VictorJuiz/thesis huggingface dataset:
Advanced High-Frequency Measurement Techniques for Electrical and Biological Characterization in CMOS

Precision measurements play crucial roles in science, biology, and engineering. In/nparticular, current trends in high-frequency circuit and system designs put extraordinary/ndemands on accurate device characterization and modeling. On the other hand, the need/nfor better point-of-care requires substantial innovation in developing miniaturized sensors/nand medical devices that ease the biological analysis without sacrificing the accuracy./nThis research presents two advanced measurement techniques for electrical and/nbiological characterization applications./nIn the first part, a novel single-element on-wafer VNA calibration algorithm is/npresented dedicated for device characterization at mm-Waves. Conventional calibration/napproaches such as thru-reflect-line (TRL) require at least three precisely-machined and/nwell-characterized standards. The necessity of probe re-positioning leads to significant/nmeasurement errors due to mechanical uncertainty as the measurement frequency/napproaches sub-THz. By exploiting on-chip impedance modulation, such an electronic/ncalibration (E-Cal) algorithm can work with single element without any prior knowledge/nof the impedance behavior. This CMOS-based approach opens a new direction in the/nfield of VNA calibration./nIn the second part, the implementation of a dielectric spectroscopy biosensor aiming/nfor single-cell analysis is presented. Most present day clinical flow cytometers use/nfluorescence-activated cell sorting (FACS), which requires bulky optical detection system/nas well as complex sample-labeling process, limiting the assay time and the wide-spread/nadoption in the point-of-care (POC) setting. To address these issues, this research/npresents the design and the implementation of a sensor-on-CMOS spectrometer that/nmeasures the microwave signature of single cell as a potentially label-free analytic tool./nThe sensor covers four frequency bands across 6.5 – 30 GHz, offering sub-aF noise/nsensitivity at 100-kHz bandwidth. Such performance is enabled with injection-locked/noscillator sensors in interferometry architecture. With microfluidic integration,/nexperiments on flow cytometry and molecular sensing are demonstrated.

Advisor: Niknejad, Ali M.
Magnetic Nano Particles and Thin Films for High Frequency Micro Inductors

The size and performance of integrated circuits have been following Moore’s law to continuously shrink and progress over the past decades while on-chip inductors have seen little advancements. This work proposes several unique approaches in the integrated magnetic cores for high frequency micro inductor developments, including: (1) spherical-shape, anti-oxidizing magnetic nanoparticle composites; (2) sputtered magnetic thin films with magnetization-induced anisotropy; and (3) rectangular-shape magnetic particles with geometry-induced anisotropy. Theoretical and simulation studies have been conducted with experimental demonstrations to validate these concepts./nChemical syntheses of spherical-shape magnetic FeNi3 particles of 100 nm in diameter, with and without a thin passivation SiO2 coating have been investigated. After the integration with micro inductors by a CMOS-compatible process, it is found that the inductance values have increased 20-45% up to 2 GHz for micro inductors after adding the magnetic nanoparticle composites. The quality factors have degraded slightly mainly due to the magnetic losses from large coercivity at about 100 Oe despite of the reduction of eddy current losses in the magnetic nanoparticle composites./nThe control of magnetization-induced anisotropy of magnetic thin films by using different magnitudes of sputtering deposition power under an external magnetic field has been studied and characterized. By reducing the sputtering power from 1000 to 150 Watts, the sputtered CoZrTaB thin films have smaller grain size and higher in-plane anisotropy and higher FMR frequency from 1.48 to 2.17 GHz. After the integration the magnetic thin films with stripline inductors, 2.5-3.5 times higher inductances and 2.5-3 times higher Q-factors than those of air-core inductors have been accomplished./nMagnetically aligned, rectangular plate-like structures have been demonstrated for geometry-induced nano magnets in micro inductors. These magnets have been analyzed in theories and simulations with experimental validations to have advantages of particles in low eddy current losses and thin films in magnetic anisotropy for high FMR. After the integration with micro inductors under an external magnetic field, the roll-off frequencies in inductance of micro inductors have reached 4.2 GHz with 10% increase in inductance.

Advisor: Lin, Liwei
Between National Law and International Norms: The Political Transformation of Human Rights in Argentina, 1955-83

This dissertation examines Argentina’s late twentieth-century transition from military authoritarianism to democracy in the broader context of the globalization of ideas about international human rights. With a focus on events between 1955 and 1983, I explain how Argentines came to create and support a human rights-based conception of the rule of law and, specifically, the criminal prosecution of their country’s former de facto leaders./nI approach this question by reconstructing an aspect of Argentine legal and political culture that has been overlooked in existing scholarship: public debates led by the country’s prominent and politically diverse lawyers over constitutionalism, revolution, national security, and universal rights. Integrating national history and the history of globalization, I argue that the remaking of Argentine democracy was part of a late twentieth-century globalization of legal order whereby legal advocates and their nonlawyer allies wielded international human rights norms not to transcend the state, as is frequently claimed, but to transform it. This national transformation, constrained by the political and legal legacies of state violence, ultimately produced a paler version of democracy than many Argentines had once envisioned but one that nonetheless served to restrain the violence of the state against its citizens. Human rights were themselves transformed in the process: a law and politics of resistance to the state became instead the state-sponsored initiative to try perpetrators of “dirty war” abuses, an initiative that continues today, along with resistance to it.

Advisor: Healey, Mark A.
Sargent, Daniel J.
States of the Wind: Dust Storms and a Political Meteorology of Contemporary China

On New Year’s Day, 2001, Beijing was struck by a massive dust storm, coursing through and glutting the city on the eve of a long-awaited Chinese century. On the backs of coursing winds and in the long, sandy wake of massive desertification afflicting inner, upwind China, dust storms portended a multi-faceted and multi-scaled environmental crisis in the coming, a shade on the glowing economic futures to which the Chinese party-state had yoked its post-Mao, post-ideological legitimacy. Combating dust storms in Beijing – and then, protecting places as far downwind as Seoul, Tokyo, and even the western US – introduced new political problems and actors into an emerging field of environmental governance, with the central government, through forestry agencies especially, scrambling to devise ways of holding the earth to the ground, against its dangerous tendency to lift into the air. In the course of this, geological, ecological, and meteorological things and processes came to the fore as problems of government./nMy dissertation explores how dust and wind, in the first decades of the 2000s, were consequential in the elaboration of various emerging topologies of power. It explores how, in the Chinese Communist Party’s brand of ecological governance, how ecology, sociology, and economy are re-assembled into elements in a shifting governmental topology, aimed at the stabilization of a shifty, desertified environment as well as the maintenance of ‘social stability’ against the economic and ecological ravages of desertification. In particular, I argue that in the ecological governance of sand and storms, new deployments of an infrastructural political logic are reorganizing both sandy landscapes and the peoples on them – each is figured as structurally unsound and in need of stabilizing state intervention. In this, environmental interventions at many scales think the country, its land, and its people, as elements in a variegated infrastructural program aimed at the control and stabilization of shifty things. It explores tree-walls, sand barriers, and sand ecology and engineering on one hand as polytechnic and scientific interventions into intervening into shifting landscapes. In tandem, it explores how ‘environment’ as a historically situated and multiple concept in China inspires new ways of ordering a populace that is also taken to be shifty and chaotic. Through multi-sited ethnography, it explores, along a dust storm’s path, the emergent topologies of power that arise to confront dust and sand. This is a contribution to political and environmental anthropology, political ecology, China studies, and science and technology studies.

Advisor: Ong, Aihwa
Design and Engineering of Pattern Formation in Gene Expression in Escherichia coli

Synthetic biology aims to develop new biological systems and devices, from the modification of existing pathways to the construction of entirely new genetic circuits. The role of the engineer in synthetic biology is to apply engineering principles to the design and analysis of proposed systems. Building biological systems de novo are the best way to demonstrate our successes on this front and so far has yielded biological devices such as synthetic promoters, toggle switches, oscillators, and logic gates. Here we aim to push the current boundaries of synthetic biology and study the principles behind engineering pattern formation in ensembles of E. coli cells. Motivated by the study of morphogenesis, we hope to develop synthetic systems with the high-minded goals of one day engineering molecular differentiation or even multicellularity. Pattern formation will be a critical part of these goals and brings an additional focus on cell-to-cell communication and signaling molecules. Here we examine two different communication mechanisms, quorum sensing and contact-based signaling, and see what types of patterns we can achieve./nUsing quorum sensing, we focus on diffusion-driven instability (Turing patterning), where a homogeneous steady state of an ensemble of cells is destabilized in the presence of diffusion. This is made possible by the conflicting interactions of the internal dynamics of the cells and the normalizing effect of diffusion between them. The work in this area thus far has centered around activator-inhibitor network theory and to date has yet to yield a biological experimental demonstration. Here we analyze the Turing mechanism and propose a new network which we call a “quenched oscillator” system and demonstrate its ability to produce diffusion-driven instability. We then propose a synthetic implementation and present work towards a partial implementation. In the process, we use zinc finger proteins (ZFPs) and small RNAs (sRNAs) to construct new synthetic inverters to put together in a ring oscillator for use in a quenched oscillator system./nInterest in contact-based signaling has risen recently with the discovery of a contact-dependent inhibition (CDI) system in E. coli. While a synthetic contact-mediated communication channel has not yet been achieved, its realization will provide a huge boost in engineering possibilities, particularly for multicellular applications. Here we develop an analytical framework based on graph theory for analyzing lateral inhibition networks, a category that CDI falls under, for the existence and stability of equitable patterns. Without an actual CDI system to use, we develop what we call a “compartmental lateral inhibition” system using diffusible molecules and engineered communication channels to simulate contact-mediated signaling for verification of our patterning analysis. The current state of our synthetic implementation is presented, highlighting experimental setup details that may prove useful for future applications in engineered multicellular ensembles.

Advisor: Arcak, Murat
Utilizing Problem Structure in Optimization Algorithms for Model Predictive Control

In this work we perform control design and demonstrate the effectiveness/nof model predictive control (MPC), an optimization based control approach/nthat is capable of satisfying state and input constraints and using forecasts/nof disturbance inputs, for the application of energy efficient control of/nheating, ventilation, and air conditioning systems in buildings. We derive/nsimplified control oriented models and express the relevant constraints/nand disturbance predictions, and show that online solution of the resulting/noptimization problems is able to reduce energy consumption while satisfying/noccupant thermal comfort constraints and limits on control actuator inputs./nWe investigate the implementation challenges of applying model predictive/ncontrol to large systems, focusing on online solution of an optimization/nproblem at every time step. We show that it is critical to take advantage of/nproblem structure in system modeling and the formulation of the constraints/nand objective function. Applying an interior point algorithm making use of/nparallel sparse linear algebra solvers performs well, solving nonlinear MPC/nproblems with tens of thousands of variables and constraints in less than a/nminute on modern multicore processors. We design an optimization modeling/ntool that allows simple expression of a MPC problem and efficient interfaces/nto compiled optimization solvers, calculating sparse derivatives and/nconstraint Jacobians automatically. Finally we examine specialized/noptimization algorithms for linear systems with polyhedral constraints,/nreusing repeated model data for time invariant systems to solve block/nbanded linear systems of equations.

Advisor: Borrelli, Francesco
This Too Shall Pass: Temporal Distance and the Regulation of Emotional Distress

Does the time perspective people adopt when reflecting on stressful events influence how they respond emotionally to these events? If so, through what cognitive pathway(s) does it have this effect? Part 1 of my dissertation examined these questions in a series of seven studies. Studies 1a, 1b, and 2 tested the hypothesis that adopting a distant-future perspective on recent stressors (relative to a near-future or control perspective) reduces emotional distress, examining four potential mediators of this effect. Study 3 built upon the prior studies by investigating whether their findings apply to a new domain and affect longer-term outcomes. Studies 4-6 centered on a key cognitive mechanism that helped to account for the distress-reducing properties of temporal distancing across our first three studies—impermanence focus. Studies 4 and 5 examined whether individual differences in impermanence focus predicted emotional reactions to negative events in a manner similar to adopting a distant-future perspective. Study 6 manipulated impermanence focus to test whether it affected emotional reactions to stressors in a manner parallel to adopting a distant-future perspective./nPart 2 of my dissertation examined boundary conditions of the buffering effects of temporal distancing—exploring conditions under which temporal distancing might amplify rather than reduce emotional distress. However, very few moderators of the link between temporal distancing and reduced distress were found, and those that were identified were weak. Taken together, these studies demonstrate that temporal distancing plays an important role in emotional coping with negative events, and that it does so by directing individuals’ attention to the impermanent aspects of these events. Moreover, temporal distancing appears to be a strategy that effectively reduces the distress associated with a wide variety of stressors, for a broad range of individuals.

Advisor: Ayduk, Ozlem
Cotangent spectra and the determinantal sphere

We explore the generalization of cellular decomposition in chromatically localized stable categories suggested by Picard--graded homotopy groups. In particular, for K(d) a Morava K-theory, we show that the Eilenberg-Mac Lane space K(Z, d+1) has a K(d)-local cellular decomposition tightly analogous to the usual decomposition of infinite-dimensional complex projective space (alias K(Z, 2)) into affine complex cells. Additionally, we identify these generalized cells in terms of classical invariants --- i.e., we show that their associated line bundles over the Lubin-Tate stack are tensor powers of the determinant bundle. (In particular, these methods give the first choice--free construction of the determinantal sphere S[det].) Finally, we investigate the bottom attaching map in this exotic cellular decomposition, and we justify the sense in which it selects a particular K(d)-local homotopy class/nSusp^{-1} S[det]^2 --> S[det]/ngeneralizing the classical four "Hopf invariant 1" classes h = (2, eta, nu, sigma) in the cofiber sequences/nSusp^{-1} S^(2n) --h-> P_k^1 --> P_k^2/nassociated to the four normed real division algebras k = (R, C, H, O) with real dimension n = (1, 2, 4, 8). We also include a lengthy introduction to the subject of chromatic homotopy theory, outlining all of the tools relevant to the statements of our original results.

Advisor: Teleman, Constantine
Essays on Development and Urbanization

This dissertation contains three chapters that examine development and urbanization in China since 1980. The first chapter investigates the impact of Special Economic Zones established since 1992 on local economic outcomes and urbanization rates. The second chapter studies local bureaucrats’ incentives while balancing the goals of economic growth and resource or environmental protection. The last chapter examines patterns of urbanization in China as related to the administrative hierarchy between urban and rural regions./nIn the first chapter, I examine the local and aggregate productivity impacts of Chinas Special Economic Zones (SEZ) program from the 1990s to 2006. Using an event study de- sign where I exploit variation in the timing of the first zone establishment across counties, I find that an SEZ increased GDP by 1% to 2% per year over 5 years. In order to assess the aggregate impact of the program, I develop a spatial equilibrium model with two sectors – agriculture and manufacturing. In the model, the economy-wide output impact of an SEZ depends on the elasticities of inter-regional and inter-sectoral labor supply, as well as the relative productivity levels of the SEZ-hosting regions and other regions. I do not find any evidence that the SEZ program induced inter-regional labor reallocation. However, the program did accelerate the shift of employment from the agricultural sector./nIn the second chapter, I explore whether Chinese bureaucrats’ policy decisions depend on connections with their superiors through the appointment of bureaucrats to office. In particular, I consider appointment as a kind act on the part of the promoter, and ask whether the promoted bureaucrat enacts policies that are in the interest of his benefactor. This framework is applied to the policy outcome of rural land conversion and air pollution. I examine whether rural land conversion is more prevalent, and whether air pollution is more abundant, when the local bureaucrat works under the Party Secretary who promoted him. My analysis exploits variation in the length of politicians terms within individual and pairs of politicians. Preliminary findings suggest that promoted land bureaucrats may exhibit reciprocal behavior, while environmental protection bureaucrats may not./nIn the last chapter, I study the impact on urbanization of the Cities Leading Counties (CLC) policy implemented in China beginning in 1983. This nationwide program granted large metropolitan governments administrative control over counties in the surrounding/nhinterland. I use annual county-level nighttime lights data to examine changes in urbanization in the hinterland after integration with a city. I find that while the policy increased urbanization in counties subsumed into cities, the cities themselves did not experience faster urbanization.

Advisor: Finan, Frederico S
Probabilistic Methods for Single Individual Haplotype Reconstruction: HapTree and HapTree-X

Identifying phase information is biomedically important due to the association of complex haplotype effects, such as compound heterozygosity, with disease. As recent next-generation sequencing (NGS) technologies provide more read sequences, the use of diverse sequencing datasets for haplotype phasing is now possible, allowing haplotype reconstruction of a single sequenced individual using NGS data. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. Furthermore, previous diploid haplotype reconstruction studies have ignored differential allele-specific expression in whole transcriptome sequencing (RNA-seq) data; however, intuition suggests that the asymmetry in this data (i.e. maternal and paternal haplotypes of a gene are differentially expressed) can be exploited to improve phasing power. In this thesis, we describe novel integrative maximum-likelihood estimation frameworks, HapTree and HapTree-X, for efficient, scalable haplotype assembly from NGS data. HapTree is built to recover an individual polyploid genome from genomic read data, and HapTree-X aims to reconstruct a diploid genome or transcriptome from RNA-seq and DNA-seq data by making use of differential allele-specific expression. HapTree-X is the first method for haplotype assembly that uses differential expression, newly allowing the use of reads that cover only one SNP./nFor triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. We evaluate the performance of HapTree-X on real sequencing read data, both transcriptomic and genomic, from NA12878 (1000 Genomes Project and Gencode) and demonstrate that HapTree-X increases the number of SNPs that can be phased and sizes of phased-haplotype blocks, without compromising accuracy. We prove theoretical bounds on the precise improvement of accuracy as a function of coverage which can be achieved from differential expression-based methods alone. Thus, the advantage of our integrative approach substantially grows as the amount of RNA-seq data increases.

Advisor: Pachter, Lior