VictorJuiz/thesis huggingface dataset:
STUDYING MEMBRANE ANCHOR ORGANIZATION IN LIVING CELL MEMBRANES

The cell membrane is a complex mixture of various lipids, proteins and other biomolecules that are all organized into a fluid 2-dimensional bilayer. A rather unique trait of this organelle is the lateral mobility of the component molecules. Surprisingly, these molecules are not necessarily distributed homogeneously in the membrane. From a physical perspective, these inhomogeneities are interesting because they indicate some level of organization in the membrane. From a biological perspective, this organization is interesting because it might be a key regulatory element in the enzymatic processes and cell signaling events that occur at the cell membrane. Due to the difficulty of studying membrane organization, not much is known about the spatiotemporal scale of these organized domains, nor is it clear what the physical driving forces are, although there are models based on observations from a variety of different methods. The key factor to overcome in studying membrane organization is the ability to probe the membrane in an informative way that does not perturb the native organization of the membrane./nMembrane anchors are lipid moieties covalently conjugated to various membrane proteins and have been implicated in the lateral sorting of anchored proteins in the membrane. Most studies on lipid anchors focus either on identifying what molecules anchored proteins colocalize with or observing how anchored proteins diffuse in the cell membrane. Truncated anchored proteins with just the anchor domain remaining can be genetically fused to fluorescent proteins and also studied to determine the extent to which the anchor-membrane interactions, as opposed to protein-protein interactions, influence their distribution in the membrane. The methods used to study these behaviors are varied and, subsequently, the observations that result from these studies are also varied and the conclusions are conflicting./nTime-resolved spectroscopy of fluorescently labeled anchor domains in living cells offers a non-invasive method to extract a wealth of information about the spatiotemporal localization of anchored proteins in a live cell. More specifically, fluorescence cross-correlation spectroscopy (FCCS) analysis and fluorescence lifetime analysis can be derived from the same data stream. In this dissertation, I review the current model of how membranes are organized and present observations made by myself and coworkers, of two instances of homogeneous colocalization of the same anchors but no heterogeneous colocalization of different anchors in Jurkat cell membranes. We conclude that the observation of two distinct non-overlapping domains existing in the same cell membrane indicate a more complex organization than the current model allows.

Advisor: Groves, Jay T
Nogales, Eva
The Effect of Multiple-Enhanced Diffusion on the Joule Heating of a Cold Non-Neutral Plasma

One proposed technique for trapping anti-atoms is to superimpose a Ioffe-Pritchard style magnetic-minimum neutral trap on a standard Penning trap used to trap the charged atomic constituents. Adding a magnetic multipole field in this way removes the azimuthal symmetry of the ideal Penning trap and introduces a new avenue for radial diffusion. Enhanced diffusion will lead to increased Joule heating of a non-neutral plasma, potentially adversely affecting the formation rate of anti-atoms and increasing the required trap depth. We present a model of this effect, along with an approach to minimizing it, with comparison to measurements from an intended anti-atom trap.

Advisor: Fajans, Joel
On the Piloted Ignition of Solid Fuels in Spacecraft Environments

The effect of environmental variables on the ignition of solid combustible materials is explored through a combination of experimental, analytical and numerical analyses. This research stems from NASA's design requirement to reduce the cabin internal pressure and increase the oxygen concentration in human space vehicles and in future lunar habitats of the Constellation Program. These new environmental conditions may result in an increased fire risk of combustible solid materials due to higher flame temperatures (attributed to enhanced oxygen) and reduced convective heat losses from heated surfaces (attributed to reduced pressure). In particular, the influence of low pressure on ignition is emphasized here because little is known concerning this topic./nA series of experiments conducted in a laboratory-scale combustion wind tunnel with externally irradiated samples of PMMA (polymethyl-methacrylate) showed that both the ignition delay time and the fuel mass flux at ignition decrease when the ambient pressure is lowered. An analytical model is used to identify the governing processes that lead to these results and then a numerical model is applied to quantify the influence of ambient variables (particularly pressure) on the piloted ignition of PMMA. The numerical model verifies the phenomenological explanations inferred from the experimental findings and the qualitative analytical results, and correctly simulates the thermo-physical mechanisms leading to ignition. It is concluded that reduced pressure environments result in: 1) smaller convective heat losses from the heated material to the surroundings due to a thickening of the thermal boundary layer next to the solid fuel surface, allowing for the material to heat more rapidly and pyrolyze faster; and, 2) a lower mass flux of volatiles required to reach the lean flammability limit of the gases at the pilot, leading to earlier ignition, due mainly to an enlarged boundary layer and a thicker fuel species profile under reduced pressures./nThe findings from this research indicate that the flammability of combustible materials is enhanced at low ambient pressures and elevated oxygen concentrations, and may have significant consequences in the assessment of their fire risk in spacecraft and other environments where these conditions are encountered such as aircrafts and high altitude cities, among others.

