VictorJuiz/thesis huggingface dataset:
Conditioning surface-based models to well and thickness data [electronic resource]

Surface-based models imitate a sequence of depositional events in time. By considering sedimentation processes, these algorithms produce highly realistic subsurface structures from a variety of environments. However, since depositional events are forward-modeled, they cannot be directly conditioned to data. Therefore, conditioning requires solving a possibly expensive inverse problem. In this study, an optimization scheme is developed that allows conditioning turbidite simulation to thickness information and well data. The methodology is applied to three real data sets.

Keywords: Energy Resources Engineering
Advisor: Caers Jef primary advisor. Thesis advisor
Durlofsky Louis advisor. Thesis advisor
Tchelepi Hamdi advisor. Thesis advisor
"Confio / I trust", surrounding the limits of time [electronic resource] : a cycle of pieces for different instrumental combinations and voices

"Confío / I trust", surrounding the limits of time is a cycle of pieces in the form of modular movements, which also function as independent works and it is for different combinations of instruments and voices. This project is the result of different stages of research and direct work with performers in some cases. The cycle is focused on a reflection concerning musical language and different types of connection with poetic expression. It is engaged with a vast conception of early Western music and its spirituality and sense of poetic melancholy --sometimes also of joy-- viewed from a contemporary perspective. This project entails a non-antagonistic reflection about the relationship between composers and performers, and creators with their work. This approach to early music could contribute to an understanding of music as a vehicle of emotions, text as the principal tool to express passions, and notation as a result of a practical human tradition. Academic contemporary music, after extensive expansions through different avant-garde movements, new instrumental techniques, extreme integration of instrumental sounds and technological means, would find a creative source in this space of encounter with early music, as a way to question, reaffirm, and spread out its potentiality.

Keywords: Music
Advisor: Ferneyhough Brian
Kapuscinski Jaroslaw
Ulman Erik
Conformational transitions in RNA probed in riboswitch systems [electronic resource]

Conformational transitions are a key phenomenon in biological processes; proteins and nucleic acids require structural malleability that not only enables them to adopt specific three-dimensional structures that impart activity, but also accommodates conformational transitions that enhance their functions and allow them to communicate with their surrounding environment. Protein conformational transitions have been extensively studied for a large number of systems, but RNA conformational transitions are less well understood. In this dissertation, I have studied conformational transitions in RNA occurring at the levels of both secondary and tertiary structure. A thiamine pyrophosphate and an adenine riboswitch have been used to follow the folding of RNA from an ensemble of partially structured heterogeneous conformers in the ligand-free state to fully folded native states in the ligand-bound state. Small angle X-ray scattering and two-dimensional chemical footprinting have been used as the primary experimental techniques to query the conformational transitions occurring in these two RNA systems. Being solution techniques, these methods are particularly suitable for probing heterogeneous ensembles of RNA structures that exist at thermodynamic equilibrium in variable salt and ligand concentrations. The results provide detailed characterization of partially folded RNA structures and the conformational transitions that mediate their conversion to natively folded forms.

Keywords: Applied Physics
Advisor: Doniach S. primary advisor. Thesis advisor
Das Rhiju advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Consequences of rewards [electronic resource] : the creation, perpetuation, and erosion of social inequality

This dissertation focuses on how status and rewards jointly impact the creation, perpetuation and erosion of social inequality. Rewards are objects or positions that come to have differential levels of prestige when they are affiliated with groups of varying status, such as certain types of educational degrees, technologies, awards, and the like. Expectations about who we are and what we should be able to achieve are formed based on a combination of both our characteristics and displayed status markers. The first study experimentally tests whether rewards have the power to create entirely new status characteristics and bases of inequality. The second study is an examination of how assessments of competence and trustworthiness systematically bias the distribution of rewards and, thereby, the perpetuation of inequality, by examining how lenders perceive loan applicants and make funding decisions in experimentally created lending markets. The third study explores whether rewards have the power to neutralize status-based inequality when low status individuals are rewarded with markers of a much higher honorific value than members of high status groups.

