order model (DDC-ROM). We compare two filters: the ROM projection, which was originally used to develop the DDC-ROM, and the ROM differential filter, which uses a Helmholtz operator to attenuate the small scales in the input signal. We focus on the following questions: ``Do filtering and differentiation with respect to space variable commute, when filtering is applied to the diffusion term?'' or in other words ``Do we have commutation error (CE) in the diffusion term?" and ``If so, is the commutation error data-driven correction ROM (CE-DDC-ROM) more accurate than the original DDC-ROM?'' If the CE exists, the DDC-ROM has two different correction terms: one comes from the diffusion term and the other from the nonlinear convection term. We investigate the DDC-ROM and the CE-DDC-ROM equipped with the two ROM spatial filters in the numerical simulation of the Burgers equation with different diffusion coefficients and two different initial conditions (smooth and non-smooth). / M.S. / We propose reduced order models (ROMs) for an efficient and relatively accurate numerical simulation of nonlinear systems. We use the ROM projection and the ROM differential filters to construct a novel data-driven correction ROM (DDC-ROM). We show that the ROM spatial filtering and differentiation do not commute for the diffusion operator. Furthermore, we show that the resulting commutation error has an important effect on the ROM, especially for low viscosity values. As a mathematical model for our numerical study, we use the one-dimensional Burgers equations with smooth and non-smooth initial conditions.

This thesis presents a performance assessment of flight operations in the North Atlantic Organized Track System (OTS) using the Global Oceanic Model. The main contributions of the study are: a) improvements to the logic of the Global Oceanic Model; b) prediction of benefits among various aircraft separation minima and operational policies to assign flights to tracks in the OTS system; and c) forecast of OTS traffic over North Atlantic from 2020 to 2040. The preliminary results show that a concept of operation with longitudinal separation minima of 15 nm and information of the flight cost matrix provides average fuel savings of 93 kilograms per flight using 2020 traffic. The fuel savings increase to 170 kilograms per flight using traffic levels expected in the year 2040. A new operational track assignment routine is developed and it could save around 40 kilograms per flight compared with the current concept of operations. The study results show a shortage of capacity of the Organized Track System in the future. The analysis shows that the OTS configuration used today and in 2020 is unable to accommodate the traffic projected in 2040. The analysis concludes that more tracks will be needed to maintain an acceptable level of service. / MS

An optimal solution of vortex-induced vibrations of structures would be a time-domain numerical simulation that simultaneously solves the fluid flow and structural response. Yet, the requirements in terms of computing power remains a major obstacle for implementing such a simulation. On the other hand, lower- or reduced-order models provide an alternative for determining structural response to forcing by fluid flow. The objective of this thesis is to provide a consistent approach for the development of reduced-order models for the lift and drag on oscillating cylinders and the identification of their parameters. Amplitudes and phases of higher-order spectral moments of the lift and drag coefficients data are combined with approximate solutions of the representative models to determine their parameters. The results show that the amplitude and phase of the trispectrum could be used to model the lift on the oscillating cylinder under different excitation conditions. Moreover, the amplitude and phase of the cross-bispectrum could be used to establish the lift-drag relation for oscillating cylinders. A forced van der Pol equation is used to represent the lift on a transversely oscillating cylinder, and a parametrically excited van der Pol equation is used to model the lift coefficient on an inline oscillating cylinder. All cases of excitations lead to close values for the damping and nonlinear parameters in the van der Pol equation. Consequently, and as shown in this thesis, different excitation cases could be used to identify the parameters in the governing equations. Moreover, the results show that the drag coefficient could be derived from the lift coefficient through a square relation that takes into account the effects of the forced motions. / Ph. D.

When designing a control for a physical system described by a PDE, it is often necessary to reduce the size of the controller for the PDE system. This is done so that real time control can be achieved. One approach often taken by engineers is to reduce the approximating finite-dimensional system using a balanced reduction method known as balanced truncation and then design a control for the lower order system. The unsettling idea about this method is that it involves discarding information and then designing a control. What if valuable physical information were lost that would have allowed a more effective control to be designed? This paper will explore an alternate balanced reduction method called LQG balancing. This approach allows for the designing of a control on the full order approximating system and then reducing the control. Along the way, the basic ideas of feedback control design will be discussed, including system balancing and model reduction. Following, there will be mention of the linear Klein-Gordon equation and the development of the one-dimensional finite element approximation of the PDE. Finally, simulations and numerical experiments are used to discuss the differences between the two balanced reduction methods. / Master of Science

Steel moment frames are a popular seismic-force resisting system, but it is believed that they are susceptible to early fracture if there is a stress concentration in the plastic hinge region, also known as the protected zone. If a defect is present in this area, it may be repaired by grinding and/or welding, but little research has investigated how the repairs affect the performance of full-scale moment connections subjected to inelastic rotations. Thus, the goals of this research were to establish the performance of full-scale moment connections with repairs and defects, then develop a method for predicting fracture of the full-scale specimens using more economical cyclic bend tests. To do this, six full-scale reduced beam section (RBS) connections were tested having arrays of repairs or defects applied to the flanges. The repairs were 0.125 in. deep notches ground to a smooth taper and 0.25 in. deep notches ground to a smooth taper, welded, and ground smooth. The defects were sharp 0.25 in. and 0.375 in. notches. In addition, 54 bend tests were conducted on beam flange and bar stock coupons having the same repairs and defects, power actuated fasteners, puddle welds, and no artifacts. Finally, Coffin-Manson low-cycle fatigue relationships were calibrated using results from the cyclic bend tests with each artifact (repair, defect, or attachment method) and used in conjunction with estimates of full-scale plastic strain amplitudes to predict fracture of full-scale specimens. All four of the full-scale moment connections with repairs satisfied special moment frame qualification criteria (SMF). One full-scale specimen with sharp 0.25 in. notches satisfied SMF qualification criteria, but the flexural resistance dropped rapidly after the qualification cycle. On the other hand, the specimen with sharp 0.375 in. notches did not satisfy SMF qualification criteria due to ductile fractures propagating from the notches. The proposed method for predicting fracture of full-scale connections was validated using the six current and six previous full-scale RBS specimens. This method underpredicted fracture for eleven of the twelve specimens. The ratio of the actual to predicted cumulative story drift at fracture had a mean of 1.13 and a standard deviation of 0.19. / M.S. / Moment connections in steel structures resist earthquake loads by permanently deforming the material near the connection. This area is called the protected zone and is critical to the safety of the structure in an earthquake. Due to this importance, no defects are allowed near the connection, which can include gouges or notches. If a defect does occur, it must repaired by a grinding or welding. These are the required repair methods, but there have be no tests to determine how the repairs affect the strength and ductility of the connection. This research tested six full-scale moment connections with defects repaired by grinding and welding, as well as unrepaired defects. A correlation was also developed and validated between the full-scale tests and small-scale bend tests of steel bars with the same defects and repairs. This relationship is valuable because the small-scale tests are quicker and less expensive to conduct than the full-scale tests, meaning other defects or repairs could be easily tested in the future. All but one of the six full-scale specimens met the strength requirements and had adequate ductility. The one test specimen that failed had an unrepaired defect. The relationship between the full-scale and small-scale tests underpredicted fracture (a conservative estimate) for the five of the full-scale tests and overpredicted fracture (unconservative estimate) for one test.