Advisor: Fernandez-Pello, Carlos
From Farm to Table to Stage: Performing Food Politics

This dissertation examines the civic function of the arts through an analysis of socially engaged performances that address issues of American food politics. Socially engaged performances - known alternately as community-based performance, theatre for social change, and activist art - seek to make people aware of the systems within which they are embedded. Food offers a particularly productive way of connecting the intimacies of social life with a larger apparatus./nWithin the discourse of socially engaged performance there is debate about the best way to connect art practice with pointed political critique. Some critics argue for an approach that values harmony and community. Other critics suggest that antagonism and autonomy are the most effective approach. The discourse of food politics has its own debates and tensions that play out along similar lines: food as means of unification versus food as emblematic of social disparity. This project is unique in that it is one of the first studies to examine food-centered performances that not only use food as material and/or metaphor, but also attend to the systemic processes of the production, distribution and consumption of food./nUsing interviews, performance analyses, and published reviews, this project examines the impact of artists' use of food and food politics in their artistic work, as well as the way artists' formal concerns and dramaturgical choices in turn impact the discourse of food politics. The research demonstrates that these performances are an ideal site through which to test the potential of socially engaged art. Through several case studies - including an installation piece that explores the space of the restaurant, a multi-media theatre piece that examines discourses of food politics, and a community-based theatre project that connects farmers and artists - this dissertation argues that the use of food not only facilitates more effective socially engaged performance, but can also expose the race and class blind spots of the food movement.

Advisor: Jackson, Shannon
"This Modern Day Slavery": Sex Trafficking and Moral Panic in the United Kingdom

The dissertation analyzes the discourse and development of the British anti-sex trafficking movement. Following the European Union's largest expansion in 2004, the United Kingdom experienced a surge in immigration from Eastern Europe, which was greeted by fears about losing British culture, stolen jobs, and rising criminal activity. From this welter of concerns, I argue, the issue of sex trafficking coalesced into a moral panic about the dangers of immigration and the sexual exploitation of women. Using qualitative research and discourse analysis, I examine the movement's depiction of the trafficking victim and its reliance on punitive policing and anti-immigration policies. Although anti-trafficking advocates claim the abolition of the African slave trade as their historical precedent, I contend that the conceptual roots of contemporary discourse lie in the white slavery panic of the Victorian era. Today's description of the trafficked woman as young, naïve, and Eastern European recalls the figure of the white slave at the same time that it demonizes migrant sex workers who do not fit the feminized and culturally-bound profile of helpless victim./nThis analysis of the United Kingdom's response to a changing demographic landscape reveals how a reaction can define the phenomenon to which it ostensibly refers. In other words, the anti-trafficking campaign produces its opposing object, "sex trafficking," by delimiting the discursive field and determining the appropriate course of defensive action. In light of the political and economic crises wracking post-millennial Britain, the realm recast itself as a hostile environment for sex trafficking and inaugurated a series of unprecedented policing measures and prostitution policy shifts. To interrogate these events I perform a contrapuntal reading that troubles both the conceptual basis of the anti-trafficking movement and its legal and tactical operations. Through this analysis, my dissertation reveals that the anti-trafficking campaign is not a reaction to the sexual traffic in women; it is part of a larger socio-legal response to Eastern Europeans seeking access to the United Kingdom as full members of the European Union. This project constitutes an expansion and repositioning of studies of sex work and migration, offering a specific analysis of the British context while emphasizing the intersection between standardized narratives and cultural ruptures.

Advisor: Constable, Marianne
Advanced MOSFET Designs and Implications for SRAM Scaling

Continued planar bulk MOSFET scaling is becoming increasingly difficult due to increased random variation in transistor performance with decreasing gate length, and thereby scaling of SRAM using minimum-size transistors is further challenging. This dissertation will discuss various advanced MOSFET designs and their benefits for extending density and voltage scaling of static memory (SRAM) arrays. Using threedimensional (3-D) process and design simulations, transistor designs are optimized. Then, using an analytical compact model calibrated to the simulated transistor current-vs.-voltage characteristics, the performance and yield of six-transistor (6-T) SRAM cells are estimated. For a given cell area, fully depleted silicon-on-insulator (FD-SOI) MOSFET technology is projected to provide for significantly improved yield across a wide range of operating voltages, as compared with conventional planar bulk CMOS technology. Quasi-Planar (QP) bulk silicon MOSFETs are a lower-cost alternative and also can provide for improved SRAM yield. A more printable "notchless" QP bulk SRAM cell layout is proposed to reduce lithographic variations, and is projected to achieve six-sigma yield (required for terabit-scale SRAM arrays) with a minimum operating voltage below 1 Volt.

Advisor: King Liu, Tsu-Jae
Regulation of mitotic progression in Saccharomyces cerevisiae by the microtubule-associated proteins Slk19 and Stu1

Mitosis is the process by which eukaryotic cells segregate their chromosomes before division. A critical stage of mitosis is anaphase, when the microtubule-based spindle segregates chromosomes into mother and daughter cells prior to cytokinesis. My dissertation research aimed to provide a better understanding of the regulation of anaphase progression and spindle function during mitosis in Saccharomyces cerevisiae./nMy research focused on two microtubule-associated proteins, Slk19 (CENP-F homolog) and Stu1 (CLASP homolog). These proteins play fundamental roles in anaphase progression, Stu1 in microtubule spindle stability and Slk19 in spindle midzone organization and Cdc14 phosphatase regulation. I found that Stu1 and Slk19 physically interact and that Slk19 regulates Stu1 localization during anaphase. In addition to its interaction with Slk19, I identified a number of other physical and genetic interactors of Stu1 through mass spectrometry, yeast two-hybrid and synthetic genetic analyses. These interactors provide insight into the role of Stu1 at kinetochores. I also investigated Stu1 function through a protein truncation analysis and purification of full-length Stu1 protein. My truncation analysis revealed that the Stu1 C-terminus is dispensable for viability but is necessary for proper protein localization. The N-terminus, however, is essential for viability. My attempts to purify Stu1 from insect cells were partially successful; the protein is extremely sensitive to proteolytic degradation, and under conditions that limit proteolysis, the protein appears to aggregate or oligomerize in solution./nI also investigated the role of Slk19 sumoylation in anaphase progression. I determined that the Cdc14 early anaphase release (FEAR) network protein Slk19 is sumoylated in vivo and that sumoylation is important for restricting Cdc14 phosphatase localization to the nucleus at the end of anaphase. A slk19 sumoylation mutant causes premature Cdc14 movement from the nucleus to the bud neck, which affects mitotic exit, as this slk19 sumoylation mutant can partially rescue the spindle disassembly defect of the mitotic exit network mutant cdc15-2. This slk19 mutant also has aberrant spindle elongation dynamics, which might be due to a change in Cdc14 function during anaphase./nIn conclusion, my dissertation research has uncovered a number of previously unrecognized interactions among mitotic proteins and has revealed a novel function of sumoylation in the regulation of Cdc14 function during anaphase through the FEAR network protein Slk19.

Advisor: Barnes, Georjana
Delayed Gamma-Ray Assay for Nuclear Safeguards

This dissertation addresses the need for new non-destructive assay instruments capable of quantifying the fissile isotopic composition of spent nuclear fuel and of independently verifying the declared amounts of special nuclear materials at various stages of the nuclear fuel cycle. High-energy delayed gamma-ray spectroscopy can provide the ability to directly assay fissile and fertile isotopes in the highly radioactive environment of the spent fuel assemblies and to achieve the safeguards goal of measuring nuclear material inventories for spent fuel handling, interim storage, reprocessing facilities, and final disposal and repository sites./nThe delayed gamma-ray assay concept is investigated within this context with the objective of assessing whether the delayed gamma-ray assay instrument can provide sufficient sensitivity, isotope specificity and accuracy as required in nuclear material safeguards applications. Preliminary system design analysis indicates that the delayed gamma-ray response is affected by multiple parameters: type and intensity of the interrogating source, the configuration of the interrogation setup, the time pattern of the interrogation, and the resolution and count rate limit of the gamma-ray detection system./nIn order to handle the variety of factors associated with the delayed gamma-ray assay of spent nuclear fuel, a high-fidelity response modeling technique is introduced. The new algorithm seamlessly combines transport calculations with analytical decay/depletion, and discrete gamma-ray source reconstruction codes. Its performance was benchmarked in the dedicated experimental campaign involving accelerator-driven photo-neutron sources and samples containing fissile and fertile isotopes./nAnalytical estimations of the intensity of the delayed gamma-ray response and the passive background rate are utilized to develop a concept of the non-destructive instrument for the assay of spent nuclear fuel. The modeling technique is then applied to more detailed parametric study. These simulations included extensive spent fuel inventories, and accounted for realistic assay configurations and instrumentation. The results of this preliminary analysis indicate that the delayed gamma-ray assay of spent nuclear fuel assemblies can be performed with available neutron generator and detection technology./nThe sensitivity of the delayed gamma-ray spectra to the actinide content of the spent nuclear fuel is investigated. The simplest analysis of the delayed gamma-ray response is based on the analysis of integrated count rates and peak ratios. More powerful analytical and numerical methods are likely needed for determining the relative concentrations of fissile and fertile isotopes in samples with complex compositions.

