VictorJuiz/thesis huggingface dataset:
Improving Cosmological Distance Measurements with Type Ia Supernovae: From Pixels to Dark Energy

In the late 1990s, precise distance measurements with Type Ia supernovae (SNe Ia) were used to show that the expansion of the universe is accelerating. One possibility is that this accelerated expansion is due to an additional form of energy referred to as “dark energy” which contributes roughly 70% of the total energy in the present day universe. The properties of dark energy are not currently well-constrained, and a wide range of different cosmological probes are currently being designed to explore the fundamental nature of the accelerated expansion of the universe. SNe Ia have remained one of the strongest cosmological probes, and upcoming experiments such as the Large Synoptic Survey Telescope (LSST) are expected to discover over 100,000 SNe Ia that can be used for cosmology. The uncertainties on cosmological parameters derived from these large samples of SNe Ia will be entirely dominated by the systematic uncertainties of distance measurements to SNe Ia. In this dissertation, we discuss several different methods of improving the systematic uncertainties in distance measurements to SNe Ia./nThis dissertation is split into three main chapters each discussing how to improve a different aspect of distance measurements to SNe Ia. In Chapter 2, we examine how instrumental calibration can affect these distance measurements, and discuss a new anomalous behaviour of CCD readout electronics related to the binary encoding of pixel values that affects most astronomical instruments currently in use. For the Nearby Supernova Factory, this anomaly introduces a dispersion in the measured B-band/U-band magnitudes of 0.11 mag/0.51 mag for the faintest 20% of measurements./nAnother major source of systematic uncertainty in distance measurements to SNe Ia is intrinsic variation of the SNe Ia. In Chapter 3, we develop a new method of parametrizing SNe Ia using manifold learning to generate a non-linear decomposition of the intrinsic diversity of their spectra near maximum light. We identify regions of the parameter space of SNe Ia where previous standardization methods such as SALT2 have biases of up to 0.3 mag, and show how correlations between host galaxy properties and distance estimates are greatly reduced when standardizing SNe Ia using our new parametrization./nFinally, in Chapter 4, we discuss how upcoming surveys such as LSST will need to rely on photometric classification to identify the majority of the transients that they discover, which means that samples of SNe Ia used for cosmology will be contaminated with other types of transients. We developed a set of techniques for photometric classification to address the fact that spectroscopic subsamples used for training classifiers are typically highly biased compared to the full samples of transients and variables that will be discovered. Using these techniques, we built a photometric classifier that won the PLAsTiCC photometric classification challenge out of 1,094 competing teams.

Advisor: Perlmutter, Saul
Matroids and convex geometry in combinatorics and algebra

This thesis is a compendium of three studies on which matroids and convex geometry play a central role and show their connections to Catalan combinatorics, tiling theory, and factorization theory. First, we study positroids in connection with rational Dyck paths. Then, we study certain matroids on the lattice points of a regular triangle in connection with lozenge tilings. Finally, we explore the connection between the atomic structure of submonoids of (N^d,+) and the geometric properties of the cones they generate./nPositroids, first studied by Postnikov in 2006, are matroids that parameterize the cells of the totally nonnegative part of a Grassmannian variety. The first part of this thesis concerns with the study of a family of positroids that can be parameterized by (rational) Dyck paths. We call such positroids (rational) Dyck positroids. Using work of Reed and Skandera, we show that Dyck positroids on the ground set [2n] are in natural bijection with unit interval orders of size n. We also offer recipes to read the decorated permutation of a Dyck positroid directly from either the antiadjacency matrix representation or the interval representation of the corresponding unit interval order. Finally, for the family of rational Dyck positroids, we provide combinatorial descriptions for some of the most relevant combinatorial objects that are in bijection with positroids./nThe second part of this thesis pertains to the study of certain class of matroids which naturally appear in the set of one-dimensional intersections of complete complex flag arrangements. More specifically, these matroids encode the dependency relations among the lines of such flag arrangements. The bases of such matroids can be thought of as certain n-subsets of lattice points of a regular n-simplex. For dimension 2, we provide various cryptomorphic characterizations of these matroids in connection with lozenge tilings of a regular triangle. We also study the connectivity of members of this family of matroids in any dimension./nFinitely generated submonoids of (N^d,+), also known as affine monoids, are crucial in the study of combinatorial commutative algebra and, in particular, toric geometry. Let C denote the class consisting of all submonoids of (N^d,+) (not necessarily finitely generated). The last part of this thesis is devoted to explore how atomic properties of a monoid M in C (and the monoid algebras M induces) are connected with the geometry of its conic hull cone(M) and with the combinatorial structure of the face lattice of cone(M). For monoids in C, we investigate two of the most important arithmetic invariants in factorization theory: the system of sets of lengths and the elasticity. We conclude this thesis studying the atomicity of monoid algebras, including the algebras induced by monoids in C. We shall provide a partial answer to a fundamental question about the atomicity of monoid algebras that Robert Gilmer asked back in the 1980's.

Advisor: Williams, Lauren K
Directional Wireless Mesh Network Design

From a system point of view, this body of work examines the design and scaling of directional wireless mesh networks. Effort has been made to look at both the physical and medium access layers of these systems and what can be done to improve the capacity of these networks so that they may perform efficiently at very large scales. This work takes a forward looking view of these networks. While much of this work is based around millimeter wave radios (especially 60 GHz), it is not limited by it. Many of the ideas are independent of frequency and therefore should apply at both lower and higher carrier frequencies./nFrom the physical layer standpoint, I show that interference is a significant limitation to system capacity even for very large antenna arrays (1000s of elements), eliminating the idea of ‘pencil beams’ that do not cause or receive interference. Limiting and mitigating interference are investigated. To limit interference, I look at how the antenna array geometry may be altered and show that of the geometries I have examined, linear arrays perform best. To mitigate interference, I show that using receiver only adaptation and transmitter beam steering can be significantly better than using beam steering for both transmitter and receiver and helps to better approach the theoretical capacity limit./nAt the medium access layer, I present a new protocol called listen-only scheduling. The principle idea behind it is that nodes in a mesh network each independently determine their listening schedules without transmission scheduling. The independent scheduling is enabled by the use of independent transmitters and receivers and could be used at any carrier frequency. It is particularly attractive for directional mesh networks because of deafness and exposed node issues. I show that theoretically it should be able to perform at least within 20–30% of the maximum theoretical throughput./nLastly, future directions for this work are presented with some preliminary work. In particular, there are opportunities for cross-layer optimization between the physical, medium access, and network layer to avoid interference, increasing system capacity. One should be able to schedule in time using link management at the medium access layer and schedule in space and time by using routing at the network layer.

Advisor: Wawrzynek, John C
A song of lysine and Pseudomonas putida

Synthetic biology attempts to make inherently chaotic biological systems both predictable and useful. To achieve this, well characterized genetic parts are necessary both to control genetic circuitry as well as to catalyze specific chemical reactions. While the discipline is maturing, the number of chemical reactions we can catalyze and the number of means to control the expression of these enzymes is still extremely limited in the context of what occurs in nature. It therefore behooves the discipline to rapidly explore nature for biological novelty so we can then leverage it for biological programming. Herein I utilize multiple functional genomics techniques to uncover novel enzymatic and regulatory elements within the lysine catabolism of the bacterium Pseudomonas putida. From these data we are able to develop novel tools for synthetic biology, improve P. putida as a chassis for metabolic engineering of bioproducts, as well as make fundamental discoveries about previously unknown enzymatic steps of the lysine catabolism of both bacteria and plants.

Advisor: Keasling, Jay D
Understanding and Controlling the Chemistry in Liquid Cell Electron Microscopy to Study Nanocrystal Shape Transformations

Nanomaterials exhibit unique size-dependent properties, and colloidal, metallic nanocrystals have been utilized in catalytic, biomedical, and optical applications. Observing the dynamics of nanocrystals in their native liquid environment requires the high spatial resolution/nof the electron microscope and encapsulation using a thin membrane such as graphene. By understanding and controlling the chemistry during liquid cell electron microscopy reactions, fundamental insights about nanoscale processes can be elucidated to improve colloidal/nsynthesis of nanocrystals./nOxidative etching of gold nanocrystals using a combination of preloaded FeCl3 and electron beam-generated radiolysis products was used as a model system for learning about the chemistry of the liquid cell environment. By collecting etching trajectories of multiple/nnanocubes and rhombic dodecahedra, with {100} and {110} facets respectively, as they transition through intermediate {hk0} facets, the initial FeCl3 concentration was found to control the chemical potential of the etching process. Using Monte Carlo simulations to help understand the trajectories, the chemical potential was found to change the intermediate facets when etching from cubes but not rhombic dodecahedra due to differences in coordination of inner surface atoms./nThe electron beam generates highly reactive radiolysis products during liquid cell imaging, so determining the electron beam's role on the chemistry of the liquid environment is useful for experimental design and reproducibility. Following the volume trajectories of/netching nanocrystals, it was found that the electron beam dose rate controls the etching rate independently of the FeCl3 control of the chemical potential. Further, at low dose rates, the electron beam generates sacrificial reductant hydrogen gas bubbles that prevent premature etching. Ex situ etching experiments using FeCl3 confirmed the dynamics observed in the/nliquid cell and provided additional insight into the liquid cell environment. Additional in situ TEM observations of the nanoscale Kirkendall effect of silver nanoparticles and electron stimulated desorption of NaCl nanocubes shows the wide range of processes that can be investigated. Although the chemistry of these liquid cell processes are not as well understood as the gold nanocrystal etching, useful insights about structural transformations were extracted./nFinally, an undergraduate research program for first-year students was designed and implemented using liquid cell TEM data. The structure of the program is presented with feedback from the participants showing quantifiable gains in self-identication as scientist.

