VictorJuiz/thesis huggingface dataset:
Germline maintenance and regeneration in the amphipod crustacean, Parhyale hawaiensis

Because the germline eventually gives rise to gametes, which have the potential to become the/nnext generation, it is arguably one of the most important cell types and understanding how the/ngermline is specified and maintained throughout an organism's lifetime is a fundamental/nquestion in biology. This dissertation investigates the underlying mechanisms of germline/nspecification, maintenance, and regeneration in the amphipod crustacean Parhyale hawaiensis./nFirst I identified additional germline markers, Ph-piwi1, Ph-piwi2, Ph-tudor, and Ph-gustavus in/nParhyale. Then I characterized the Parhyale adult germline stem cell (GSC) niche by using a/ncombination of molecular markers (for germline and stem cell niche components) and using cell/nproliferation assays. I generated an antibody to Parhyale Vasa, which was instrumental in/nconfidently identifying germline cells. In the Parhyale adult ovaries, this GSC niche likely/nresides within the germline ridge. Understanding where the putative GSC niche is important for/nevolutionary comparisons and can give clues as to how germline regeneration occurs. Finally, I/ninvestigate the potential role of bone morphogenetic protein (BMP) signaling in Parhyale/ngermline maintenance and regeneration. This study provides insight into germline specification,/nthe GSC niche, and adult regeneration in the amphipod crustacean, Parhyale hawaiensis.

Advisor: Patel, Nipam
Exactly Solvable Stochastic Models in Elastic Structures and Scalar Conservation Laws

This dissertation presents new results concerning two models with deterministic dynamics but involving a stochastic initial condition or environment. The first concerns a well-known family of PDE called scalar conservation laws, where, given a random initial condition, we provide a statistical description of the solution as a stochastic process in the spatial variable at later time. This confirms a special case related to a conjecture by Menon and Srinivasan [G. Menon and R. Srinivasan. "Kinetic Theory and Lax Equations for Shock Clustering and Burgers Turbulence". In: Journal of Statistical Physics 140.6 (2010)]. The second involves a model from condensed matter physics for a one-dimensional elastic structure driven through a periodic environment with quenched phase disorder. In collaboration with M. Mungan [D.C. Kaspar and M. Mungan. Subthreshold behavior and avalanches in an exactly solvable charge density wave system". In: EPL (Europhysics Letters) 103.4 (2013) and D.C. Kaspar and M. Mungan. "Exact resluts for a toy model exhibiting dynamic criticality". (2014). Submitted.] the author obtained some basic results for this model and a more detailed description for an approximation to it which is a nonstandard sandpile system. We report some of these results here, with some additional introductory material targeted at a mathematical, rather than physical, audience. In each case some questions for future inquiry are identified, and it is argued that rigorous analysis of toy models such as those considered here is productive in the continued development of the field of statistical mechanics.

Advisor: Rezakhanlou, Fraydoun
From Spiders to Languages: a Phylogenetic Journey

The parallels between biological and linguistic evolution have been recognized for a long time. In this work, contemporary phylogenetic methods are applied to address empirical questions in both fields. Additionally, the parallel histories and methodologies between biological systematics and historical linguistics are reviewed and novel approaches for coding linguistic data for contemporary phylogenetic methods are suggested./nBiogeography of Orsolobidae The biogeography of the spider family Orsolobidae was used as a case study to test the ‘drowned’ New Zealand hypothesis and to assess the importance of the breakup of Gondwana in its diversification. A molecular phylogeny of Orsolobidae and numerous outgroups was dated using both fossil node and substitution rate calibrations. The resulting divergence age estimates are consistent with the Gondwana breakup, while they reject the ‘drowned’ New Zealand hypothesis./nLinguistic characters and phylogenetics The history and methods of biological systematics and historical linguistics are briefly reviewed while underlining their similarities and differences. Novel coding methods are proposed for lexical, phonological and morphological linguistic characters and how they can be analyzed with computational phylogenetic methods./nClassification of Tupí-Guaraní A new internal classification is suggested for the Tupí-Guaraní language family based on lexical data analyzed with Bayesian phylogenetic methods. The dataset is coded using a novel cognate presence-absence method which includes items that have undergone semantic shift. The results largely agree with the lower subgroups of previous classifications, but suggest a significantly different higher structure of the family, with Kamaiurá sister to all other languages. Our results also suggest a Tupí-Guaraní homeland between the Xingu and Tocantins rivers and new hypotheses for the spread of the family in South America.

Advisor: Gillespie, Rosemary G.
Computational Modeling in Three Dimensions of Multi-DOF Ship Motion in a Viscous Fluid

The prediction of roll motion of a ship with bilge keels is particularly difficult because of the nonlinear characteristics of viscous damping. Flow separation and vortex shedding caused by bilge keels significantly affect the roll damping and the magnitude of the roll response. To predict roll damping and motion of a ship, the Slender-Ship Free-Surface Random Vortex Method (SSFSRVM) was employed. It is a free-surface viscous-flow solver with low computational cost so that it can run on a standard desktop computer. It features a quasi-three dimensional formulation that allows the decomposition of the three-dimensional hull problem into a sequence of two-dimensional computational planes, in which the two-dimensional free-surface Navier-Stokes solver FSRVM can be applied. In this work, the SSFSRVM methodology has been further developed to model multi-degrees of freedom of free-body motion in the time domain. This version of SSFSRVM model does not require the assumption of small amplitude motion, and is capable of having viscosity turned on or off in the solution procedure. Because FSRVM uses a grid-free formulation, there is no issue with numerical viscosity./nWe validated the SSFSRVM in simulating the free roll decay motion of a naval vessel without forward speed. The numerically predicted vorticity distributions at different time instants near a bilge keel closely matched experimental PIV images. We found that the SSFSRVM model is capable of predicting the roll motion of a hull, and capturing the behavior of the vortical structures in the fluid. Further, we examined how the roll decay coefficients and the flow field were altered by the span of the bilge keels, based on the time-domain simulation of the coupled hull and fluid motion. Plots of vorticity contours and iso-surfaces along the three-dimensional hull were presented to reveal the motion of fluid particles and vortex filaments near the keels. In addition, the generation of the quadratic roll damping was investigated by showing the bilge-keel hydrodynamic moment and the pressure distribution on the hull surface and bilge keels./n/nFinally, the predicted roll time histories of a naval hull with three different forward speeds were compared with those obtained from experimental measurements. The numerical predictions were in good agreement with the experimental measurements for all three speeds. In addition, the numerical model also successfully produced the divergent waves with the same angles as those measured in the experiment, and accurately predicted the locations of the peaks and troughs of the divergent waves. The motion of the sonar-dome and bilge-keel vortex filaments, as well as their interactions, were presented to investigate the effect of forward speed. Significant influences of forward speed on the roll motion and roll damping were noted and explained.

Advisor: Yeung, Ronald W
Attosecond spectroscopic studies of atomic and molecular dynamics

Isolated attosecond pulses with photon energies in the extreme ultraviolet have provided a new capability to study few-femtosecond and sub-femtosecond dynamics in atomic and molecular systems. A novel regime of attosecond transient absorption measurements, in which the near-infrared pulse follows the attosecond pulse, is reviewed. The observed timescales of the decay of an absorption feature and oscillations due to quantum beating are derived and experimental considerations for these measurements are discussed. Attosecond transient absorption spectroscopy is then applied to observe quantum beating between the 2s22p5(2P3/2)3d and 2s22p5(2P1/2)3d electronically excited states of neon. The quantum beating is observed more prominently in one of the absorption features, and theoretical models of the effect of the near-infrared pulse are proposed to explain this asymmetry and characterize the observed beating. In the model that most closely agrees with the measurement, the beating is detected via Rabi cycling induced by the near-infrared pulse through an intermediate state (likely one of the 3p states), and this mechanism is shown to be strongly dependent on the spectrum of the near-infrared pulse./nThe isolated attosecond pulses used in these experiments are characterized using the photoelectron streaking method and the duration of these pulses is measured by iteratively reconstructing the streaking spectrograms. The effect on the streaking spectrogram of various pulse characteristics, such as duration, chirp, and the presence of satellite pulses, is described. Streaking spectrograms using low photon energy attosecond pulses are typically asymmetric. The reasons for this asymmetry are discussed and the challenges of reconstructing these low energy pulses are addressed. Finally, attosecond pulses are used to investigate superexcited states, or doubly excited states above the ionization potential, of the nitrogen molecule (N2). These states can decay via two competing channels, autoionization and predissociation. Time-of-flight mass spectrometry is applied to measure lifetimes of these states. Preliminary results are presented and improvements to the experimental design are proposed.

Advisor: Leone, Stephen R
Neumark, Daniel M
Minor China: Affect, Performance, & Contemporary China in the Global

In our globalized moment, cultural production emerging from China and other non-Western locations has become of central concern for critical theory, art history, and cultural studies. In order to counteract previous decontextualized and over-universalizing discussions of contemporary Chinese art, most art history, theatre, and performance studies scholars have emphasized how art and culture emerged within specific historical and political contexts. However, by repeatedly relying on contextualization, the Chinese are reproduced as lacking imagination, contradictions, and complexity. By examining the historical emergence of this discourse, I demonstrate the limits of past approaches in order to explore other methodological possibilities./nIn contrast to other scholars who have situated contemporary Chinese performance and art within over-determined modes of contextualization, this dissertation locates alternative methodological possibilities in affect and feelings. This project argues that historical contextualization reproduces presumptions around the Chinese state as authoritarian and its subjects as conscious actors. Thus, I develop a method called minor China that privileges the realms of affect, fantasy, and the immaterial over such presumptions. The minor, akin to the musical structure that feels melancholic and less prevalent than the major, focuses on such contours to direct attention to the assumptions that frame how we write about Chinese culture and the state. I develop the minor from the recent theoretical turns towards minor feelings and affects, from scholars such as Lauren Berlant, Sianne Ngai, Steven Shaviro, and Eve Sedgwick. As I engage these analytics for their methodological capabilities, I situate minor contours to understand what they offer for cultural and political economic analyses of China.

Advisor: Jackson, Shannon
Tides in Close Binary Systems

We consider three aspects of tidal interactions in close binary systems. 1) We first develop a framework for predicting and interpreting photometric observations of eccentric binaries, which we term tidal asteroseismology. In such systems, the Fourier transform of the observed lightcurve is expected to consist of pulsations at harmonics of the orbital frequency. We use linear stellar perturbation theory to predict the expected pulsation amplitude spectra. Our numerical model does not assume adiabaticity, and accounts for stellar rotation in the traditional approximation. We apply our model to the recently discovered Kepler system KOI-54, a 42-day face-on stellar binary with e=0.83. Our modeling yields pulsation spectra that are semi-quantitatively consistent with observations of KOI-54. KOI-54's spectrum also contains several nonharmonic pulsations, which can be explained by nonlinear three-mode coupling. 2) We next consider the situation of a white dwarf (WD) binary inspiraling due to the emission of gravitational waves. We show that resonance locks, previously considered in binaries with an early-type star, occur universally in WD binaries. In a resonance lock, the orbital and spin frequencies evolve in lockstep, so that the tidal forcing frequency is approximately constant and a particular normal mode remains resonant, producing efficient tidal dissipation and nearly synchronous rotation. We derive analytic formulas for the tidal quality factor and tidal heating rate during a g-mode resonance lock, and verify our results numerically. We apply our analysis to the 13-minute double-WD binary J0651, and show that our predictions are roughly consistent with observations. 3) Lastly, we examine the general dynamics of resonance locking in more detail. Previous analyses of resonance locking, including my own earlier work, invoke the adiabatic (a.k.a. Lorentzian) approximation for the mode amplitude, valid only in the limit of relatively strong mode damping. We relax this approximation, analytically derive conditions under which the fixed point associated with resonance locking is stable, and further check our analytic results with numerical integration of the coupled mode, spin, and orbital evolution equations. These show that resonance locking can sometimes take the form of complex limit cycles or even chaotic trajectories. We also show that resonance locks can accelerate the course of tidal evolution in eccentric systems.

Advisor: Quataert, Eliot J
Circuit-QED and Quantum Feedback Control

Quantum computation and quantum information are an emerging research field that involves both physics, computer science, and engineering. The quantum nature of our world can be harnessed to dramatically improve the way we store, transmit, and process information. The first part (Chap. 1) of this thesis presents the theory behind quantum information science and gives a survey of some fascinating topics in this area. The second part (Chap. 2 and 3) studies dissipative quantum systems, which helps us understand the challenges facing all real quantum information processors. The third part (Chap. 4 and 5) discusses how we may use control strategies to fight dissipation and protect quantum information. The last part (Chap. 6 and 7) of this thesis describes circuit-QED systems, a solid state implementation of quantum computers that has become increasingly popular over the years due to great controllability and scalability. Most of my independent contributions are contained in Chap. 3, 4, 5, and Sec. 6.3.1, 7.3.

