VictorJuiz/thesis huggingface dataset:
Reflective Impulse Radios: Principles and Design

Emerging wireless sensor networks display a severe asymmetry between the up and down links. An alternative communication architecture, reflective impulse radio, is proposed to address such design challenges. It operates from the principles of passive transmission and pulse based modulation, readily used in radio frequency identification (RFID) and ultra wide-band (UWB) technologies respectively. By employing both schemes in conjunction however, it achieves ultra low power consumption and high data rate simultaneously./nThis dissertation begins by examining future wireless sensor applications and presenting the link asymmetry. The alternative architecture is then introduced and its operation principles explained. A step-by-step design procedure follows, accompanied by the implementation of a miniature biomedical implant transmitter as a design example. Potential challenges and mitigation techniques are also discussed. Key advantages of the proposed architecture include ultra low power consumption, simple circuitry (hence high reliability and low cost), and broad range of scalability. Measurement results of the biomedical example are subsequently presented, before a short conclusion is given in the end./nWhile originated for wireless sensor networks, the proposed architecture can be applied to many other applications facing similar communication challenges.

Advisor: Rabaey, Jan M
The Evolution and Stability of Massive Stars

Massive stars are the ultimate source for nearly all the elements necessary for life. The first stars forge these elements from the sparse set of ingredients supplied by the Big Bang, and distribute enriched ashes throughout their galactic homes via their winds and explosive deaths. Subsequent generations follow suit, assembling from the enriched ashes of their predecessors. Over the last several decades, the astrophysics community has developed a sophisticated theoretical picture of the evolution of these stars, but it remains an incomplete accounting of the rich set of observations. Using state of the art models of massive stars, I have investigated the internal processes taking place throughout the life-cycles of stars spanning those from the first generation (“Population III”) to the present-day (“Population I”). I will argue that early-generation stars were not highly unstable to perturbations, contrary to a host of past investigations, if a correct accounting is made for the viscous effect of convection. For later generations, those with near solar metallicity, I find that this very same convection may excite gravity-mode oscillations that produce observable brightness variations at the stellar surface when the stars are near the main sequence. If confirmed with modern high-precision monitoring experiments, like Kepler and CoRoT, the properties of observed gravity modes in massive stars could provide a direct probe of the poorly constrained physics of gravity mode excitation by convection. Finally, jumping forward in stellar evolutionary time, I propose and explore an entirely new mechanism to explain the giant eruptions observed and inferred to occur during the final phases of massive stellar evolution. This mechanism taps into the vast nuclear fusion luminosity, and accompanying convective luminosity, in the stellar core to excite waves capable of carrying a super-Eddington luminosity out to the stellar envelope. This energy transfer from the core to the envelope has the potential to unbind a significant amount of mass in close proximity to a star's eventual explosion as a core collapse supernova.

Advisor: Quataert, Eliot
Geometric invariant theory and derived categories of coherent sheaves

Given a quasiprojective algebraic variety with a reductive group action, we describe a relationship between its equivariant derived category and the derived category of its geometric invariant theory quotient. This generalizes classical descriptions of the category of coherent sheaves on projective space and categorifies several results in the theory of Hamiltonian group actions on projective manifolds./nThis perspective generalizes and provides new insight into examples of derived equivalences between birational varieties. We provide a criterion under which two different GIT quotients are derived equivalent, and apply it to prove that any two generic GIT quotients of an equivariantly Calabi-Yau projective-over-affine variety by a torus are derived equivalent./nWe also use these techniques to study autoequivalences of the derived category of coherent sheaves of a variety arising from a variation of GIT quotient. We show that these autoequivalences are generalized spherical twists, and describe how they result from mutations of semiorthogonal decompositions. Beyond the GIT setting, we show that all generalized spherical twist autoequivalences of a dg-category can be obtained from mutation in this manner./nMotivated by a prediction from mirror symmetry, we refine the main theorem describing the derived category of a GIT quotient. We produce additional derived autoequivalences of a GIT quotient and propose an interpretation in terms of monodromy of the quantum connection. We generalize this observation by proving a criterion under which a spherical twist autoequivalence factors into a composition of other spherical twists./nFinally, our technique for studying the derived category of a GIT quotient relies on a special stratification of the unstable locus in GIT. In the final chapter we establish a new modular description of this stratification using the mapping stack from the quotient of the affine line by the multiplicative group to the quotient stack X/G. This is the first foundational step in extending the methods of GIT beyond global quotient stacks X/G to other stacks arising in algebraic geometry. We describe a method of constructing such stratifications for arbitrary algebraic stacks and show that it reproduces the GIT stratification as well as the classical stratification of the moduli stack of vector bundles on a smooth curve.

