VictorJuiz/thesis huggingface dataset:
Electrical neural stimulation and its application to high-resolution retinal prosthesis [electronic resource]

Nervous system enables perception of sensory information, cognition, control of body organs and motor functions by means of signal transmission across the body-wide neural networks. Electrical nature of neural signaling provides an opportunity for control of the signals using external electric field. It enables introduction of information into the diseased neural systems, thereby augmenting and restoring (to some extent) its function. Prosthetic and therapeutic applications of electrical neural stimulation continue to expand. They currently include augmented sensory inputs, such as cochlear and retinal prostheses, treatment of essential tremor and chronic pain with deep brain stimulation, bladder control, and many others. Retinal degenerative diseases lead to blindness due to slow demise of photoreceptors, while other retinal neurons survive to a large extent, which provides an opportunity for reintroduction of information into the visual system by electrical stimulation of the inner retinal neurons. This work describes the dynamics of the extracellular electrical stimulation of spiking neurons and of neural networks, and application of such electro-neural interfaces to retinal prosthesis. Biophysical modeling of the active membrane properties of neurons in external electric field and generation of the action potential was based on Hodgkin-Huxley formalism of ion channel dynamics. Strength-duration relationship calculated for various pulse shapes predicted the existence of the stimulation upper threshold due to reversal of the sodium ionic current at high stimulation strengths. This phenomenon was experimentally confirmed in retinal ganglion cells (RGCs) using the patch clamp recordings. Besides the direct stimulation of RGCs, two types of the network-mediated responses have been identified in the whole-mount retina: originating in the photoreceptors and in the inner retinal neurons. Selectivity of the direct and network-mediated stimulation of RGCs as a function of the electrode location (above, below and inside the retina), geometry (bipolar vs. monopolar), pulse polarity and duration was assessed. These results defined the current configuration of the photovoltaic retinal prosthesis. Each pixel in such implant converts pulsed near-infrared illumination into pulses of electric current flowing through the retina and stimulating the nearby neurons. A computational model describing the optoelectronic properties of such pixels in biological tissue was developed and experimentally verified. Thresholds and selectivity of the network-mediated retinal stimulation have been then measured with photovoltaic arrays. These results provide foundation for further optimization of the photovoltaic retinal prosthesis towards 3-dimensional electro-neural interfaces, to restore high visual acuity and contrast sensitivity in patients blinded by retinal degeneration.

Keywords: Physics.
Advisor: Doniach S. primary advisor. Thesis advisor
Palanker Daniel primary advisor. Thesis advisor
Huguenard John advisor. Thesis advisor
Electrodynamic and thermodybamic modeling of the lightning channel [electronic resource]

Lightning is a form of of an electric breakdown of air caused by the strong electric field that is induced by charge accumulation in the cloud during a thunderstorm. During lightning, a current of tens of thousands of amperes flows in the lightning channel and a charge of several coulombs is transfered between different parts of the cloud or between the cloud and the ground. These high-current and high-energy phenomena cause various effects that influence our daily life and the Earth's electromagnetic environment, including near-Earth space. For this reason it is of great interest to improve our understanding of the characteristics of the lightning channel and the fundamental physics underlying the development of lightning. Lightning consists of physical processes that span a wide range of spatial and temporal scales. Despite decades of research, many questions concerning the fundamental physics of lightning remain unanswered. This lack of understanding is caused by a combination of factors including the difficulty in obtaining high-quality experimental data and the intrinsic complexity in the physical processes involved. In this work, a numerical model is constructed to handle the electrodynamics and the thermodynamics of the lightning channel as well as the complex geometrical structure of the lightning channel. This model is applied to investigate three lightning processes: the subsequent return stroke, the leader step and the large scale geometrical structure of the lightning channel. The study of the subsequent return stroke reveals that the current and optical waves may propagate along the channel at significantly different speeds. This result has a profound impact on the calculated return stroke electromagnetic radiation, which in turn affects many aspects of lightning-related studies, including lightning geolocation and lightning-upper-atmosphere coupling. The model also predicts a finite time delay between the return stroke current and optical wavefront. The leader-step study focuses on reproducing the ground-station recordings of the electric field pulse associated with single leader steps. It is demonstrated that a parsimonious model is sufficient to capture the observed characteristics of the waveforms. In the study of the large-scale structure of the lightning channel, a probabilistic model is used to determine the growth and branching of the lightning channel. The model is then applied in a Monte-Carlo type algorithm to determine the probability distribution of the lightning strike locations on the ground given the location of the initial channel in the cloud. The protection efficiency of a metallic rod on the ground is investigated by comparing the estimated probability distributions using simulations that are with or without the metallic rod present on the ground.

