VictorJuiz/thesis huggingface dataset:
Yeast and chemostats, balls and urns [electronic resource] : two comments on the dynamics of adaptive evolution
Keywords: Statistics

Kao & Sherlock (2008) present three-color data on yeast evolutionary dynamics. Four of their experiments depict one hundred million yeast cells; four depict one billion yeast cells. Each shows the adaptive evolution of an initially neutral population for about five hundred generations. Each cell in their experimental populations fluoresces one of three colors (red, yellow, or green). Their data show subpopulations so-defined evolving through time. Our work deals with the Wright-Fisher model (Fisher 1922; Wright 1931) and its use in modeling the Kao-Sherlock data (2008). In particular we use the model in an attempt to approximate the adaptive characteristics of the subpopulations that underlie the red, yellow, and green Kao-Sherlock subpopulations. We introduce our work on these data in Chapter 2. Specifically, we describe the data in detail and review the model and its continuous time approximation. We also review briefly previous work pertinent to our work here. Chapter 3 deals with two mathematical features of the Wright-Fisher model. We bound the means of certain stopping times relating to the process. Such bounds show that the process with selection spends little time in the central part of its domain; it spends most of its time near the boundaries of such. We then discuss approximating the mean of the process with selection. We show how typical calculations break down and discuss the assumptions underlying our approximation. Chapter 4 then applies the results of Chapter 3 to the Kao-Sherlock yeast data. We discuss issues relating to data fitting and parameter estimation and arrive at an approach based on sequential non-linear regressions. We give our results in the context of additional recent results by Kvitek & Sherlock (unpublished) and discuss pros and cons relating to in silico versus experimental approaches. In the end each informs the other. Model-based results allow the direct comparison of assumptions and outcomes. In Chapter 5 we consider an urn model of simplified adaptive dynamics. Imagine an urn containing one ball. On closer inspection we see that it has a "0" printed on it. We select the ball from the urn. Seeing the "0" we return it to the urn along with a new "1" ball. We repeat this indefinitely. At each step we: 1. Select a ball at random from the urn making a mental note of its number; 2. Throw the selected ball back into the urn and then add a brand-new ball. The new ball sports a number one greater than that on the selected ball. In Chapter 5 we derive bounds for the expected dynamics of this process. In addition, we take pains to build a tenuous connection between this process and the process underlying our conception of adaptive evolution. We close by suggesting several possible interesting research directions involving urn models in population genetics.
3D velocity and scalar field diagnostics using magnetic resonance imaging with applications in film-cooling [electronic resource]
Keywords: Mechanical Engineering

A new Magnetic Resonance Imaging (MRI) technique was developed to measure the three-dimensional, time-averaged scalar concentration distributions in turbulent mixing applications. The diagnostic was initially developed and tested in a turbulent free shear layer experiment where it was validated using planar laser induced fluorescence (PLIF) experiments. The remainder of the study examined a three-dimensional mixing flow motivated by trailing edge film cooling of an aircraft gas turbine blade. A modern slotted trailing edge cutback geometry was added in which coolant was discharged from rectangular slots separated by tapered lands. Water, and water with copper sulfate were the working fluids, and the MR-based experiments were conducted at Reynolds numbers based on airfoil chord and bulk velocity from 100,000-250,000. The magnetic resonance concentration (MRC) technique was further refined in the film cooling apparatus to reduce the uncertainty to under 6.0% in concentration and to provide robust measurement of the surface concentration. Combined magnetic resonance velocimetry (MRV) and MRC measurements were acquired for a generic trailing edge cutback geometry. The effect of variations in the blowing ratio and Reynolds number were examined. Reynolds number was found to have no significant effect while the variations in blowing ratio produced relatively small changes. Combined MRV and MRC data sets were analyzed in detail for insight into the mean flow structures primarily responsible for rapid mixing of the mainstream and coolant flows. Longitudinal vortices formed inside the slot feed channels and at the edges of the lands played a critical role as did the separation bubble behind the slot lip. Three modifications to the breakout geometry were designed with the goal of minimizing the adverse effects of these flow structures. Performance improvements with the redesigned trailing edge geometries indicate as much as a 40% improvement in the averaged surface effectiveness using a non-dimensional performance parameter.
60 GHz 4-Element RF beamforming receiver array [electronic resource]
Keywords: Electrical Engineering