Advisor: Alivisatos, A. Paul
Reading and Misreading: The Social Life of Libraries and Colonial Control in Vietnam, 1865-1958

This dissertation examines the cultural and political history of French colonial libraries and print control in Vietnam from 1865 to 1958. I analyze the changing mission of colonial libraries as a hybrid of state documentation and public space for self-directed education and social life. I also embed libraries within the multilayered landscape of print control—the politics of production, dissemination, and preservation of print matter. I follow the dynamic debates on print control among colonial and post-colonial government administrators, librarians, archivists, translators, publishers, and readers. These diverse actors investigated the content, language, and influence of ‘good reading’ and initiated projects to disseminate reading matter through translation, publishing, and libraries. Administrators also policed cases of ‘misreading,’ the violation of proper library decorum or consumption of politically subversive texts./nThe chapters follow a historical and thematic chronology: the builders, the readers, print industry, print control, and decolonization. Focused primarily on the state-initiated Central Library in Hanoi and Saigon, this dissertation advances a two-part argument on the history of colonial libraries and print control in Indochina. First, to build libraries is to build the state. Libraries legitimized the authority of the state as infrastructures of symbolic modernity, print control, and documentary heritage. Second, library users shaped the everyday mission and social function of the library beyond the hegemonic aspirations of colonial and post-colonial states. As seen in the Hanoi and Saigon Central Library Reading Rooms in 1920s to 1950s, readers transformed the tranquil space intended for administrative research into a dynamic public space for study and social life. This two-part argument reveals the significance of the library as an institution of state-building, print control, and public reading culture./nThis dissertation is the first comprehensive history of the library in French colonial Indochina during the long twentieth century. It offers the following contributions: (1) a critical investigation into the role of libraries as an institution of state documentation, popular education, and literacy in French or Vietnamese vernacular script, quốc ngữ (2) an analysis of the relationship between building the modern nation state and building libraries, (3) a cultural history of Vietnamese print market, reading practices, and urban public spaces, and (4) a study of the major cultural institution of libraries across colonial/post-colonial divides and through periods of war.

Advisor: Zinoman, Peter
Design and Physics of VCSELs for Emerging Applications

Vertical cavity surface emitting lasers (VCSELs) have been widely employed in short distance optical interconnects. Recently however a series of emerging applications are creating a rapidly growing demand for compact, low cost and high-performance light sources. 3D imaging and proximity sensing capabilities based on time of flight and structured light schemes are currently being deployed in a vast amount of consumer hand held devices, in particular in cell phones. Here VCSEL arrays of various sizes, densities and powers are being employed in volumes of multiple hundreds of millions per year. At the same time, wavelength tunable VCSELs with wide tuning range, fast tuning speed and single mode continues wavelength tuning are of tremendous interest for swept source optical coherence tomography (SS-OCT)./nThis work investigates a series of VCSEL architectures that specifically address the requirements of the above-mentioned applications. Inhouse epitaxial growth by metal organic chemical vapor deposition was developed (chapter 2) to supply the wide variety of VCSEL structures investigated and in particular to enable the realization of devices that depend on regrowth steps. Optical pumping of high contrast grating (HCG) enabled devices was tested (chapter 3) as this method has proven successful in DBR based devices. Wavelength tunable VCSELs with a MEMS actuated HCG as sole top reflector where demonstrated (chapter 4 & 5). These devices showed single mode emission and continues electrostatic tuning covering a wide wavelength range. Thus, proving their concepts promising for application as sources in SS-OCT. Two different VCSEL architectures with lithographically defined current apertures have been investigated, one based on a buried InGaP heterostructure (chapter 5) and one based on a buried tunnel junction (chapter 6). Substituting the native oxide confined current aperture by a lithographic aperture of such kind enables a wealth of potential performance improvements. Improvements in reliability, thermal resistance, emitter uniformity, array density, high-power single mode emission and coherently coupled arrays can be reasonably expected of such devices. In combination with the HCG reflector lasing in a stable, single polarization can be achieved. At last, VCSEL arrays were fabricated at 850 nm and 940 nm wavelength in chapter 7.