Keywords: Electrical Engineering.
Advisor: Inan Umran S. primary advisor. Thesis advisor
Close Sigrid
Lehtinen Nikolai G. advisor. Thesis advisor
Electronic nematicity in iron-based superconductors [electronic resource]

Emerging evidence for the presence of strongly anisotropic electronic states in the underdoped regime of both cuprate and iron-based high temperature superconductors suggests the possibility of an important role for electronic nematic order in these materials. The central theme of my thesis work has been the experimental study of electronic nematicity in iron-based superconductors via measurement of resistivity anisotropy. To do this, I have developed several new experimental techniques, on the one hand enabling detwinning of sub-mm size single crystals in the broken-symmetry orthorhombic state, and on the other hand revealing the nematic susceptibility in the high-symmetry tetragonal state. A major part of my thesis work has involved measurement of the elastoresistance; that is, the change in the resistance of a material as a consequence of the strains that it experiences. In this thesis, I will show how differential elastoresistance measurements can directly reveal the nematic susceptibility of a material in the tetragonal state. I will introduce the appropriate tensor formalism necessary to describe these measurements, and describe an experimental technique to determine these coefficients using piezoelectric stacks to provide anisotropic bi-axial strain. Results in the tetragonal state of various underdoped families based on the parent compound BaFe2As2 explicitly demonstrate that the tetragonal-to-orthorhombic structural transition in these materials is fundamentally driven by an electronic nematic instability. These results also suggest that the resistivity anisotropy in the paramagnetic orthorhombic state is dominated by the Fermi surface anisotropy, rather than an anisotropy in the scattering rate. Finally, similar measurements of a wide variety of optimally doped iron-pnictides and iron-chalcogenides reveal that a divergence of the nematic susceptibility in the B2g symmetry channel appears to be a generic feature of optimally-doped iron-based superconductors. In addition to the above, I also employ a mechanical detwinning technique to reveal the resistivity anisotropy in the orthorhombic state of the same Fe-based superconductors. For the isovalently-substituted material BaFe2(As1-xPx)2, these measurements reveal a strong coupling between external stress and both the Neel temperature and the superconducting critical temperature.

Keywords: Materials Science and Engineering.
Advisor: Clemens B. M. (Bruce M.) primary advisor. Thesis advisor
Fisher Ian primary advisor. Thesis advisor
Devereaux Thomas Peter
Electronic phases in iron-based high temperature superconductors [electronic resource]

High temperature superconductivity (HTSC) is a topic that has fascinated physicists for decades not only due to the intricate underlying properties of nature that it reflects, but also to the challenging nature of the physics problem it presents. For over two decades, condensed matter physicists have wrestled the cuprate problem as the only material family of HTSC. The discovery of the iron-based superconductors (FeSCs) in 2008 brought a fresh perspective to the field, as now comparison and contrast can be made between the two families in the hope of identifying the bare minimal ingredients for the HTSC phenomenon. In this regard, one of the key findings early on was that the FeSC share a phase diagram that is arguably similar to the cuprates, that is, the parent compound is a magnetically ordered state, which is suppressed with doping before superconductivity emerges in a dome-like fashion. In this dissertation, I approach the FeSC problem from two major perspectives using the technique of angle-resolved photoemission spectroscopy: i) understanding the electronic correlation strength in the normal state, and ii) understanding the nature of the electronic phases in proximity to superconductivity. Through a comprehensive and systematic study of many FeSC families, I find that FeSCs are not Fermi liquids, nor are they strongly correlated like the doped Mott insulators of the cuprates, but rather moderately correlated, for which theoretical models of both itinerant and localized components are necessary for capturing the essential physics. For the second perspective, I find direct evidence for an electronic nematic phase bounded by the structural transition and Fermi surface reconstruction associated with the spin density wave order. Furthermore, I present direct spectroscopic evidence that these two orders compete with superconductivity in an underdoped FeSC. These results are similar to the competing nature of the pseudogap to superoconductivity in the cuprates, suggesting that phase competition may play a non-trivial role for HTSC.