Mm-wave technology is attractive for non-destructive high resolution imaging, high data rate communication, and automobile radar applications. For example, the large available bandwidth at the unlicensed 60 GHz band can potentially support up to 7 Gb/s in IEEE 802.11ad. However, one fundamental problem in mm-wave technology is the high signal path loss. Multiple-antenna arrays can be exploited to compensate for this drawback. Since CMOS technology has evolved to a stage where its performance is comparable to the traditional III-V compound semiconductor counterpart, low cost, lower power design and integration of an mm-wave wireless circuit in CMOS technology has become feasible. In this work, we first characterize the on-chip passive elements and active elements in a 65-nm CMOS technology. Slotted ground CPW and MSL lines are proposed which provide high Q ($> 20$) performance or flexible design capabilities. Two low noise amplifiers (LNA) with and without cascode devices are implemented and compared. The LNA without the cascode device turns out to be a better option. It is shown that the cascode device will degrade noise figure, bandwith, and linearity. The noise figure without the cascode device is only 3.8 dB with 16.2 dB gain at 59 GHz, 8.7 GHz bandwidth, and 8.3 mA current consumption under the 1 V supply. A 4-element RF beamforming receiver front end with four off-chip antennas is implemented in 65-nm CMOS. The front end is digitally controlled and based on the proposed phase oversampling vector modulation (POVM) method. The receiver front end includes 4 LNAs, 4 POVMs, and power combining networks. Four off-chip antennas are wire bonded to the receiver. Different substrate materials are experimented and compared for the antenna design, including RO4003, FR4, and RT5880 materials. Compared to start-of-the-art work, we achieve high phase resolution ( .5^o$), very low NF (5.6 dB) with high gain (18.5 dB) for the beamformer at 56 GHz, and demonstrate truly spatial power combining and beam steering by using antennas. Compared with the conventional exhaustive lookup table method, the proposed POVM uses a semi-lookup table method. It uses a very small lookup table consisting of $\emph{only}$ basic oversampling vectors, and utilizes the linearity characteristics to adaptively select the weighting coefficients to compensate for the non-idealities in circuits, antenna array, and interfaces.
Achieving collision avoidance and fairness in CSMA-based wireless mesh networks [electronic resource]
Keywords: Electrical Engineering

CSMA-based wireless mesh networks are vulnerable to collisions. Even a single unicast flow can exhibit excessive collisions from hidden terminals. Furthermore, fairness objectives for single-hop networks can cause undesirable behaviors for mesh networks. Mesh networks of wireless sensors suffer from undesirable protocol interactions due to these challenges. Inter-protocol collisions and unfair channel usage between protocols cause the behavior of one protocol to change depending on other protocols. These inter-protocol interactions complicate the design of large sensor network systems. Motivated by these problems, this dissertation presents grant-to-send, a novel collision avoidance mechanism for wireless mesh networks. Rather than announce packets it intends to send, a node using grant-to-send announces packets it expects to hear others send. This dissertation provides evidence that inverting collision avoidance in this way greatly improves wireless mesh performance without significant overhead. Grant-to-send is simple to implement, and is compatible with existing hardware. Grant-to-send is also general enough to replace protocol-specific collision avoidance mechanisms common to sensor network protocols. While these individual mechanisms only avoid intra-protocol collisions, grant-to-send provides a MAC mechanism which can address both intra- and inter-protocol collisions. This dissertation also proposes a fairness scheme for mesh networks, which can be applied to protocol fairness. The fairness scheme combines and modifies traditional flow-based fairness techniques such as fair queueing and fair scheduling. However, the complexities of wireless make these mechanisms insufficient by themselves. This dissertation therefore proposes two new mechanisms that address these limitations, channel decay and fair cancellation, and shows that the fairness scheme can significantly improve protocol fairness. Together, this dissertation shows that achieving collision avoidance and fairness can make mesh networks perform better, more reliable, and thus easier to design.
Acquisition of sociolinguistic knowledge in a Mandarin-English dual immersion school [electronic resource]
Keywords: Linguistics

As children acquire language and encounter new speakers and linguistic situations, they also acquire the knowledge of sociolinguistic variation necessary to achieve communicative competence (Romaine 1984). When children enter school, they encounter new speakers, a new set of linguistic situations and styles, and sometimes new language varieties or even entirely new languages. Children's exposure to new languages is particularly intense in language immersion models; in the dual-language immersion model, students dominant in different languages interact in the same classroom, and spend time learning in each language. The "dual" in dual-language simplifies the more complex reality of many such programs, in which multiple varieties of languages are in fact present (Rubinstein-Avila 2002). In dual-language immersion classrooms where teachers and students speak a range of dialects, participants must learn to negotiate between varieties as well as between languages. The present study seeks to investigate what sociolinguistic knowledge children can acquire in the early elementary school years of a Mandarin-English dual-language immersion program, by examining how sociolinguistic meaning is reflected and negotiated in the linguistic practice and metalinguistic discourse of members of the school community. This question is addressed through ethnographic and quantitative analysis of teacher and student language use, corrective feedback, and other metalinguistic discourse. The present research draws on data from a year-long participant-observation study of first-grade and second-grade classes (ages 5-8) at a Mandarin-English dual-language immersion program in the United States. Analysis of language use and metalinguistic discourse at the school establishes that, rather than simply imitating the speech of their teachers or classmates, students in the early elementary grades can make use of sociolinguistic information present in stylistic variation and metalinguistic discourse to target and acquire a variety distinct from that used by the speakers around them. This analysis of the variation present in a dual-language immersion school setting also suggests that the sociolinguistic information present in classrooms is more rich and varied than has been previously assumed, and equips students to competently navigate a range of linguistic situations.
Action and knowledge [electronic resource]
Keywords: Philosophy