Advisor: Vujic, Jasmina
Consuming Hygge at Home: Perception, Representation, Practice

Comparative research on the relationship between everyday spaces of consumption and cultural metaconcepts offers insight into how consumers experience and construct meaning through the use of space. In practice theory, metaconcepts, the "structuring structures" of consumer meaning and emotion, are understood to operate at the individual, group, and cultural level. Consumers engage cultural metaconcepts -- in this case, the Danish concept of hygge and coziness, its typical American translation --!through banal acts, such as making morning coffee, and exceptional consumption, such as remodeling one's home. Likewise, metaconcepts act across social scale. The emotional experience of hygge can be experienced alone or in a group, but the concept is also strongly linked to Danish identity and to the home. Therefore, the ideal of hygge influences the everyday purchases that constitute the majority of middle-class consumption. Through everyday consumption, hygge has a strong relationship to the material arrangement and use of the home. Hygge influences everything from the size and shape of the dining table to the relationship of the living room to the front door. These material arrangements shape both social relationships and consumption, reinforcing cultural ideals and norms. Previous research on hygge, homeyness, and atmosphere, however, has lacked a comparative perspective, making it difficult to identify cultural differences in the metaconcepts that drive much normal, routine, and habitual consumption. From a review of literature from fields including cultural geography, anthropology, sociology, and architecture, I identify seven concepts that typify scholarly approaches to the home. I then conduct a two-part analysis for understanding the intangible, multivalent, and fleeting concepts of hygge and coziness in a sample of seventeen everyday domestic settings near Copenhagen, Denmark and Portland, Oregon. First is a comparative research video ethnographic method designed to invoke wide-ranging discussion and involve participants in the creation of research representations. Second is a historical survey of representations of hygge and coziness in popular media, including the Danish magazine Bo Bedre, the American magazine Sunset, and the book The Not So Big House by American author and architect Sarah Susanka. This research offers a contribution to interdisciplinary theory in marketing research and studies of domestic space along with concrete findings applicable to the marketing of domestic goods, homes, restaurants, bars, and other products and services. It also offers a rapid ethnographic method of use to scholars and market research professionals alike.

Advisor: Cranz, Galen
Studies of Auction Bidding with Budget-Constrained Participants

Consider a first-price, sealed-bid auction where participants have affiliated valuations and private budget constraints; that is, bidders have private multidimensional types. We offer sufficient conditions for the existence of a monotone equilibrium in this environment along with an equilibrium characterization. Hard budget constraints introduce two competing effects on bidding. The direct effect depresses bids as participants hit their spending limit. The strategic effect encourages more aggressive bidding by participants with large budgets. Together these effects can yield discontinuous equilibrium strategies stratifying competition along the budget dimension. The strategic consequences of private budget constraints can be a serious confound in interpreting bidding behavior in auctions. Evidence from an experimental auction market lends support to the strategic importance of budget constraints.

Advisor: Kariv, Shachar
Continuum Modeling and Finite Element Analysis of Cell Motility

Cell motility, and in particular crawling, is a complex process, with many as yet unknown details (\textit{e.g.}, sources of viscosity in the cell, precise structure of focal adhesions). However, various models of the motility of cells are emerging. These models concentrate on different aspects of cellular behavior, from the motion of a single cell itself, to -taxis behaviors, to population models. Models of single cells seem to vary significantly in their intended scope and the level of detail included./nMost single cells are far too large and complex to be globally amenable to fine-scale modeling. At the same time, cells are subject to external and internal influences that are connected to their fine-scale structure. This work presents a continuum model, including the use of a continuum theory of surface growth, that will predict the crawling motion of the cell, with consideration made for the appropriate fine-scale dependencies./nThis research addresses several modeling aspects. At the continuum level, the relationships between force and displacement in the bulk of the cell are modeled using the balance laws developed in continuum mechanics. Allowances are made for the treatment of and interaction between multiple protein species, as well as for the addition of various terms into the balance laws (\textit{e.g.}, stresses generated by protein interactions). Various assumptions regarding the nature of cell crawling itself and its modeling are discussed. For instance, the extension of the lamellipod/detachment of the cell is viewed as a growth/resorption process. The model is derived without reference to dimensionality./nThe second component of the presentation concerns the numerical implementation of the cell motility model. This is accomplished using finite elements, with special features (\textit{i.e.}, ALE, discontinuous elements) being used to handle certain stages of the motility. In particular, the growth assumption used to model the crawling motility is represented using ALE, while the strong discontinuities that arise out of the growth model are represented using the discontinuous elements. Results from representative finite element simulations are shown to illustrate the modeling capabilities.

Advisor: Papadopoulos, Panayiotis