Keywords: Physics.
Advisor: Shen Zhi-Xun primary advisor. Thesis advisor
Devereaux Thomas Peter
Fisher Ian advisor. Thesis advisor
Electronic structures of novel complex materials studied by angle resolved photoemission spectroscopy [electronic resource]

Electronic Structure is the key factor for identifying new material or phases and understanding the underlying physics behind emergent phenomena. In the investigation of the electronic structures of novel complex materials, the angular resolved photoemission spectroscopy (ARPES) serves as a powerful tool. The thesis summarizes two of my graduate research projects, which both involves probing electronic structures and analyzing underlying physics on novel complex materials with state-of-the-art ARPES techniques: In the first part, I would summarize our investigation on the materials with non-trivial topology. I would start from our initial work on the three-dimensional topological insulators where we identified the characteristic surface states and verified that they are robust from perturbations. Following the line of search, we discovered three-dimensional topological insulators with other interesting properties, including the strongly inversion asymmetric topological insulator BiTeCl, and the strongly correlated topological Kondo insulator SmB6. We further extended our research to Na3Bi and Cd3As2, where we found them hosting a three-dimensional Dirac point and are first examples of topological Dirac semimetals, a three-dimensional analogue of graphene. In the second part of my thesis, I would discuss the ARPES study on the electron correlation level in the iron chalcogenide family Fe(Se, Te). For the parent compound FeTe, we discovered "peak-dip-hump" spectra with heavily renormalized quasiparticles in the low temperature antiferromagnetic state, characteristic of coherent polarons seen in other correlated materials. The increase of Se ratio leads to an incoherent to coherent crossover in the electronic structure. Furthermore, the reduction of the electronic correlation in Fe(Se, Te) evolves in an orbital-dependent way, where the dxy orbital is influenced most significantly. Finally, in comparison with other members of iron chalcogenides (AxFe2-ySe2, A=K, Rb, Cs; and monolayer FeSe film on SrTiO3 substrate), we found the strong correlation behavior is universal in all iron chalcogenides. Specifically, the dxy orbital is always heavily renormalized and loses spectral weight upon raising temperature. Several physical models of the orbital dependent physics and electron correlations would be discussed.

Keywords: Physics.
Advisor: Shen Zhi-Xun primary advisor. Thesis advisor
Devereaux Thomas Peter
Qi Xiaoliang advisor. Thesis advisor
The empire that wasn't [electronic resource] : the Grand Duchy of Tuscany and empire, 1574-1609

This dissertation considers the Grand Duchy of Tuscany's long-distance activities during the reigns of Grand Dukes Francesco I (r. 1574-1587) and Ferdinando I (r. 1587-1609), including long-distance commercial and imperial projects, military adventures, diplomacy and espionage, collecting, and information-gathering, to explore how the vast empires and emergent global economy of the late sixteenth and early seventeenth century functioned in practice, the role of small powers in these systems, and the wide range of prospects contemporaries saw. The projects and adventures of Tuscan affiliated diplomats, spies, mariners, and merchants who traveled to Morocco, Syria, Iran, Muscovy, India, China, Japan, Spanish America and Brazil reveal an early modern world still very much in flux, open to an almost limitless array of possibilities. This case study of Tuscany's role demonstrates both the breadth of Tuscan ambition and the centrality of politics to structuring participation in the global economy and overseas empire in the early modern world, which in turn suggests a need to revise traditional nationalist and determinist accounts of Europe's engagement with the broader world.

Keywords: History.
Advisor: Findlen Paula primary advisor. Thesis advisor
Como David R.
Riskin Jessica advisor. Thesis advisor
Empirical analyses of energy efficiency policies and the cost dynamics of renewable energy [electronic resource]

A large set of economic policies attempts to improve the cost-benefit calculus of actions that increase the efficiency of electricity consumption or decrease the environmental externalities associated with electricity generation. This dissertation provides three advances in the economic analysis of relevant policies. The first develops a method by which to more comprehensively evaluate consumer-facing energy efficiency policies. A main point of the dissertation is that consumer-facing energy efficiency policies include an embedded behavioral policy and thus may affect the decision-making processes that consumers apply in choosing among alternative energy-consuming goods. These changes in decision-making processes may imply losses in individual-level welfare. Accordingly, policies motivated by externality concerns could yield "negative dividends". This outcome obtains if the policy yields cumulative losses in individual-level welfare that are larger than the gains in externality reductions. The dissertation demonstrates these concepts and the evaluation method by using unique data from a stated choice experiment that studies how participants' choices of hypothetical light bulbs change in response to the Energy Star label. This label highlights energy efficient alternatives in the marketplace. The second advance in the dissertation is a method with which policymakers can design better consumer-facing energy efficiency policy instruments. It explicitly considers the impact of candidate instruments on consumers' decision-making processes. The third and final advance improves methods with which to estimate the cost dynamics of maturing technologies and is most applicable to the assessment of policies supporting the deployment of renewable energy-based electricity generation. Estimates of inter-temporal break-even prices for maturing technologies must reflect expected decreases in the cost of manufacturing capacity, but price guidance in the literature does not include these expectations. The dissertation addresses this gap by developing a central measure of costs, the Economically Sustainable Price (ESP), which can be interpreted as the long-run marginal cost of manufacturing and delivering one unit of output. Along a long-run equilibrium trajectory of manufacturing capacity additions, one would expect prices to equal the ESP. The dissertation provides methods to estimate and forecast ESPs from publicly available cost data. The methods are illustrated with an application to solar photovoltaic (PV) module cost data. Aside from estimating the first cost-based learning curve for solar PV modules, this example provides several policy-relevant findings about the cost- and price-dynamics of this good.