Keywords: Sociology.
Advisor: Cook Karen S. primary advisor. Thesis advisor
Correll Shelley Joyce advisor. Thesis advisor
Ridgeway Cecilia L. advisor. Thesis advisor
A conservative meshless framework for conservation laws with applications in computational fluid dynamics [electronic resource]

Mesh generation, which is essential to most traditional numerical discretizations, often remains the bottleneck of the simulation process. Many researchers have developed meshless algorithms to circumvent mesh generation. Unfortunately, almost all existing meshless methods suffer from the lack of formal discrete conservation, which can lead to unpredictable numerical errors in the presence of discontinuities. This thesis addresses the issue of non-conservation in existing meshless methods. It focuses on the formulation and implementation of a novel conservative meshless scheme and its applications in computational fluid dynamics (CFD). The scheme, first of such nature documented in the literature, is formulated based on obtaining derivative approximations using function values and generated coefficients satisfying a set of reciprocity and polynomial consistency conditions. The required coefficients are generated by the solution of a global quadratic program. They minimize an upper bound of a representation of the global discretization error in addition to satisfying the necessary conditions. A generalization of the derivative approximation allows the use of arbitrary consistent interface values in the derivative operator while maintaining discrete conservation. This creates a flexible framework within which a wide variety of numerical flux schemes, such as those previously developed for finite volume discretization, can be used with no additional costs. The practicality of this new framework is demonstrated by solving compressible flow problems using, without modifications, a piece of software designed for finite volume discretization. The meshless numerical results show superconvergence and compare well with those obtained using meshed finite volume discretizations and other meshless schemes, highlighting the validity of the new framework and its potential to be applied to problems of greater complexity and scale.

Keywords: Aeronautics and Astronautics
Advisor: Jameson Antony
Iaccarino Gianluca advisor. Thesis advisor
MacCormack R. W. (Robert William)
Consistency and convergence rate of Markov chain quasi Monte Carlo with examples [electronic resource]

Markov Chain Monte Carlo methods have been widely used in various scientific disciplines for generation of samples from distributions that are difficult to simulate directly. The random numbers driving Markov Chain Monte Carlo algorithms are modeled as independent $\mathcal{U}[0,1)$ random variables. The class of distributions that could be simulated are largely broadened by using Markov Chain Monte Carlo. Quasi-Monte Carlo, on the other hand, aims to improve the accuracy of estimation of an integral over the multidimensional unit cube. By using more carefully balanced inputs, under some smoothness conditions the estimation error is converging at a higher rate than plain Monte Carlo. We would like to combine these two techniques, so that we can sample more accurately from a larger class of distributions. This method, called Markov Chain quasi-Monte Carlo (MCQMC), is the main topic of this work. We are going to replace the IID driving sequence used in MCMC algorithms by a deterministic sequence which is designed to be more uniform. Previously the justification for MCQMC is proved only for finite state space case. We are going to extend those results to some Markov Chains on continuous state spaces. We also explore the convergence rate of MCQMC under stronger assumptions. Lastly we present some numerical results for demonstration of MCQMC's performance. From these examples, the empirical benefits of more balanced sequences are significant.

Keywords: Statistics
Advisor: Owen Art B. primary advisor. Thesis advisor
Lai T. L. advisor. Thesis advisor
Wong Wing Hung advisor. Thesis advisor
Context-dependent interactions in an ant-plant-hemipteran symbiosis [electronic resource]

The cost-benefit outcomes of potentially mutualistic interactions between species can range on a continuum between mutualism and parasitism, depending on context. Here I use ecological, behavioral, physiological, theoretical, phylogenetic, and comparative approaches to understand the effects of context on the strength of an ant-plant-hemipteran mutualism. I examine how the strength of mutualism changes with variation in the density and behavior of individuals, the ontogenetic stage of individuals, resource availability in the surrounding environment, and the evolutionary history of a partner guild. The mutualism studied here occurs among the widespread neotropical tree Cordia alliodora, ants of the genus Azteca, and phloem-sucking scale insects of the superfamily Coccoidea. The ants live and tend scale insects inside specialized, hollow branch nodes of the tree, the scale insects excrete a concentrated sugar that forms a key component of the ants' diet, and the ants defend the trees against leaf-eating herbivores. In Chapter 1, I examine the indirect effects of increased densities of scale insects on the tree, and find that higher densities of scale insects increase the effectiveness of ant defense against leaf-eating herbivores. In Chapter 2, I investigate how ant defense of trees changes as trees and ant colonies grow in the course of ontogeny, and find that larger trees suffer from higher herbivore pressure and less effective ant defense. In Chapter 3, I consider the effects of water availability and covariation in tree growing-season duration on the mutualism, and find that as water availability increases, the strength of the mutualism decreases. In Chapter 4, I reconstruct the evolutionary history of the Azteca ant symbionts of the tree in Middle America, and, through the use of comparative methods, I find that the effectiveness of defense that ants provide to trees is conserved across the ant phylogeny. Taken together, these results show that biotic, abiotic, and evolutionary context can strongly affect the strength of an ant-plant-hemipteran mutualism, and that the direction of these effects may be predicted from key contextual variables.