This dissertation mounts a defense of the claim, made by Elizabeth Anscombe in her monograph Intention, that when an agent is acting intentionally, he knows what he is intentionally doing immediately---without observation or inference. We can separate out three elements, which build on each other, in this claim: the agent is acting, is acting intentionally, and has knowledge of what he is doing. The progress of the dissertation roughly follows this rough division. The first two chapters are concerned with articulating what is at stake in the characterization of an agent as acting. Since someone can be doing something without its being the case that she will have done it, and the knowledge claim concerns the doing rather than the having done of an action, we should first of all investigate what is predicated of someone who is said to be underway toward an end. I begin in the first chapter at a further remove from intentional action, with an investigation of not necessarily agential process-claims in general; the second chapter begins the transition to acting intentionally be applying the considerations of the first to the agential context. The third and fourth chapters explicitly turn to acting intentionally. The third begins by addressing an argument meant to establish that intentional action is compatible with ignorance of what one is doing, and in doing so formulates a criterion for performing non-basic actions intentionally. The fourth chapter takes up teleologically basic actions and supplements the criterion of the third to give a sufficient and necessary condition on acting intentionally. The final pair of chapters addresses the knowledge element of the claim. In the fifth, I articulate the concern that the nature of action is such as to render it only knowable theoretically, and examine several theories that attempt to account for knowledge of action observationally or inferentially. This concern is viable in the context of the causal theory of action; in the sixth chapter, I endorse in its place a metaphysically modest teleological theory. With that in place, space is opened up for a neo-expressivist account of knowledge of intention in action, which, when combined with the results of the preceding chapters, redeems the knowledge claim.
Adaptive decision making in information networks [electronic resource]
Keywords: Electrical Engineering

The goal of this thesis is to develop techniques that enable us to analyze network precesses in which nodes of the network make decisions based on local and limited information. Such processes arise naturally in many information networks such as the World Wide Web (WWW), online social networks, and sensor networks. First we study a stochastic version of the online bipartite matching problem in which the sequence of arrivals are i.i.d samples of a given distribution. We use the ideas of offline statistics and adaptivity to give the first algorithm for this problem that improves the 1 − 1/e competitive ratio of the celebrated algorithm by Karp, Vazirani, and Vazirani, for the stochastic version in its general form. We also model and study the evolution of cooperation in populations with local interactions. Every node of the network corresponds on an individual choosing whether to cooperate or defect in a repeated prisoner's dilemma game. The players try to learn the best action by imitating those neighbors who have higher payoffs. We show that when the interactions take place on graphs with large girth, cooperation is more likely to emerge as a result of local clustering of cooperators. We also consider the practical problem of constructing well-connected sensor networks by locally moving the sensors. We design decentralized algorithms in which sensors identify the critical edges and then move in directions that improve connectivity in more critical regions. In our algorithms, nodes determine their movement direction only with local information exchange with their neighbors.
Adhesion and time-dependent fracture in integrated circuit technologies [electronic resource]
Keywords: Materials Science and Engineering

In order to maintain scaling in accordance with Moore's Law, a number of novel materials are being integrated at both the device and interconnect levels in modern microprocessors. The successful integration of these new materials requires that they tolerate the inherent stresses present in the structure, as well as the environments, temperatures, and loads associated with fabrication and packaging. This dissertation presents results from several studies focused on the fracture properties of materials at both the device and interconnect levels in modern integrated circuits. Innovative methods for performing thin film adhesion measurements on high strength films are introduced and were used to measure interface fracture energies as high as 35 J/m^2. Additionally, a novel technique for quantifying the effects of environment and temperature on the kinetics of thin film interface debonding is described and was used to quantify growth rates on the order of 1 nm / sec. Using these techniques, combined with surface science measurements of the resulting fracture surfaces, correlations between thin film fracture properties and other device or film properties are explored. While this dissertation specifically addresses materials used in integrated circuits, the techniques and concepts outlined here are applicable to a number of emerging nanoscience and energy technologies. At the device level, a correlation between adhesion and work function tuning behavior of bilayer metal gate electrodes on high-k films is explored. Angle-resolved X-ray photoelectron spectroscopy of the high-k and metal gate fracture surfaces provides strong evidence of a diffusion mechanism responsible for this behavior. At the interconnect level, effects of Cu electroplating chemistry and diffusion barrier composition on barrier adhesion and stress-induced voiding in Cu films are examined, and the critical role of electroplating impurities and interfacial oxygen is addressed. Additionally, the first evidence of time-dependent environmentally assisted debonding of Cu / barrier interfaces in oxidizing and reducing environments is reported and modeled. The kinetics of debonding vary over six orders of magnitude depending on environment and temperature, demonstrating the important role that environment may play in determining defect growth in Cu interconnects.
Advanced chemistry and understanding of acene-containing conjugated polymers for functional electronics [electronic resource]
Keywords: Chemical Engineering

Conjugated organic polymers and small molecules could potentially be employed as active material for high-throughput, low-cost and large-area device fabrication through solution processing. Electronic devices employing organic systems, such as organic light emitting diodes (OLEDs), organic photovoltaic cells (OPVCs) and organic thin-film transistors (OTFTs) for sensors and displays, have seen improved performances and commercialization in the recent decade. Continuous material innovation is the key towards the achievement of higher and better performances. Among various high-performing materials, large fused ring linear acenes, such as pentacene (Pn) and anthradithiophene (ADT) have maintained the benchmark for charge transport. Okamoto et al have since employed these structures into polymer backbones for solution-processable functional materials. This thesis explores in details the utility of Pn and ADT as building blocks in conjugated polymers. A variety of material and device characterization was carried out for the new materials developed. These include: (A) regio-regular Pn-containing copolymers. The direction of conjugation-extension (from 2,9- or 2,10-positions) was found to impact molecular order and charge-transport properties. (B) 2,8-conjugation-extended ADT-cyclopentadithiophene copolymers. Adjusting the bulkiness of the central substituents on the acene was found to impact molecular packing and charge-transport properties. Triisobutylethynyl-functionalized ADT achieved a photovoltaic power conversion efficiency of 2.7% in a polymer:fullerene bulk heterojunction device. (C) 5,11-conjugation-extended ADT copolymers. To explore impact on polymer electronic and packing behavior, ADT was incorporated with its long molecular axis orthogonal to the polymer backbone via in situ desilylation and Horner Emmons condensation. Using the first methodology, copolymerization with diketopyrrolopyrrole resulted in a low-bandgap polymer due to extended electron delocalization in the direction orthogonal to backbone. This polymer showed out-of-plane layered packing structure, and a high transistor hole mobility of 0.11 cm2 V-1 s-1. The second methodology enabled the development of an ADT monomer precursor exhibiting high ambient stability. Both 5,11-conjugation extended polymers yielded photovoltaic power conversion efficiencies of around 0.8 %. Through the development of these novel monomers and polymer, this thesis demonstrates the synthetic versatility that could be applied to pentacene and ADT in polymers, and the resulting ability to engineer the materials' energy levels and packing behavior. It shows that acene-containing polymers are promising materials for organic electronic devices.
Aeroacoustics of turbulent mixing layers [electronic resource]
Keywords: Mechanical Engineering

Jet noise is an important contributor to overall aircraft noise. The flow near the jet nozzle is a spatially developing mixing layer and influences flow dynamics further downstream. The present study focuses on the influence of inflow conditions on mixing layer development and noise generation mechanisms using large-eddy simulations. Large-eddy simulations of spatially developing, turbulent mixing layers with splitter plate included in the computational domain are presented. Different inflow condition cases with initially laminar boundary layers (abbreviated as LBL) and turbulent boundary layers (abbreviated as TBL) are considered. Effect of heating, keeping the velocity ratio fixed, is analyzed for both. For each case, the mean and turbulent intensity profiles collapse when plotted in similarity coordinates. The development distance to achieve self-similarity in the mean velocity profile is found to be shortest for cases with turbulent exit boundary layers. The growth rate of the shear layer and peak self-similar values of the turbulent intensities are found to be in agreement with available experiments. It is observed that with heating, the initial instability is accelerated but the saturation self-similar amplitude of Reynolds stress components do not vary. The saturation amplitudes of density fluctuations were found to increase proportionally to difference in free-stream densities whereas near-field pressure fluctuations were found to decrease with heating. A simple scaling is suggested for the near-field pressure fluctuation amplitude. The observed scaling laws were also confirmed by simulation data from two-dimensional direct numerical simulations. For LBL, sound radiation is observed in downstream direction peaked roughly at 30 degrees. The vortex pairing and breakdown to turbulence contribute significantly to the radiated sound. For TBL, the acoustic field near the shear layer is significantly weaker and noise due to passage of boundary layer eddies over the trailing edge is observed. For both the cases, a reduction in overall sound pressure levels in the far-field is observed with heating. Analysis of relative importance of Reynolds stress autocorrelation tensor components is presented to explain the effects of heating.