Keywords: Management Science and Engineering.
Advisor: Sweeney James L. primary advisor. Thesis advisor
Beshears John (John Leonard) advisor. Thesis advisor
Reichelstein Stefan
Weyant John P. (John Peter) advisor. Thesis advisor
Enabling multivariate investigation of single-molecule dynamics in solution by counteracting Brownian motion [electronic resource]

Although single-molecule fluorescence spectroscopy has developed into a mature toolkit that allows one to follow the dynamical behaviors of individual biomolecules in exquisite detail, its application in the solution phase is often limited by Brownian diffusion of the nanometer-sized biomolecules to only a 1-millisecond observation window. To remove this limitation while avoiding potential perturbation via immobilization, a device known as the Anti-Brownian ELectrokinetic (ABEL) trap has been developed to counteract Brownian motion that combines position-sensitive fluorescence detection and closed-loop feedback based on electrokinetic forces in a microfluidic geometry. This dissertation describes my work on recent methodology developments and new applications of the ABEL trap technology. First, we describe an optimal redesign of the feedback control strategy that operates close to the ultimate physical limits imposed by diffraction, shot-noise, photobleaching and information bandwidth provided by fluorescence emission. This advanced system greatly improves the capability to hold individual proteins and oligonucleotides in buffer solution and enables multivariate interrogation of single-molecule dynamics for as long as 30 seconds in a non-perturbative aqueous environment. Next, we combine multimodal fluorescence detection with the ABEL trap and illustrate its power using single organic fluorophores and a photosynthetic protein as examples. Direct observation of the synchronized dynamics of different fluorescence parameters reveals the internal states of a single nano-emitter and the interconversions between these states on a 1-second timescale in solution. Last, we show that by applying machine-learning techniques to the ABEL trap's photon data stream, a single molecule's diffusive and electric-field-induced motion parameters can be extracted in real-time during its residence in the trap. We demonstrate how this new measurement paradigm enables molecule-by-molecule sensing of size and charge heterogeneity and their fluctuations at the nanoscale. Two biophysical applications are illustrated: resolving the heterogeneous molecular mixture along a multimeric protein dissociation pathway and real-time visualization of the binding/unbinding interactions between single DNA strands.

Keywords: Electrical Engineering.
Advisor: Moerner W. E. (William Esco)
Fan Shanhui
Solgaard Olav advisor. Thesis advisor
Engineering intestinal microenvironments [electronic resource]

Intestinal tissue engineering efforts are motivated by both traditional regenerative medicine incentives and the need for physiologically-relevant in vitro models for scientific study. In this work, engineering of the biomechanical and biochemical cues provided by the in vitro microenvironment is used to improve the yield and functionality of primary intestinal cultures and to establish cell line-based intestinal models that can more accurately model healthy tissue function. In whole, this demonstrates the tremendous impact that microenvironmental cues can have on intestinal cell viability, development, maturation, and ultimately in the establishment of physiologically-relevant functionalities in vitro. Furthermore, the achievements presented in this work directly constitute significant advancements in the field of intestinal tissue engineering and provide valuable insight for the continued development of in vitro culture techniques for autologous tissue expansion and the establishment of a new generation of preclinical drug screening models with improved physiological accuracy.

Keywords: Bioengineering.
Advisor: Heilshorn Sarah primary advisor. Thesis advisor
Cochran Jennifer R. advisor. Thesis advisor
Dunn Alexander Robert advisor. Thesis advisor
Engineering photonic crystal cavities in III-V semiconductors for X(2) frequency conversion [electronic resource]

Nonlinear optics has traditionally been associated with large, high power devices and applications. Engineering photonic devices with high nonlinearities at low input powers and in a compact size is more challenging, but opens up a range of new applications and possibilities in spectroscopy, sensing, imaging and quantum information processing. Photonic crystal cavities provide a promising platform for achieving such lower power operation, as the low mode volumes and high quality factors allow significant intensity buildup within the cavities for very low input powers, in a device footprint on the order of a few microns. In this dissertation, we investigate the potential of photonic crystal cavities fabricated in III-V semiconductors for nonlinear frequency conversion via the second order nonlinear susceptibility of the semiconductor.

Keywords: Applied Physics.
Advisor: Byer R. L. (Robert L.)
Vuckovic Jelena primary advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor