VictorJuiz/thesis huggingface dataset:
Modifications to flux balance analysis to enable large scale integrated modeling [electronic resource]

Metabolism is the cellular system that converts surrounding material and energy gradients into the molecules needed to sustain life. All the processes of cell maintenance and replication rely on metabolic products to function. For this reason, quantitative metabolic models contribute greatly to our understanding of biological systems, and underlie many of our predictive capabilities for microbial cells. Therefore, to increase understanding and expand predictions, we must advance quantitative models of metabolism and how cell processes use metabolic products. The metabolic modeling method Flux Balance Analysis (FBA) facilitated the first genome-scale microbial models. FBA consists of a detailed stoichiometric mass balance over hundreds of small molecule reactions. Classic FBA presents a cell-as-metabolism perspective so far as the interface with and function of all other cellular processes are contained in a single summary biomass reaction. A screen for host-dependencies of bacteriophage --- bacterial virus --- prompted my investigation of how infecting pathogens exploit host metabolic resources. Viruses lack metabolic infrastructure, so new viral particles are necessarily built using macromolecular precursors and energy from the host cell. To computationally model viral use of host metabolites, a previously developed model of bacteriophage T7 macromolecular replication was combined with an FBA model of host E. coli metabolism. To enable solution of the combined system, I developed an algorithm to simulate the differential equation and linear optimization models simultaneously with mutual constraint. However, difficulties with FBA in integrated models arise from the biomass reaction. Previously the biomass reaction gave FBA power by abstracting cell process interaction and regulation detail, but in order to do so it assumed a long-time, steady-state, and population average function of metabolism. These assumptions are inconsistent with dynamic and single-cell applications. By relaxing the rigid biomass reaction and its assumptions, I developed FBA methods suited to integrated and whole-cell modeling applications. The first component of this solution was my introduction of a flexible (flexFBA) objective to encourage, rather than require, proportional production of cell process reactants. The second update is to link the processes' use of reactants and return of byproducts across simulation time steps (tFBA). In combination, these modifications make FBA relevant on a much shorter timescale. For example, flexFBA and tFBA can simulate transitions between metabolic steady states, and avoid FBA artifacts due to small copy number enzymes.

Keywords: Chemical Engineering.
Advisor: Covert Markus primary advisor. Thesis advisor
Spormann Alfred M. primary advisor. Thesis advisor
Spakowitz Andrew James advisor. Thesis advisor
The moduli space of real curves and a Z/2-equivariant Madsen-Weiss theorem [electronic resource]

Galatius, Madsen, Tillmann, and Weiss proved that the classifying space of the category of 2-cobordisms is equivalent to the loopspace of a particular Thom spectrum. We show that this is in fact a Z/2-equivariant equivalence, where we equip all spaces with a Z/2-action which is motivated by complex conjugation of complex curves. In order to do this, we prove an equivariant delooping theorem which shows that grouplike topological monoids with Z/2-action are Z/2-equivalent to loopspaces. Furthermore, we motivate our choice of Z/2-action by showing that it determines a Z/2-space BDiff_g whose fixed points classify real curves.

Keywords: Mathematics.
Advisor: Galatius Søren
Church Thomas (Thomas Franklin) advisor. Thesis advisor
Cohen Ralph L.
Molecular and stable isotopic analyses of the fatty acyl components of the pottery of Çatalhöyük, Turkey [electronic resource] : understanding the relationships between animal domestication, ceramic technology, environmental variation and their roles in the secondary products revolution