Advisor: Chang-Hasnain, Constance
Computational fluorescence and phase super-resolution microscopy

Light microscopy is an important driving force for new biological discoveries because of its capability of visualizing micro-scale cell structures and interactions. Fundamentally, optical resolution is bounded by the diffraction limit, preventing observation of biological events with an even smaller scale. However, computational imaging approaches are efficient tools to surpass this limit. In recent years, optimization formulation has become more popular because of its flexibility and efficacy toward information retrieval. In this thesis, we leverage the power of optimization algorithms and new experimental schemes to tackle super-resolution microscopy, both improving existing methods and developing new techniques. We first apply rigorous optimization algorithm analysis to a super-resolution phase microscopy technique, Fourier ptychography. A more accurate noise model and the self-calibration algorithm ensure a better reconstruction quality for this technique. Next, we incorporate optimization into the study of a super-resolution fluorescence microscopy technique, structured illumination microscopy. Super-resolution reconstruction is achieved even with a series of random unknown illumination patterns, which is not possible without proper optimization formulation. Next, we leverage the experience of the previous two projects to propose a super-resolution microscopy method for phase and fluorescence contrast with multi-fold resolution improvement in both 2D and 3D using an unknown speckle illumination composed of high-angle plane waves from Scotch tape as a patterning element. The result is a practical method for achieving multimodal super-resolution with >2x resolution gain, surpassing the limit of the traditional linear structured illumination microscopy. All these outcomes are within the realm of computational super-resolution microscopy, where the optimization algorithm is jointly designed with optics for efficient information retrieval to achieve super-resolution microscopy.

Advisor: Waller, Laura
Optimizing for Robot Transparency

As robots become more capable and commonplace, it becomes increasingly important that they are transparent to humans. People need to have accurate mental models of a robot, so that they can anticipate what it will do, know when and where not to rely it, and understand why it failed. This helps engineers ensure safety and robustness of the robot systems they develop, and enables human end-users to interact more safely and seamlessly with robots./nThis thesis introduces a framework for producing robot behavior that increases transparency. Our key insight is that a robot's actions do not just influence the physical world; they also inevitably influence a human observer's mental model of the robot. We attempt to model the latter---how humans might make inferences about a robot's objectives, policy, and capabilities from observations of its behavior---so that we can then present examples of robot behavior that optimally bring the human's understanding closer to the true robot model. In this way, our framework casts transparency as an optimization problem./nPart I introduces our framework of optimizing for robot transparency, and applies it in three ways: communicating a robot's objectives, which situations it can handle, and why it is incapable of performing a task. Part II investigates how transparency is useful not just for safe and seamless interaction, but also for learning. When humans teach a robot, giving human teachers transparency regarding what the robot has learned so far makes it easier for them to select informative teaching examples.

Advisor: Dragan, Anca D
Abbeel, Pieter
The Dynamics of Flexible Risers Transporting Fluids in Subsea Environments

As water depths for oil and gas exploration and extraction increase, structures such as flexible risers, mooring lines, and umbilical cables are increasingly being used in subsea environments. Compared to conventional fixed-type structures and vertical risers, the dynamics of flexible risers is significantly more complex. In particular, these flexible structures may be prone to dynamic instabilities. Furthermore, there has been increasing interest on safety, which makes it imperative to design more robust risers in order to avoid situations where the static configurations of risers can lose their stability./nThe focus of this work, therefore, is to provide a comprehensive study of the dynamics, stability, and vibration of flexible risers. We use Kirchhoff's theory of an extensible, flexible rod that resists torsion to develop a set of nonlinear equations for the dynamics of risers. Furthermore, we extend our model to take into account the cross-sectional shearing by using a Cosserat rod theory. The resulting model incorporates drag and the effects of the fluid being transported internally besides all other forces acting on the risers. We perform static analyses and linear stability analyses for a variety of applications of risers such as a catenary-type riser, a lazy wave-type riser, a steep wave-type riser, and a vertical riser./nBased on configurations obtained from static analysis, we perform a comprehensive investigation regarding their stability. First, we identify the effects of external current and internal fluid on the stability of a static configuration and find an interesting phenomena where the internal fluid being conveyed can destabilize some static configurations. We also suggest a potential means to stabilize the destabilized configurations. Furthermore, we look into the torsional stability of risers in order to capture the critical point where the twisted or hockled configurations are observed under certain conditions and the effects of design parameters on the onset of the resulting torsional instability. Finally, we investigate the variation in the dynamic characteristics of a flexible riser as the riser transitions from a vertical riser to a catenary-type riser and also find a potentially efficient way to remove the instability for vertical risers by introducing a small horizontal offset. Our principal results from this work are expected to provide effective and useful guidelines for the design of marine flexible risers.

Advisor: O'Reilly, Oliver