VictorJuiz/thesis huggingface dataset:
Optical techniques for integrated control and recording of neural activity [electronic resource]

A long-standing objective of psychiatry has been the ability to both control and record the activity of precisely-defined populations of brain cells on the millisecond timescale most relevant for neural computation. Recent advances bring that goal increasingly near by leveraging the genetically-precise techniques of molecular biology with the high-speed, multiplexed command afforded by optical technologies to introduce and utilize light-sensitive neural activity control integrated with fast neural circuit imaging. In this thesis, I present exemplars of these technological advances and demonstrate their utility in illuminating the neural circuit basis of behaviors relevant to understanding psychiatric disease. I first show how fast neural circuit imaging may be integrated with optical neural control tools to develop insight into the role of genetically, developmentally, or projection defined populations of brain cells in mediating circuit-level physiological changes. I then demonstrate computational methods to analyze the resultant imaging data and apply fast circuit imaging to delineate links between hippocampal physiology and behavior in an animal model of depression. Finally, I present the development of a novel class of optically-activated, genetically-targetable control tools that permit optical control of G-protein coupled intracellular signaling; and the use of these molecular devices to determine causal roles of neuromodulatory inputs in reward processing. The development of these and similar optical modalities further improves the precision of questions addressable by the neuroscientist, and potentially the extent of disease treatable by the clinician.

Keywords: Bioengineering.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Endy Andrew D. advisor. Thesis advisor
Kobilka Brian K. advisor. Thesis advisor
Malenka Robert C. advisor. Thesis advisor
Optimal controller synthesis for decentralized systems [electronic resource]

Optimal control theory can be classified, broadly speaking, as either centralized or decentralized. Centralized systems are generally thought of as a single decision maker, taking all sensor measurements and deciding all actuator inputs. By contrast, decentralized systems are typically characterized by multiple subsystems which each make decisions based on different sets of information. Optimal control, as the name suggests, is aimed at finding control policies which minimize a particular norm of the closed-loop map. For centralized problems, the only constraint on the set of admissible control policies is that the resulting system be internally stable. These types of problems have been solved for quite some time, and a variety of methods now exist to explicitly construct the optimal policies. Decentralization imposes additional constraints on admissible policies. These constraints can, in many cases, make the optimization problem intractable. Thus, for decentralized problems, our goal is two-fold. First, we try to identify classes of systems for which tractable representations of the optimization problem exist. Second, we need to synthesize the optimal decentralized controllers. This research is focused at decentralized problems which are represented by subsystems connected over graphs. The decentralization property is given as sparsity constraints on the admissible control policies. For such systems, there exists a simple condition which is sufficient for tractability of the optimization problem. For these systems, we provide a method for constructing the optimal decentralized controllers. These results provide significant insight into the structure of the optimal controllers. Moreover, they establish the state dimension of the optimal policies.

Keywords: Aeronautics and Astronautics
Advisor: Lall Sanjay primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Rock Stephen M. advisor. Thesis advisor
Optimization of organic solar cells [electronic resource]

Organic solar cell is a promising technology because the versatility of organic materials in terms of the tunability of their electrical and optical properties and because of their relative insensitivity to film imperfections which potentially allows for very low-cost high-throughput roll-to-roll processing. However, the power conversion efficiency of organic solar cell is still limited and needs to be improved to be competitive with grid parity. In this thesis, I'll discuss major factors to limit efficiencies of bilayer organic solar cells such as light absorption, exciton diffusion and open circuit voltage. Light trapping enhances light absorption and increases efficiencies with thinner devices structure. The technique is particularly important in organic solar cells because internal quantum efficiency of organic solar cells is low with thick films while absorption is weak with thin films. V-trap configuration is a simple and effective light trapping scheme for organic solar cells since there is no need to modify active layers, thinner films achieve high efficiencies and no tracking system is necessary. The effects of total internal reflection in shaped substrates and the comparison with shapes other than V-shape will be also provided in Chapter 2. Exciton diffusion is a main bottleneck in bilayer organic solar cells and thus the exciton diffusion length (LD) is an important parameter that determines efficiency. However, different groups report different LDs because there are many factors that affect the diffusion length or because there is a systematic error in the measurement Abstract v method. The photocurrent spectroscopy method to estimate LD in Chapter 3 and the effect of molecular packing on LD will be discussed in Chapter 4. Even when light absorption and exciton diffusion are optimized, the efficiency of a single junction organic solar cell is too low for commercial applications. Multijunction cells are a way to achieve the efficiencies needed. I'll discuss the practical efficiencies of tandem organic solar cells in the case of a series-connected tandem cell and an unconstrained (multi-terminal) tandem cell. In practical cases, unconstrained tandem cells result in higher efficiencies because of the increased freedom in choosing materials and device structures without requiring current matching. Semitransparent solid state dye sensitized cells are demonstrated as a route to realize three terminal tandem cells in Chapter 5. Curved focal plane arrays on stretchable silicon mesh networks can lead to realize high performance optical system with simple design. In Chapter 6, I show that curved focal plane arrays have optical advantages such as small number of elements, bright and accurate imaging for off-axis locations. Fabrication method is briefly introduced.

