VictorJuiz/thesis huggingface dataset:
Trapping ultracold gases near cryogenic materials with rapid reconfigurability [electronic resource]

We demonstrate an atom chip trapping system that allows the placement and high-resolution imaging of ultracold atoms within microns of any 100 µm-thin, UHV-compatible material, while also allowing sample exchange with minimal experimental downtime. The sample is not connected to the atom chip, allowing rapid exchange without perturbing the atom chip or laser cooling apparatus. Exchange of the sample and retrapping of atoms has been performed within a week turnaround, limited only by chamber baking. Moreover, the decoupling of sample and atom chip provides the ability to independently tune the sample temperature and its position with respect to the trapped ultracold gas, which itself may remain in the focus of a high-resolution imaging system. As a first demonstration of this system, we have confined a 200-nK cloud of 10,000 rubidium 87 atoms within 100 µm of a gold-mirrored 100-µm-thick silicon substrate. The substrate was cooled to 35 K without use of a heat shield, while the atom chip, 100 µm away, remained at room temperature. Atoms may be imaged and retrapped every 16 s, allowing rapid data collection.

Keywords: Applied Physics.
Advisor: Lev Benjamin L. primary advisor. Thesis advisor
Fisher Ian
Hollberg Leo (Leo William)
Ultrafast photoemission studies of the topological insulator Bi2Se3 [electronic resource]

Most macroscopic properties of a material (electrical, thermal, and optical) can be understood on the basis of its band structure and the dynamical behavior of its electrons. However, resolving electron dynamics directly is difficult using conventional techniques because the underlying interactions typically occur on a femtosecond timescale. Ultrafast photoemission spectroscopy is an experimental technique which can probe electronic band structure with femtosecond time resolution. This dissertation presents work using this technique to study dynamic phenomena in the topological insulator Bi2Se3, a fascinating material due to the coexistence of its insulating bulk and metallic surface electronic structures. It will demonstrate three types of novel measurements that can be performed with ultrafast photoemission spectroscopy which are unattainable by other methods: (1) By performing two-photon photoemission (2PPE) spectroscopy, it is possible to resolve unoccupied band structure above the Fermi level. In Bi2Se3 this reveals a second, topologically protected surface state. (2) Time-resolved 2PPE (tr2PPE) is used to record real-time "movies" of the electron relaxation which follows optical excitation. This allows for the identification of intra- and inter- band electron scattering pathways in the material. Temperature-dependent tr2PPE measurements are performed on the conduction band to help understand the role of electron-phonon coupling. A model of fundamental electron-phonon scattering processes is implemented to describe the results. (3) In a time- and angle- resolved photoemission spectroscopy (trARPES) experiment, intense optical excitation is used to drive coherent motion of A1g optical phonon modes in Bi2Se3. These modes lead to periodic binding energy shifts in the bulk conduction band and surface state. A slight red-shift of the phonon frequency is observed in the surface state, which is used to deduce a softening of the phonon due to the abrupt termination of the crystal at its surface.

Keywords: Physics.
Advisor: Shen Zhi-Xun primary advisor. Thesis advisor
Devereaux Thomas Peter
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
Ultrafast X-ray tomography of breathing mode excitations in semiconductor nanocrystals [electronic resource]

Femtosecond x-ray scattering techniques are used to directly visualize ultrafast strains and changes in atomic-scale structure in nanoscale CdSe and CdS spheres and rods. We construct a tomographic view of photo-induced lattice displacements and nanoscale shape changes by measuring multiple lattice reflections. Large amplitude tensile strains at the percent level are observed, associated with a rapid expansion followed by contraction along the nanocrystal radial direction. These morphological changes occur simultaneously with the first steps in the melting transition on hundreds of femtosecond time-scales. This work represents the first direct, real-time probe of the dynamics of these strains in few-nanometer scale particles, with bulk thermodynamic elastic constants remaining sufficient to describe their response despite the extreme excitation conditions.

Keywords: Chemistry.
Advisor: Lindenberg Aaron Michael primary advisor. Thesis advisor
Hodgson Keith
Pande Vijay advisor. Thesis advisor
Understanding and preventing degradation in organic photovoltaics [electronic resource]

Organic photovoltaics (OPVs) are an emerging photovoltaic technology with the potential for low-cost, high-throughput processing. The record laboratory efficiency for these solar cells are now at 9.2% which is approximately half of the efficiency of a traditional rooftop solar module; however, the stability of OPV needs to also reach a lifetime comparable to a 25-year traditional rooftop solar module to be competitive. Here I present the three major modes of degradation in OPV power conversion efficiency for solar cells tested at one-sun illumination in a controlled atmosphere. The first mode is a photo-induced burn-in that occurs in the first few hundred hours of operation and decreases efficiency by ~25%. This burn-in can be avoided by creating a highly aggregated blend of the polymer electron donor material and fullerene electron acceptor material. The second mode is thermal degradation that occurs above the Tg of the material. In the first portion of thermal degradation, the polymer donor material adheres to the top electrode and degrades performance by blocking the transport of electrons. This degradation can be mitigated by making the top electrode the electron withdrawing electrode. The last mode of degradation is long-term degradation and appears to be related to the amount of oxygen that the OPV device is exposed to. The three modes of degradation are shown to be general for several OPV material sets. Lastly, the talk will present rules for highly stable OPV devices and by following these rules we can produce OPVs with a lifetime in excess of 15 years and OPVs with less than half of the typical burn-in.

Keywords: Materials Science and Engineering.
Advisor: McGehee Michael
Heilshorn Sarah advisor. Thesis advisor
Salleo Alberto
Understanding mechanisms of microglia regulation [electronic resource] : neural progenitor cells and molecular changes in the aging systemic environment regulate microglial activity

Microglia are the resident immune cells of the central nervous system. This unique population of cells has been implicated in some way in every neurodegenerative disorder, but they are also essential for proper neural development and for maintaining homeostasis in the healthy adult brain. To assume such distinct roles, the range of microglial effector functions is impressively diverse, and includes the capacity for proliferation, motility, the secretion of both pro- and anti-inflammatory factors, and phagocytosis. The execution of these functions is based upon the detection of signals from their microenvironments, which microglia are particularly well equipped to recognize. Thus microglia are remarkably versatile in terms of both their sensory abilities for external cues and their functions in response to these signals. Understanding the mechanisms by which these cells are controlled is therefore a primary goal in the field of microglial biology and will also be essential for harnessing microglial functions in disease states. The studies presented in this dissertation aim to elucidate the regulation of microglial behavior through extrinsic signaling mechanisms at multiple levels: the first at the level of a defined molecular niche within the brain, and the second within the context of the systemic signaling environment of the organism as a whole. In the first study, we demonstrate the integral relationship between microglia and neural progenitor cells (NPCs). Microglia are known to influence some functions of NPCs, which in the adult mammalian brain reside within specific neurogenic niches. We found that NPCs themselves are in fact capable of secreting a distinct profile of immunomodulatory proteins and are powerful modulators of microglial activity and functions. In the second study, we investigate mechanisms of microglial regulation in the aging organism. We found that aging is accompanied by a general increase in neuroinflammation and microglial dysfunction. Some of these microglial alterations may be mediated, in part, by age-related changes in the levels of bloodborne proteins of the systemic environment. Furthermore, we show that manipulation of the molecular composition of the systemic environment through heterochronic parabiosis can accelerate in young animals, or reverse in old animals, microglial aging phenotypes. Collectively, this work highlights the regulation of microglial phenotypes and functions through signaling mechanisms occurring at both the cell-to-cell and system-wide level. These findings will not only expand our general understanding of microglial biology but could also have implications for the development of therapeutic interventions to control microglia in disease states.

Advisor: Wyss-Coray Anton primary advisor. Thesis advisor
Andreasson Katrin
Palmer Theo advisor. Thesis advisor
Steinman Lawrence advisor. Thesis advisor
Understanding the deformation behavior of lithiated silicon and related advances in nanoindentation [electronic resource]

In the first part of this dissertation, silicon micropillar lithiation/delithiation studies were employed to assess the robustness of amorphous silicon, relative to crystalline silicon, to lithiation- and delithiation-induced fracture. Even the largest pillars showed no lithiation-induced interior or exterior cohesive fracture. Delithiation of fully lithiated pillars produced internal cohesive fracture initiated by delamination of the pillar/substrate interface at the base of the pillar sidewall. Finite element modeling, indicating concentrated triaxial tensile stresses that move inward and upward with progression of delithiation, provided explanation for the observed fracture evolution. The research findings demonstrate that amorphous silicon is quite robust to fracture during lithiation; the critical size for fracture of amorphous silicon particles upon lithiation is determined to exceed ~2.3 [mu] m. The second part of this dissertation is focused on nanoindentation-based lithiated silicon deformation behavior studies. Prior to indenting lithiated silicon films, advances to general nanoindentation techniques were proposed. A new physically based function for nanoindentation indenter tip shape calibration was developed. The function, which accounts for the rounded shape at the indenter tip as well as the pyramidal shape away from the tip, fits calibration data well and returns physically meaningful calibration constants. Next, modifications to the Agilent Technologies Nanoindenter XP stage were implemented to make possible nanoindentation studies of blistered lithiated silicon films immersed in paraffin oil. Lithium-silicon alloy films of various compositions were probed. Young's modulus and the hardness were found to decrease as lithium content increased. Indentation creep testing was executed on unlithiated, amorphous silicon and heavily lithiated silicon, and the results indicate that lithiated silicon creeps readily compared to unlithiated silicon. In all cases, the viscoplastic flow behavior of lithiated silicon is consistent with power law creep with a large stress exponent (> 20). Interpreting the measured large stress exponents with a model for thermally activated, shear-driven local atomic rearrangement, the activation volume for the transformation is found to be comparable to the volume of a molecular unit of Li15Si4.

Keywords: Materials Science and Engineering.
Advisor: Cui Yi
Nix William D. primary advisor. Thesis advisor
Dauskardt R. H. (Reinhold H.) advisor. Thesis advisor
Underwater [electronic resource] : essays on American indebtedness

This dissertation asks and answers three questions about the nature of mortgage debt and debtors in the contemporary United States. 1) Do individuals from different class backgrounds manage mortgage debt differently? 2) Do existing theories of mortgage debt, mostly in economics and finance, accord with how individuals actually manage debt? 3) And, finally, does consumer solvency or price better predict mortgage default? My findings have implications for theories of consumer credit in economic sociology and inequality as well as relevance to contemporary debates about how to reform housing finance policy in the United States.

Keywords: Sociology.
Advisor: Grusky David B. primary advisor. Thesis advisor
Cook Karen S. advisor. Thesis advisor
Granovetter Mark S. advisor. Thesis advisor
Uneasy border state [electronic resource] : the politics and public policy of Latino illegal immigration in metropolitan California, 1971-1996

This dissertation explores the roots of modern American politics and policy of backlash towards Latino illegal immigration in late twentieth century California, the state with the largest Latino undocumented immigrant population. Drawing on research in dozens of largely untapped archival collections of local, state, and federal officials, agencies, and legislative bodies, and advocates, as well as published media, government, legal, and academic and think tank research sources, I explain evolving debates over labor market impacts, social and fiscal policy, federal immigration policy implementation, local and state immigration policy, and immigration law enforcement. I trace underexplored historical relationships between policymakers at various levels of government and diverse political advocates, political institutional and economic processes, legal developments, and political outcomes of policy shifts. I argue that from the early 1970s to the mid-1990s, Latino illegal immigration transformed from a predominantly liberal political issue into a conservative one in metropolitan California. Economic concerns, over labor market competition and increasingly over fiscal impacts, remained the core focus of debate yet conservatives increasingly seized upon and recast economic concerns in a cultural framework and embraced a cultural politics of illegal immigration law and order. The complex structure of modern American federalism made it extremely difficult to address California illegal immigration concerns, helping to fuel the political contentiousness of debate and fragmented local and state policymaking.

Keywords: History.
Advisor: Camarillo Albert primary advisor. Thesis advisor
Jiménez Tomás R. (Tomás Roberto)
White Richard
Universal communication and clustering [electronic resource]

Information theory has a history of marrying elegant mathematical models with a wide scope of applications. In an attempt to follow this tradition, we start with questions of universality in communications, and end with surprising connections to clustering, compression, and prediction. Two specific information theoretic scenarios are considered: universal pattern decoding for an unknown codebook across an unknown channel, and universal encoding and decoding across a modulo-additive channel with noiseless feedback. In both settings, fundamental limits are established, and practical algorithms and tools are constructed to achieve these bounds. Applications are briefly discussed both for evaluating the semantic similarity of search queries, and for comparing human populations based on the genotypes of various individuals.

Keywords: Electrical Engineering.
Advisor: Weissman Tsachy primary advisor. Thesis advisor
El Gamal Abbas A. advisor. Thesis advisor
Goldsmith Andrea
Using Neuroimaging and Optogenetics to Better Understand the Neural Circuit Basis of Major Depression

Depression is a leading global health problem that affects hundreds of millions of people. Though the psychiatric disorder has been known to exist for centuries, its treatment still has yet to be perfected. The inability to clearly define the neurobiological mechanism of depression results in the lack of precise tools for the diagnosis and treatment of depressed patients. Advances in neuroscience research are working towards redefining depression in the language of brain circuits by characterizing the disease's structural, functional, and electrochemical profile. In the pioneering work of Helen Mayberg, one promising brain region that has been shown to be metabolically overactive in depression and therapeutically receptive via deep brain stimulation is the subgenual cingulate cortex. In this thesis, I describe the use of graph theoretical analysis of structural imaging data from depressed humans and optogenetic fMRI in the rat to evaluate the changes in whole-brain connectivity associated with depression, especially with respect to the subgenual cingulate and its associated brain regions. In the graph analysis, it was found that the structural correlation brain network in depressed patients was inefficient and less densely connected than in healthy controls. However, some regions, such as the amygdala and ventral frontal cortex, were found to be hyperconnected. In the optogenetic fMRI study, ventromedial prefrontal cortex (the rodent analog to the subgenual cingulate gyrus) stimulation was able to drive behaviors associated with depression and alter the functional connectivity of the region to other areas in the brain, such as the anterior prefrontal cortices, striatum and amygdala. Together, these studies indicate structural and functional abnormalities of the circuitry between the frontal cortices and subcortical limbic system, a collection of brain regions that control emotion, behavior, and reward processing. The presented data supports and expands upon Helen Mayberg’s hypothesis of an overactive subgenual cingulate cortex in depression. Both graph analysis and optogenetic fMRI require further research and development, but they have the potential to be useful tools in the deciphering of the neural circuit basis of depression and in the creation of impactful clinical tools to help manage the debilitating disorder.

Keywords: Ferenczi, Emily
bioengineering
neuroscience
psychiatric disease
depression
neural circuits
optogenetics
functional magnetic resonance imaging
fMRI
graph theoretical analysis
Thesis
Advisor: Deisseroth Karl
Singh Manpreet
Utilizing photonic crystal Fabry-Perot sensors for high resolution sensing with applications in atomic force microscopy [electronic resource]

Atomic Force Microscopes are known for their high spatial resolution images and are widely used in research and the semiconductor industry. Quantitative Atomic Force Microscopy is a technique which quickly measures the interaction force between the probe and sample, extracting mechanical properties in addition to topography. This technique offers the benefits of nanoindentation while maintaining the high speed and throughput of tapping mode imaging. The challenge of increasing the force resolution of Atomic Force Microscopes for quantitative imaging can be met by miniaturization of the Atomic Force Microscope system and has long been a goal in the field. This thesis outlines how photonic crystal fiber sensors achieve this miniaturization to offer improved resolution and stability and presents improvements and theory relevant to these probes which have applications outside the field of Atomic Force Microscopy. The first part of this work discusses how the properties of a Fabry-Perot sensor are enhanced through control of the reflected phase of its constituent mirrors. This brings up many questions about the fundamental limits of reflected phase in highly reflective mirrors which are addressed through theory, an in-depth analysis of photonic crystals alongside selected mirror alternatives and a discussion of efficiently engineering the desired mirror properties through rigorous coupled wave analysis. Confidence in the ability to engineer mirrors with reflected phase capable of providing better sensors necessitated the testing of our theory through experimental validation which was achieved by precise measurements of Fabry-Perot reflected spectra. The middle of this thesis consists of this methodology alongside experimental results to offer confidence in the theory and limits we initially present. Finally, the fiber facet photonic crystal atomic force microscope is presented. These probes were fabricated using in the Stanford Nanofabrication Facility using standard CMOS fabrication techniques and assembled in the Stanford Nanocharacterization Laboratory using a focused ion beam. These probes use photonic crystal mirrors for high sensitivity and are assembled directly on optical fiber for low measurement noise through fiber coupled detectors. They are thus capable of extracting the tip sample interaction force at a resolution of 10 pN/rtHz with every tap in an image.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Fejer Martin M. (Martin Michael) advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Validation and sensitivity analysis of simulations of particle deposition in human airways [electronic resource]

The airway is a major entry port into our body. Airborne particles such as tobacco smoke, dust, pollen, bacteria are breathed with every breath. Particles are also used for medical treatment in the form of inhaled aerosols to treat diseases such as asthma. The effect of these particles on our health is highly dependent on where they deposit in our airway. Where particles deposit depends on many different factors including the particles' size, how we breath and differences in our airway geometry. We study the sensitivity of deposition to these factors through simulation. First, we start with the surface of a realistic human airway obtained from segmenting an MRI scan, breathing in from the mouth. The flow field is computed using an unstructured LES fluids solver and is validated against an Magnetic Resonance Velocimetry experiment. We can vary the flow field intensity to model different breathing conditions. Particles of size 1 to 10 microns are injected as Lagrangian point particles after the flow field is developed. Their trajectories are integrated until they either exit the airway into high generations of the bronchial tree or they are deposited on the airway wall. The deposition statistics are then analyzed. Finally, to study the sensitivity to perturbations in airway geometry, we constructed a parameterized synthetic airway that can perturbed. We studied the effects of constrictions and expansions in the main bronchi to particle distribution.

Keywords: Computational and Mathematical Engineering.
Advisor: Iaccarino Gianluca primary advisor. Thesis advisor
Shaqfeh Eric S. G. (Eric Stefan Garrido) primary advisor. Thesis advisor
Darve Eric advisor. Thesis advisor