Keywords: Biology.
Advisor: Dirzo Rodolfo primary advisor. Thesis advisor
Gordon Deborah (Film producer) primary advisor. Thesis advisor
Mooney Harold
Ward Philip
Contracting over actions [electronic resource]

I consider models in which contracts are written over the verifiable actions taken by an agent in multiple decisions. The principal's preferences over actions depend on underlying states of the world, but only the agent observes the states. The principal cannot audit the agent's information or punish her ex post for having taken inappropriate actions. Moreover, the principal is uncertain about the agent's preferences conditional on the states. Chapter 2 extends the concept of a quota contract to account for discounting and for the possibility of infinitely many periods: a discounted quota fixes the number of expected discounted plays on each action. Discounted quotas are optimal contract forms, even if arbitrary dynamic transfer payments are available, if the agent is assumed to have state-independent preferences. I recursively characterize the optimal discounted quotas for an infinitely repeated problem with independent and identically distributed states. Then I give a more explicit description of these contracts in the limit as interactions become frequent, and when only two actions are available. In Chapter 3 I allow the agent's preferences to depend on the states of the world. Under a variety of assumptions on the timing of the game and on the set of possible agent utility functions, I solve for the max-min optimal mechanisms -- those which maximize the principal's payoff against the worst possible agent preference type. These mechanisms are characterized by a property which I call "aligned delegation." Max-min optimal mechanisms may take the simple forms of simultaneous ranking mechanisms, sequential quotas, or budgets.

Advisor: Skrzypacz Andrzej
Wilson Robert
Bulow Jeremy advisor. Thesis advisor
Contracting over actions [electronic resource]

I consider models in which contracts are written over the verifiable actions taken by an agent in multiple decisions. The principal's preferences over actions depend on underlying states of the world, but only the agent observes the states. The principal cannot audit the agent's information or punish her ex post for having taken inappropriate actions. Moreover, the principal is uncertain about the agent's preferences conditional on the states. Chapter 2 extends the concept of a quota contract to account for discounting and for the possibility of infinitely many periods: a discounted quota fixes the number of expected discounted plays on each action. Discounted quotas are optimal contract forms, even if arbitrary dynamic transfer payments are available, if the agent is assumed to have state-independent preferences. I recursively characterize the optimal discounted quotas for an infinitely repeated problem with independent and identically distributed states. Then I give a more explicit description of these contracts in the limit as interactions become frequent, and when only two actions are available. In Chapter 3 I allow the agent's preferences to depend on the states of the world. Under a variety of assumptions on the timing of the game and on the set of possible agent utility functions, I solve for the max-min optimal mechanisms -- those which maximize the principal's payoff against the worst possible agent preference type. These mechanisms are characterized by a property which I call "aligned delegation." Max-min optimal mechanisms may take the simple forms of simultaneous ranking mechanisms, sequential quotas, or budgets.

Keywords: Business.
Advisor: Skrzypacz Andrzej
Wilson Robert
Bulow Jeremy advisor. Thesis advisor
Contributions of the deltoid and rotator cuff to shoulder mobility and stability [electronic resource] : a 3D finite element analysis

The shoulder bones provide few constraints on motion. Therefore, stability must be maintained by muscles and ligaments. Shoulder mobility allows versatility of function, but makes the shoulder prone to injury. A better understanding of the role of muscle in shoulder mechanics is needed to improve the treatment of shoulder injuries and pathologies. Computational models provide a valuable framework for characterizing joint mechanics. Previous shoulder models have used simple representations of muscle architecture and geometry that may not capture the details needed to fully understand muscle function. The purpose of this dissertation was to create a detailed 3D finite element model of the deltoid and the four rotator cuff muscles. This model was then used to characterize the muscle contributions to joint motion and stability. The model was constructed from magnetic resonance images of a healthy shoulder. From the images, the 3D geometry of the muscles, tendons and bones was acquired. A finite element mesh was constructed and the 3D trajectories of the muscle fibers were mapped onto the finite element mesh. A hyperelastic, transversely-isotropic material model was used to represent the nonlinear stress-strain relationship of muscle. Bone motions were prescribed and the resulting muscle deformations were simulated using an implicit finite element solver. To characterize muscle contributions to joint motion, we calculated moment arms for each modeled muscle fiber. We found that 3D models predicted substantial variability in moment arms across fibers within each muscle, which is not generally represented in line segment models. We also discovered that for muscles with large attachment regions, such as deltoid, the line segment models under constrained the muscle paths in some cases. As a result, line segment based moment arms changed more with joint rotation than moment arms predicted by the 3D models. Glenohumeral instability is common, and difficult to treat. To better understand the mechanics of instability we used the 3D model to investigate the role of the muscles in stabilizing the glenohumeral joint by simulating joint translations. We found that at the neutral position, anterior deltoid provides the largest potential to resist anterior translation which counters the conclusions of conventional line segment models. This is the result of compression generated by muscle contact, which must be considered when characterizing the ability of muscle to resist joint translation. This dissertation provides a new computational method for analyzing shoulder mechanics, and demonstrates the importance of 3D analysis when investigating the complex function of shoulder muscles.

Keywords: Mechanical Engineering
Advisor: Delp Scott primary advisor. Thesis advisor
Blemker Silvia Salinas advisor. Thesis advisor
Kuhl Ellen
Controlled vapor deposition of azide-terminated siloxane monolayers [electronic resource] : a platform for tailoring oxide surfaces

The controlled deposition of mixed, azide-terminated siloxane monolayers onto oxide surfaces provides a platform for the covalent attachment of alkyne-terminated species such as oligonucleotides using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. A convenient method for the vapor deposition of dense siloxane monolayers onto oxide surfaces was developed. A selectively deuterated silane, (CD3O)3-Si-(CH2)13-CH3, was synthesized and then vapor deposited in the presence of controlled amounts of water vapor from the in situ dehydration of MgSO4[multiplication dot]7H2O at 110°C. Monolayer densification was characterized using ellipsometry, Fourier transform infrared (FTIR) spectroscopy, water contact angle, and electrochemical capacitance measurements. The formation of dense, completely hydrolyzed monolayers required excess amounts of silane and water reactants. The optimized vapor deposition conditions were used to form mixed, azide-terminated monolayers. Dilution of the azide groups with unreactive methyl groups was achieved from the co-deposition of two silanes. Enrichment of the monolayers with the higher vapor pressure silane reactant was observed. Quantitative CuAAC reactions of the azide groups in mixed monolayers were demonstrated with azide surface compositions up to approximately 40%. Steric hindrance presumably prevented the quantitative reaction of a purely azide-terminated monolayer. Alkyne-terminated oligonucleotides were covalently attached to azide-terminated monolayers on glass followed by hybridization with complementary oligonucleotides. However, the azide-terminated monolayers were susceptible to the nonspecific adsorption of oligonucleotides even after thorough rinsing in aqueous detergents and buffers. A two-step reaction sequence was developed that involved one CuAAC reaction to attach oligonucleotides at low density followed by a second CuAAC reaction with ethynyl phosphonic acid to make the surface more resistant to nonspecific adsorption.

Keywords: Chemical Engineering
Advisor: Bao Zhenan primary advisor. Thesis advisor
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Frank C. W. advisor. Thesis advisor
COSA-1, a meiotic crossover site associated protein [electronic resource]

The formation of crossovers during meiosis is important both for the reassortment of genetic traits, and for creating a physical connection between homologous chromosomes to ensure faithful segregation. This thesis explores the role of a novel protein, COSA-1 (crossover site associated-1), in forming crossovers in the nematode C. elegans. cosa-1 was isolated in a screen for dead embryos, signaling missegregation of the autosomes, and a high incidence of males, signaling missegregation of the X chromosome. Interestingly, obvious orthologs of COSA-1 are only present in metazoans with the notable exception of Drosophilids. Thus no obvious orthologs of COSA-1 exist in the common model organisms, S. cerevisiae, S. pombe, D. melanogaster, and A. thaliana, making C. elegans one of the few organisms in which COSA-1 could have been isolated and studied. Yet, COSA-1 is conserved into humans suggesting the study of COSA-1 will have implications for human reproduction. Not only does C. elegans cosa-1 play a crucial role in promoting the formation of crossovers, evidenced by the lack of chiasmata in the cosa-1 mutant, GFP::COSA-1 exhibits an interesting localization pattern to presumptive crossover sites. In particular, unlike other crossover promoting proteins MSH-5 and ZHP-3, GFP::COSA-1 does not exhibit an initial broader localization but instead localizes to just 6 foci, 1 focus for the 1 crossover on each of the 6 chromosomes. This localization of GFP::COSA-1 to 6 foci was robust under various conditions. Mathematical modeling of the relationship between irradiation dose and COSA-1 foci revealed a relationship between obligate crossover, the phenomenon in which at least one crossover is formed per chromosome, and crossover interference, the phenomenon in which the formation of a crossover inhibits the formation of other crossovers nearby. In addition, analysis of GFP::COSA-1 foci in mutants that form extra crossovers, in particular rtel-1 and dpy-28, revealed a separation between the number of GFP::COSA-1 foci, 6, and the number of COs made, more than 6, suggesting that interference is still operating on GFP::COSA-1foci. Thus GFP::COSA-1 may serve as a better readout for crossover interference than crossovers per se. The ability to visualize GFP::COSA-1 in live worms holds great potential for elucidating the mechanisms involved in crossover interference, crossover distribution, and crossover designation.

Keywords: Genetics
Advisor: Villeneuve Anne
Bejerano Gill
Fire Andrew Zachary advisor. Thesis advisor
Pringle John