An extensive study of the organic residue associated with the Neolithic pottery of Çatalhöyük has further confirmed the timing of dairy production on-site after following the methods of a previous study (Evershed et al. 2008). By utilizing gas chromatography (GC) on 313 potsherds, and high temperature-GC/mass spectrometry (HT-GC/MS), GC-combustion-IRMS (GC-C-IRMS) and GC-thermal conversion-IRMS (GC-TC-IRMS) on subsets of that pottery collection from the Neolithic site of Çatalhöyük in central Turkey, the first well-dated stratigraphic record of both compound-specific [delta] 13C and [delta] D values of C16:0 and C18:0 fatty acids has now been established. The combination of this new information with the faunal and stable isotope records of the same site has provided a more detailed account of changes in animal management strategy over time. This study provides an in-depth look at some of the oldest dairy residues found to date as well as environmental and social factors that may have contributed or resulted from the transition to secondary product use during the Neolithic. In addition, a newly developed palaeoenvironmental proxy may provide a direct link between changes in local precipitation levels and changes in subsistence practices by assessing stable hydrogen isotope ([delta] D) values of fatty acids extracted from pottery residues. The origins of the fatty acids were determined based on their [delta] 13C values as arising largely from ruminant adipose and dairy fats. A [delta] D record was constructed, based on a subset of ruminant adipose fats only, which showed most negative isotopic values from ~6900 to 6600 cal BC indicative of wet conditions, followed by a drying trend which reached a maximum at or just after 6280 cal BC, coincident with the 8.2 ka (~6200 cal BC) cold, dry climate event. The drying trend is consistent with that observed in the [delta] 18O record from the nearby lake Eski Acıgöl carbonates. Thus, [delta] D analysis of archaeological residues may be useful in assessing broader environmental and climatic changes directly from cultural residues.

Keywords: Environmental Earth System Science.
Advisor: Dunbar Robert B.
Chamberlain C. Page advisor. Thesis advisor
Evershed Richard advisor. Thesis advisor
Hodder Ian advisor. Thesis advisor
Molecular-to-process level approaches to advancing carbon capture and storage [electronic resource]

The current work includes two projects which are quite different in application, discipline, and method, but connected in general motivation to improve carbon capture and storage (CCS) and promote cross-disciplinary, multi-scale research. The need to reduce carbon dioxide (CO2) emissions is one of the most significant environmental challenges facing society. CCS has the potential to mitigate gigatons (Gt) of anthropogenic CO2 emissions, and is regarded as a key method for global-scale CO2 emissions reduction. Improving the economic and environmental viability of CCS technologies will require the collaboration of researchers across disciplines and scales. The current work addresses the need for cross-disciplinary research by synthesizing interdisciplinary research from the molecular- to the process-scale. The first project includes a fundamental, molecular-level investigation of CO2 adsorption dynamics in carbon sorbents, with the aim of applying results to process optimization models. Understanding CO2 adsorption and transport is crucial to the development of successful carbon capture technologies, as well as other applications such as CO2 sequestration. This work investigates the use of an improved potential model to directly treat CO2 electrostatic and geometric properties, thereby more accurately describing the fluid-fluid and fluid-wall interactions which determine adsorption capacity and dynamics. CO2 interactions with pure and hydroxyl-functionalized slit and step carbon pores are simulated to investigate pore entrance effects and tradeoffs between pore size, chemistry, capacity, and transport. Furthermore, the molecular simulation results are linked to the process scale through a parametric study using a finite volume based adsorption process simulator, to investigate the potential impact of kinetic parameters on PSA-based carbon capture processes. The second project includes a high-level evaluation of the life-cycle energy efficiency of various proposed mineral carbonation processes. This study builds a holistic, transparent life-cycle assessment model of a variety of aqueous mineral carbonation processes using a hybrid process model and economic input-output life-cycle assessment approach (hybrid EIO-LCA). The model incorporates reaction chemistry to allow for a systematic investigation of the tradeoffs inherent in carbonation processes. The investigation of such tradeoffs can provide guidance for the optimization of the life-cycle energy efficiency of various proposed mineral carbonation processes.

Advisor: Wilcox Jennifer
Brandt Adam (Adam R.) advisor. Thesis advisor
Pitera Jed
Moments of automorphic L-functions and related problems [electronic resource]

We present in this dissertation several theorems on the subject of moments of automorphic L-functions. In chapter 1 we give an overview of this area of research and summarize our results. In chapter 2 we give asymptotic main term estimates for several different moments of central values of L-functions of a fixed GL_2 holomorphic cusp form f twisted by quadratic characters. When the sign of the functional equation of the twist L(s, f \otimes \chi_d) is -1, the central value vanishes and one instead studies the derivative L'(1/2, f \otimes \chi_d). We prove two theorems in the root number -1 case which are completely out of reach when the root number is +1. In chapter 3 we turn to an average of GL_2 objects. We study the family of cusp forms of level q^2 which are given by f \otimes \chi, where f is a modular form of prime level q and \chi is the quadratic character modulo q. We prove a precise asymptotic estimate uniform in shifts for the second moment with the purpose of understanding the off-diagonal main terms which arise in this family. In chapter 4 we prove an precise asymptotic estimate for averages of shifted convolution sums of Fourier coefficients of full-level GL_2 cusp forms over shifts. We find that there is a transition region which occurs when the square of the average over shifts is proportional to the length of the shifted sum. The asymptotic in this range depends very delicately on the constant of proportionality: its second derivative seems to be a continuous but nowhere differentiable function. We relate this phenomenon to periods of automorphic forms, multiple Dirichlet series, automorphic distributions, and moments of Rankin-Selberg L-functions.

Keywords: Mathematics.
Advisor: Soundararajan Kannan
Conrey J. B. advisor. Thesis advisor
Venkatesh Akshay
Monitoring matrix cracking in composite laminates using built-in piezoelectric sensors [electronic resource]

Fiber reinforced composite materials use has increased tremendously in many applications from aerospace structures to sporting goods. These materials have many advantages, but the major challenge in composites design is their damage mechanics. Matrix cracking develops first, decreasing structural performance and promotion of other damage development. The state-of-the-art inspection techniques cannot quantify crack density and they require the component to be off-service. For better design, safety, and maintenance of composite structures it is desirable to monitor the increase of cracks in-service. The objective of this investigation is to determine the quantity of matrix cracks in a composite laminate rapidly and in-service using built-in piezoelectric actuators and sensors. A diagnostic method was proposed which compared the sensed signal before and after the presence of matrix cracks and related these signal changes to crack density. It was found that change in the signal's Power Spectral Density can be used to quantify crack density, and its sensitivity was dependent on the actuator to sensor orientation. This orientation dependence was found to be the same as that of the laminate's stiffness degradation. A crack density quantification model was developed that uses signal changes and theoretical laminate stiffness parameters. The model was tested on two layup configurations, and its crack density estimates matched experimental crack density values within established error bounds.

Keywords: Aeronautics and Astronautics.
Advisor: Chang Fu-Kuo primary advisor. Thesis advisor
Cantwell Brian advisor. Thesis advisor
Christensen R. M. (Richard M.) advisor. Thesis advisor
Springer George S. advisor. Thesis advisor
A monolithic mass tracking formulation for bubbles in incompressible flow [electronic resource]

This dissertation presents a novel method for treating bubbles in free surface incompressible flow that relies on the conservative advection of bubble mass and an associated equation of state in order to determine pressure boundary conditions inside each bubble. It is shown that executing this algorithm in a traditional manner leads to stability issues similar to those seen for partitioned methods for solid-fluid coupling. Therefore, the problem is reformulated monolithically. This is accomplished by first proposing a new fully monolithic approach to coupling incompressible flow to fully nonlinear compressible flow including the effects of shocks and rarefactions, and then subsequently making a number of simplifying assumptions on the air flow removing not only the nonlinearities but also the spatial variations of both the density and the pressure. The resulting algorithm is quite robust, has been shown to converge to known solutions for test problems, and has been shown to be quite effective on more realistic problems including those with multiple bubbles, merging and pinching, etc. Notably, this approach departs from a standard two-phase incompressible flow model where the air flow preserves its volume despite potentially large forces and pressure differentials in the surrounding incompressible fluid that should change its volume. The proposed method allows bubbles to readily change volume according to an isothermal equation of state. This method is then extended to model both large and small scale bubble dynamics. Small under-resolved bubbles are evolved using Lagrangian particles that are monolithically two-way coupled to the surrounding flow in a manner that closely approximates the analytic bubble oscillation frequency while converging to the analytic volume as predicted by the well-known Rayleigh-Plesset equation. A novel scheme is presented for interconverting between these under-resolved Lagrangian bubbles and the larger well-resolved Eulerian bubbles. A novel seeding mechanism is also presented to realistically generate bubbles when simulating fluid structure interaction with complex objects such as ship propellers. The proposed framework for bubble generation is general enough to be incorporated into all grid-based as well as particle-based fluid simulation methods.

Advisor: Fedkiw Ronald P.
Grzeszczuk Radek
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
More with Less: Prioritizing U.S. Navy global presence with reductions in defense spending

After a decade of war, America’s defense budget is almost certain to see reductions over the next several years. The full impact of austerity on the Navy as the principle vehicle of U.S. power projection however must be approximated in the context of an evolving geopolitical landscape. Although the Navy is unrivaled in size, capability, and reach, the development of anti- access/ area denial (A2/AD) weapon systems by rising powers in two strategically critical theaters—the Persian Gulf and the Asia Pacific—represents a growing problem. Maritime power dynamics are changing: China’s naval ascendancy combined with its ambitions in the South China Sea risks sparking a naval arms race, while Iranian belligerence in the Gulf threatens the free flow of oil in an already volatile part of the world. If the Navy is to continuing advancing a strategy of global engagement, it must find a way to projecting power even in a constrained future resource environment.
How can the Navy continue to promote U.S. interests while operating on a reduced budget? Using scenario analysis under three different budget cases—status quo, sequestration, and a hypothetical compromise solution—this paper assesses the outlook for U.S. naval presence and power projection in the Persian Gulf and Asia Pacific over the remainder of the decade.
To preserve its global dominance and regional influence, the Navy must invest in developing counter A2/AD systems and continue to emphasize power projection. Rather than shrink from a forward deployed posture, the Navy must adopt a prioritized engagement strategy that allocates ships with region-specific capabilities against region-specific security concerns. By maintaining forward presence, and by focusing on its core-competency—power projection—even with fewer ships, the Navy can do more with less.

Keywords: Center for International Security and Cooperation
CISAC
United States Navy
budget
austerity
defense
scenario analysis
Thesis
Advisor: Blacker Coit D.
Motivating older Americans to walk [electronic resource] : an application of socioemotional selectivity theory

Mounting evidence suggests that active lifestyles may help to maintain physical and cognitive independence in old age by preserving good health. Walking is among the most cost-effective and accessible means of exercise. However, older Americans fall far short of meeting the daily recommendations for walking. In my dissertation research, I examine the relevance of socioemotional selectivity theory to the promotion of healthy lifestyles among older adults. In four studies, I examine whether or not considering older adults' preferential attention to positive information may effectively enhance interventions aimed at promoting walking. In Study 1, I compared the effectiveness of positive, negative, and neutral messages to encourage walking (as measured with pedometers). Older adults who were informed about the benefits of walking walked more than those who were informed about the negative consequences of failing to walk, whereas younger adults were unaffected by framing valence. In Study 2, I examined within-person changes in walking in response to positively- or negatively-framed messages over a 28-day period. Once again, positively-framed messages more effectively promoted walking than negatively-framed messages in older adults, and the effect was sustained across the intervention period. Study 3 extended this research to a less affluent population of older adults living in neighborhoods with many obstacles for health behaviors. The effectiveness of positively- compared to negatively-framed messages varied by ethnicity and neighborhood walkability. In Study 4, I examined whether selective adherence to positively-framed health recommendations among older adults was associated with neural and cognitive processes. Brain regions implicated in motivation and memory tracked with the processing of emotionally-valenced compared to neutral information across participants. Older adults remembered positively-framed information about walking better than negatively-framed information. Brain activation and explicit memory were associated with walking. Together, these studies suggest that consideration of age-related changes in preferences for positive and negative information may inform the design of effective interventions to promote healthy lifestyles.

Keywords: Psychology.
Advisor: Carstensen Laura L. primary advisor. Thesis advisor
Bandura Albert
Thomas Ewart A. C. advisor. Thesis advisor
Multimode optical fiber-tip photonic crystal pressure sensors [electronic resource] : toward low-cost, high-precision optical sensing

With advantages in electromagnetic interference immunity, compactness, and tolerance to harsh environments, optical fiber sensors are suitable for a wide variety of applications, especially in corrosive, explosive, and radiative environments. Multimode fiber systems are attractive for their cost savings over single-mode fiber systems, but they also come with challenges associated with the presence of multiple spatial modes in a fiber: modal noise and mode averaging. In the context of pressure sensing, we report on the benefits of designing multimode fiber Fabry-Pérot Interferometers using short optical cavities: the mitigation of mode-averaging-induced sensitivity loss and phase uncertainty, and the mitigation of modal noise, which we further addressed by filtering. In light of the performance-cost tradeoff with multimode sensing, we pursued high sensitivity devices to maximize the benefits of such a low-cost system. Using single-crystal silicon, a material prized for its excellent optical and mechanical properties, we fabricated static pressure diaphragms with photonic crystals on its surface for high broadband reflectance, and assembled them on metallized fiber tips in an extrinsic Fabry-Pérot Interferometer configuration to create highly sensitive pressure sensors that had optical sensitivities that were up to ten times that of a sensor made with bare fiber and a pure silica diaphragm.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Brongersma Mark L. advisor. Thesis advisor
Vuckovic Jelena advisor. Thesis advisor
Multi-objective optimization using hyper-dual numbers [electronic resource]

High-fidelity analysis tools can provide accurate predictions of the performance of a design. However, these tools often have a higher computational cost when compared to lower-fidelity tools. This can greatly increase the computational expense of tasks that require many repeated calls to the analysis tool, such as numerical optimization methods or uncertainty quantification techniques. There are various strategies that can be employed to reduce the computational cost. One strategy is to make use of additional information, such as the gradient (first-derivative information) or Hessian (second-derivative information). Gradient-based optimization methods can converge faster and require fewer function evaluations than non-gradient based methods. Optimization methods that use the Hessian, or an approximation to the Hessian, can further improve the rate of convergence and may require even fewer function evaluations. Response surfaces created using a few evaluations of the high-fidelity tool can also be used as surrogates for the high-fidelity analysis to reduce the computational cost. More accurate response surfaces can be created, using fewer sample locations, by incorporating first-derivative information. Including second-derivative information may provide a further benefit, provided it can be computed accurately and efficiently. Generalized complex numbers can be used to compute effectively exact first derivatives, by reducing the truncation error to below machine precision. Higher-dimensional extensions of generalized complex numbers can produce effectively exact second (or higher) derivatives, provided they have the property that multiplication is commutative. This dissertation develops a new number of this type, called hyper-dual numbers, in order to produce exact second derivatives. The mathematics of hyper-dual numbers enable first- and second-derivative calculations that are free from both subtractive cancellation error and truncation error, and therefore exact. This dissertation develops the mathematical properties of hyper-dual numbers and discusses their implementation in several programming languages. The implementations allow hyper-dual numbers to be easily applied to codes of arbitrary complexity. This is demonstrated on a 3D, parallel, unstructured computational fluid dynamics code, and the resulting derivative calculations are validated against exact results. Hyper-dual numbers are then applied to a multi-objective optimization method and two response surface creation methods.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Jameson Antony
Senesky Debbie advisor. Thesis advisor