Advisor: Teleman, Constantin
Spatial Frustration: Using Pharmacological and Mechanical Disruption of Membrane Receptor Transport to Probe Cell Signaling Dynamics on Supported Lipid Bilayers

Micron-scale spatial reorganization of cell membrane receptor protein clusters is emerging as an important early modulator of inter- and intracellular signaling input. Detailed within is an in-vitro investigative technique utilizing cultured cells, nanolithograpically-patterned supports for fluid biomolecule-functionalized phospholipid bilayer membranes and inverted optical microscopy. This method allows the user to visualize and, if desired, restrict the formation and transport of these transient macroclusters as they coalesce on the membrane of a stimulated cell. Multi-color fluorescence imaging allows the simultaneous tracking of multiple molecules, permitting real-time analysis of coupling between surface receptors and intracellular signaling and structural proteins. The two systems examined are the T cell immunological synapse and ephrinA1-EphA2 interactions in highly invasive breast cancer cells. In both cases, it is demonstrated that induced restrictions of receptor-mediated cytoskeletal reorganization is sufficient to alter downstream signaling outcomes, and the molecular mechanisms of feedback coupling are investigated.

Advisor: Groves, John T
Pattern formation in photosynthetic membranes: a physical and statistical approach

Photosystem II (PSII) and its associated light-harvesting complex II (LHCII) are highly concentrated in the stacked grana regions of photosynthetic thylakoid membranes from plants and green algae. PSII-LHCII supercomplexes can be arranged in disordered packings, ordered arrays, or mixtures thereof. The physical driving forces underlying array formation are unknown, and statistically robust methods of identifying arrays in micrographs are lacking, complicating attempts to determine a possible functional role for arrays in regulating light harvesting or energy conversion efficiency. This dissertation introduces new computational tools for studying the nano- and mesoscale organization of the membrane proteins that comprise the photosynthetic apparatus, and applies them to illuminate the origins of the diversity of local structural motifs in this adaptive biomaterial. First, we introduce a coarse-grained model of protein interactions in coupled photosynthetic membranes, focusing on a small number of particle types that feature simple shapes and potential energies motivated by structural studies. Reporting on computer simulations of the model's equilibrium fluctuations, we demonstrate its success in reproducing diverse structural features observed in experiments, including extended PSII-LHCII arrays. Free energy calculations reveal that the appearance of arrays marks a phase transition from the disordered fluid state to a system-spanning crystal. The predicted region of fluid-crystal coexistence is broad, encompassing much of the physiologically relevant parameter regime. Our results suggest that grana membranes lie at or near phase coexistence, conferring significant structural and functional flexibility to this densely packed membrane protein system. Upon extending this model to include simple representations of the membrane morphology and protein components found in thylakoid margins and stroma lamellae, we find that LHCII stacking and crowding in the grana are also primary determinants of the segregation of protein components between stacked and unstacked regions of the thylakoid membrane. In addition, we develop a statistical pipeline for identifying PSII crystals in nanometer-resolution micrographs of thylakoid membranes that would assist in future experimental tests of the predictions put forth in this dissertation; we validate our method on atomic force microscopy measurements of grana membranes isolated from Arabidopsis thaliana wild-type and soq1 mutant plants. As a whole, this work creates a foundation for future rigorous biophysical investigations of the structure, function, and dynamics of the photosynthetic apparatus.

Advisor: Geissler, Phillip L
Continuum approach for modeling and simulation of fluid diffusion through a porous finite elastic solid

The diffusion of liquid and gas through porous solids is of considerable technological interest and has been investigated for decades in a wide spectrum of disciplines encompassing chemical, civil, mechanical, and petroleum engineering. Porous solids of interest are made of either natural materials (e.g., soil, sand) or man-made materials (e.g., industrial filters, membranes). In both cases, liquids (e.g., water, crude oil) and gases (e.g., air, oxygen, natural gas) are driven through the voids in the porous solid by naturally or artificially induced pressure. Nafion⃝R is an important example of a well-characterized man-made porous medium due to its extensive use in proton- exchange membrane fuel cells. Here, while the fuel cell is in operation, a mixture of air and water diffuses through the pores of a Nafion⃝R membrane. The efficiency of the fuel cell is affected by the variation in water concentration. In addition, high water concentration has been experimen- tally shown to cause substantial volumetric deformation (swelling) of the membrane, which may compromise the integrity of the device./nIn this dissertation, a continuum approach for modeling diffusion of fluid through a porous elastic solid is proposed. All balance laws are formulated relative to the frame of a macroscopic solid resulting from the homogenization of the dry solid and the voids. When modeling only liquid diffusion through the macroscopic solid, the displacement of the macroscopic solid and the liquid volume fraction are chosen to characterize the state of the porous medium, and Fick's law is used as the governing equation for liquid flow. When modeling multiphase diffusion through the macroscopic solid, the displacement of the solid, the gas pressure and the liquid saturation are chosen as state variables, and both fluid diffusions are assumed to follow Darcy's law. Both single phase and multiphase diffusion models are implemented in the finite element method, and tested with various loading conditions on different types of materials. Numerical simulation results are presented to show the predictive capability of the two models.

Advisor: Papadopoulos, Panayiotis
Improving the Efficacy of Arms Control: From Risk Reduction to Uncertainty Management

My dissertation research addresses a role for decision-­making theory in international politics. Specifically, It examines the effect of uncertainty--as distinct from risk--on the negotiation of arms control agreements. This work is driven by the following paradox and foreign policy impediment: current best practices for arms control negotiations recommend strategies for risk reduction, including limiting the scope, scale, and duration of agreements, but these strategies are inconsistent with the overarching goals of arms control, which include the pursuit of long-­term peace and stability. When goals and strategies for arms control negotiations instead provide effective "uncertainty management," we get broader and more durable agreements./nThis project is also motivated by the fact that we have little empirical information on the efficacy of arms control agreements in general, and none that speak to the optimization of these agreements in order to meet long-­term security goals. My research aims to fill that gap so we can best consider the most effective role for arms control./nDrawing on case studies of successful and unsuccessful nuclear and conventional arms control negotiations and a novel dataset consisting of 43 bilateral and multilateral negotiations and agreements, my findings suggest that current arms control practices tend to fail not for lack of ambition; they fail because the more modest goals which allow agreements to be reached more quickly and easily result in an efficiency that comes at a price. The durability of arms control agreements is better facilitated by including a wide range of treaty terms, including confidence and security building measures (CSBMs) that work in concert to manage multiple sources of uncertainty over time. This means that if we want negotiations to succeed and agreements to survive, we need to strike a better balance between long-­ and short-­term goals. It may also mean that we need to scale back expectations for what can be achieved in the short-­term and develop new ways of extending what are thought of as "insignificant" achievements, like CSBMs.

Advisor: Weber, Steve
Role of retinoic acid signaling in homeostatic synaptic plasticity

Homeostatic synaptic plasticity (HSP) is a form on non-Hebbian plasticity that allows neurons to sense their global level of activity and modulate their own function to keep firing rate within a working range. In particular, chronic elevation or reduction of network activity activates compensatory mechanisms that modulate synaptic strength in the opposite direction (i.e. reduced network activity leads to increased synaptic strength). Among the many mechanisms that mediate homeostatic synaptic plasticity, retinoic acid (RA) has emerged as a novel signaling molecule that is critically involved in homeostatic synaptic plasticity induced by blockade of activity. In neurons, global silencing of synaptic transmission triggers RA synthesis. RA then acts at synapses by a non-genomic mechanism that is independent of its well-known function as a transcriptional regulator, but operates through direct activation of protein translation in neuronal dendrites. Protein synthesis is activated by RA-binding to its receptor RARα, which functions locally in dendrites in a non-canonical manner as an RNA-binding protein that mediate RA's effect on translation./nIn this dissertation I demonstrate the critical role that translational regulation operated by RA plays in synaptic scaling, a post-synaptic form of homeostatic plasticity which consists in the regulation of receptor abundance on the post-synaptic membrane in response to activity blockade. In this context, my work has focused on the regulation of both excitatory and inhibitory transmission operated by RA in order to elucidate whether this molecule, normally only associated with neural development, plays a pivotal role in the modulation of excitation and inhibition balance in the adult brain. Since, abnormalities in this balance have been linked to several pathological conditions such as autism and Fragile-X mental retardation, my work described here emphasizes the primary role of the dynamic regulation of the excitation/inhibition balance in neural networks mediated by RA.

Advisor: Ngai, John
Chen, Lu
Dissecting the Operating Mechanism of a Biological Motor One Molecule at a Time

Double-stranded DNA viruses, including most bacteriophages and mammalian herpesviruses, package their genomes into a pre-formed protein capsid during their self-assembly. DNA is compacted to near-crystalline densities at the end of packaging. This remarkable mechanical task is performed by a powerful ATP-driven molecular machine known as the packaging motor. Bacteriophage Phi29, a model system for studying DNA packaging, has a 19.3-kbp genome and its packaging motor is composed of a connector, an RNA scaffold, and a pentameric ring ATPase./nRing ATPases of the ASCE superfamily perform a variety of cellular functions. An important question about the operation of these molecular machines is how the ring subunits coordinate their chemical and mechanical transitions. Here we present the first comprehensive mechanochemical characterization of a homomeric ring ATPase - Phi29 gp16 - which translocates dsDNA in cycles composed of alternating dwells and bursts. We use high-resolution optical tweezers to determine the effect of nucleotide analogs on the cycle. We find that ATP hydrolysis occurs sequentially during the burst and that ADP release is interlaced with ATP binding during the dwell, revealing a high degree of coordination among ring subunits. Moreover, we show that the motor displays an unexpected division of labor: although all subunits of the homo-pentamer bind and hydrolyze ATP during each cycle, only four participate in translocation whereas the remaining subunit plays an ATP-dependent regulatory role./nSeveral viral packaging motors have been shown to slow down as the capsid fills up with DNA, but it remains unclear how the packaging velocity is regulated. Here we use high-resolution optical tweezers to monitor the base-pair-scale packaging dynamics at various degrees of capsid filling. By comparing the burst duration at various degrees of capsid filling and different external forces, we estimate an internal force of ~20 pN at 100% filling, much lower than the motor's stall force. We find that the motor's step size is continuously modulated by capsid filling, in quantitative agreement with measurements of DNA rotation by the Phi29 packaging motor. In addition, we find the motor switches on and off at high filling by entering into long-lived pauses, which may allow DNA relaxation within the capsid. Together, our results reveal that the motor is not passively stalled by a large internal force at high filling as suggested by previous models. Instead, the motor is actively throttled down via several mechanisms in response to DNA encapsidation. The intricate crosstalk between the motor and the capsid plays a key role in orchestrating the molecular events leading to packaging termination and virus maturation, and may represent a general design principle shared by different viruses.

Advisor: Bustamante, Carlos J.
Debt and the safety net: Personal borrowing in the shifting landscape of public responsibility

Over the past thirty years, as the rise in the cost-of-living has outpaced earnings and the welfare state has undergone a major transformation from providing a social safety to promoting personal responsibility, growing numbers of families and individuals have resorted to acquiring more debt to cover living expenses. This dissertation examines the relationship between personal debt and changes in the welfare state, across nations and within the United States. The trend of short-term borrowing in the context of public spending on social benefits is examined using data from Organisation for Economic Cooperation and Development (OECD). An inverse relationship between public spending and consumer debt was predicted but did not appear. Instead, a patterning of the public spending/consumer debt types loosely based on Esping-Andersen's 1990 welfare state regime typology emerged, with liberal welfare states tending to have more consumer debt than conservative or social democratic states. In the United States, credit card debt and ownership of credit cards by social assistance recipients have risen steadily over the past 20 years. Furthermore, analyses revealed clear and significant demographic and economic behavioral characteristics of payday loan borrowers, namely that social assistance recipients are approximately three times more likely than non-recipients to take out a payday loan.

Advisor: Gilbert, Neil
Semantic Representation in the Human Brain

The goal of the human sensory system is to build a useful internal representation of the world. In vision, this means that the brain categorizes and identifies all the objects and actions that are being observed. In language, it means that the brain understands the meaning of each word that is being perceived, and integrates across words to understand the meaning of a narrative. Both of these processes can be seen as extracting the meaning, or semantic content, from a dense stream of sensory information. We know very little about how the brain accomplishes these feats. Indeed, entire fields of research (computer vision and natural language processing) are devoted to reproducing on a computer feats of understanding that the human brain accomplishes with ease. We may be able to gain insight into these processes by studying how the semantic information extracted from visual and linguistic stimuli is represented in the brain./nThis dissertation describes three functional magnetic resonance imaging (fMRI) experiments that have helped to reveal how visual and linguistic semantic information are represented across the human cerebral cortex. These experiments relied on a relatively new fMRI analysis methodology known as voxel-wise modeling (VM). Although this methodology was developed for modeling how the brain represents the structure of visual information, it was adapted here for modeling representation of the extremely complex semantic information present in natural movies and natural narrative stories./nThe first experiment (Chapter 2) showed that information about object and action categories present in natural movies is represented in a low-dimensional semantic space that is shared across subjects. Projecting this semantic space across the cortex revealed that semantic information is represented in broad cortical gradients that cover a surprising amount of the cortical surface. The second experiment (Chapter 3) showed that information about the semantic content of narrative spoken stories is also represented in a low-dimensional space that is shared across subjects. To model the complex cortical maps for this semantic space a new technique was developed called PrAGMATiC (Probabilistic And Generative Model of Areas Tiling the Cortex). This new technique revealed that the cortical semantic maps can be explained by about 230 functional areas that cover much of the prefrontal cortex, temporoparietal junction, precuneus, and temporal cortex. Finally, the third experiment (Chapter 4) showed that a novel hierarchical logistic regression (HLR) model could accurately decode the categories of objects and actions present in natural movies from fMRI responses.

Advisor: Gallant, Jack L