Advisor: Whaley, Birgitta
Improved Fuel Transport Selectivity in Polymer Electrolyte Membranes

In polymer electrolyte membrane (PEM) fuel cells, fuel crossover through the membrane is a significant problem that contributes to reduction in cell efficiency and accelerated membrane degradation. The need for high water content in the membrane to produce acceptable conductivities leads to excessive fuel crossover while also limiting cell operating temperature to <100°C where platinum catalysts are easily contaminated by CO. This work focused on the study of transport functions in PEMs in an effort to reduce fuel crossover through the replacement of water with an alternative proton solvent./nThe heterocycle imidazole was incorporated into Nafion® membranes as an alternative proton solvent because of its ability to form hydrogen bond networks similar to water, and its high proton conductivity (10-2 to 10-1 S/cm) at temperatures around 150°C. Imidazole must be covalently bonded to the membrane to prevent loss due to leeching by water, or sublimation at high temperatures. In this work, imidazole in the form of 4(5)-hydroxymethyl imidazole (ImOH) was imbibed into the perfluorosufonic acid membrane, Nafion®./nIn this work, incorporation of ImOH into the membranes is shown improved the thermo-mechanical properties, as studied using dynamic mechanical analysis, while reducing water and methanol transport kinetics, as observed using dynamic vapor sorption and nuclear magnetic resonance. Study of the membrane using small angle x-ray scattering linked these results to changes in membrane morphology. Ex-situ study of methanol transport through the membrane was confirmed using in-situ electrochemical fuel crossover measurements on operational direct methanol fuel cells. The results showed that the use of ImOH as an immobilized proton solvent results in around a 50% reduction in methanol fuel crossover.

Advisor: Devine, Thomas M
Kerr, John B
Investigations of Organometallic Reaction Mechanisms Using Ultrafast Time-Resolved Infrared Spectroscopy

Ultrafast time-resolved infrared spectroscopy provides a powerful tool for studying the photochemistry of organometallic complexes. The studies described herein focus on the mechanisms of photochemically initiated organometallic reactions with a particular emphasis on two topics: the role of spin states and spin state changes in organometallic reactions, and the primary photochemical dynamics of complexes containing metal-metal bonds (e.g. transition metal dimers and clusters). Many of these studies seek to uncover trends in reactivity based on the spin states of organometallic reaction intermediates, with the goal of being able to offer some level of predictive insight into the reactivity of complexes as classified by their spin multiplicity. The reactivity of various coordinatively unsaturated reaction intermediates are studied with respect to bond activation, electron transfer, excited state photoisomerization, and other classes of reactions important to organometallic catalysis. A second focus, which shares some degree of overlap with the topic of spin state changes, is the primary photochemistry of complexes containing metal-metal bonds. Several of the studies reported herein use time-resolved infrared spectroscopy to examine the primary photochemical processes occurring upon excitation of transition metal dimers and clusters, and often spin state changes also found to play an important role. Results of computational chemistry calculations are frequently used to facilitate interpretation of the experimental results by computation of structures, relative energies, infrared spectra, and spin-orbit coupling for the complexes studied experimentally. Additional studies outside these two primary areas of focus also investigated the ring-slippage of cyclopentadienyl ligands and the CO-delivery properties of a popular CO-Releasing Molecule.

Advisor: Harris, Charles B
A Statistical Process Control Approach to Energy Efficiency in Buildings

Statistical Process control is a technique often used in manufacturing in order to determine whether a process is changing based upon most recent measurements. In this thesis, I will cover how this is applicable to energy efficiency in buildings, and construct the framework that allows for this viewpoint to be effective in understanding how buildings consume energy. I will discuss how to effectively baseline a buildings energy performance, predict that performance in basic and advanced ways, and then use that prediction to determine when building parameters are out of line. I outline a methodology for determining when building operation parameters have changed, attempt to identify them, and suggest potential problems, given a top-down monitoring methodology combined with a bottom-up fault diagnostics approach. The approach explored in this talk will combine Shewhart and other control charts with modern monitoring techniques in order to explore the efficacy of this approach. I conclude by developing new modifications on the idea of control charts and by using those modifications to produce an analysis of the campus energy use at the University of California, Berkeley.

Advisor: Wright, Paul K