Keywords: Electrical Engineering
Advisor: Peumans Peter
McGehee Michael
Wong Hon-Sum Philip
Optimizing the decision rule of a GPS integrity monitoring system for improved availability [electronic resource]

The Global Positioning System, which was created by the United States Department of Defense specifically for guiding munitions, has disseminated into many applications of the present. Using a differential, ground based augmentation scheme has enabled GPS guidance to be used for the ultra-safety requisite use of landing aircraft. The civil incantation of this project is called LAAS, for Local Area Augmentation System. The military desired a comparable system for their use, and has instituted the JPALS program, for Joint Precision and Approach Landing System. The object is to deliver an integrity monitor to satisfy the stringent requirements of difficult military operation. Although the distinction of emphasis might seem to be on the inherent danger of physical conflict, since the landing platform is expected to be distant from any combat, it is actually the electro-magnetic conflict which takes precedence in this thesis. The JPALS land-based, or sea-based, Integrity Monitor must be designed to endure radio frequency interference, RFI. The potential of RFI to undermine the operation of a landing system is quite real. The intrinsic obligation of an Integrity Monitoring System is to bound the errors associated with the guidance being provided. To this end, the system must determine if any of measurements are faulty, and if those fault(s) indicate the presence of a potentially hazardous position error. Hardware and software can be used to mitigate the impact of radio frequency interference to a GPS based landing system. Beam-steering antennas can be used to emphasize the satellites' signals, and to simultaneously deemphasize a jamming source. The focus of this thesis is in the software algorithms. How can we enhance the performance of our system in its robustness to interference, by optimizing the decision rule it uses to exclude satellites, and receivers, thereby maximizing the amount of useable information, and minimizing the error limits that are broadcast to the approaching aircraft.

Keywords: Mechanical Engineering
Advisor: Enge Per primary advisor. Thesis advisor
Kenny Thomas William advisor. Thesis advisor
Pullen Samuel P.
Option pricing and hedging with transaction costs [electronic resource]

The traditional Black-Scholes theory on pricing and hedging of European call options has long been criticized for its oversimplified and unrealistic model assumptions. This dissertation investigates several existing modifications and extensions of the Black-Scholes model and proposes new data-driven approaches to both option pricing and hedging for real data. The semiparametric pricing approach initially proposed by Lai and Wong (2004) provides a first attempt to bridge the gap between model and market option prices. However, its application to the S& P 500 futures options is not a success, when the original additive regression splines are used for the nonparametric part of the pricing formula. Having found a strong autocorrelation in the time-series of the Black-Scholes pricing residuals, we propose a lag-1 correction for the Black-Scholes price, which essentially is a time-series modeling of the nonparametric part in the semiparametric approach. This simple but efficient time-series approach gives an outstanding pricing performance for S& P 500 futures options, even compared with the commonly practiced and favored implied volatility approaches. A major type of approaches to option hedging with proportional transaction costs is based on singular stochastic control problems that seek an optimal balance between the cost and the risk of hedging an option. We propose a data-driven rule-based strategy to connect the theoretical approaches with real-world applications. Similar to the optimal strategies in theory, the rule-based strategy can be characterized by a pair of buy/sell boundaries and a no-transaction region in between. A two-stage iterative procedure is provided for tuning the boundaries to a long period of option data. Comparing the rule-based strategy with several other existing hedging strategies, we obtain favorable results in both the simulation studies and the empirical study using the S& P 500 futures and futures options. Making use of a reverting pattern of the S& P 500 futures price, we refine the rule-based strategy by allowing hedging suspension at large jumps in futures price.

Keywords: Statistics
Advisor: Lai T. L. primary advisor. Thesis advisor
Rajaratnam Balakanapathy advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Organometallic catalysis for controlled olefin polymerization and oligomerization [electronic resource]

My Ph.D. work primarily involves the synthesis of ethylene-based oligomers and ethylene-styrene copolymers using organometallic catalysis. Chapter 1 reviews selective ethylene oligomerization that produces 1-hexene and 1-octene, with particular emphasis on the chromium-based catalytic systems and the mechanism by which they operate. Its application to the preparation of value-added chemicals is also covered. Chapter 2 and Chapter 3 present investigations on selective ethylene oligomerization with a Cr(PNP)Cl3/MAO catalyst system (PNP = Ph2PN(iPr)PPh2) in the presence of dialkyl zinc as an effective strategy for the co-generation of 1-octene and functionalized ethylene oligomers. Transmetallation with ZnMe2 during Cr-catalyzed ethylene tetramerization generated end-labeled 1-alkenes in Cn> 10 along with 1-octene, while that with ZnEt2 or ZnBu2 produced a mixture of end-labeled linear alkanes and 1-alkenes in Cn> 10 as well as 1-octene. Labeling studies with D2O provided a mechanistic test for metallacycle intermediates. Mechanistic proposals are presented to explain the formation of end-labeled products in the presence of various types of zinc alkyls. Chapter 4 and Chapter 5 examine a series of titanocenes [CpTiCl3, CpTiCl2TEMPO, CpNTiCl3, CpNTiCl2TEMPO, where Cp = C5H5, CpN = C5H4CH2CH2N(CH3)2, and TEMPO = 2,2,6,6-tetramethylpiperidine-N-oxyl] for styrene homopolymerization and ethylene-styrene (ES) copolymerization at 70 °C and 120 °C to determine the influence of the pendant amine group and the hydroxylaminato ligand on comonomer incorporation and distribution. Titanocenes bearing the pendant amine ligand were active for ES copolymerization, whereas complexes lacking the pendant group afforded only mixtures of homopolymers, revealing the critical role of the pendant amine donor on the copolymerization behavior. At 120 °C, the titanocene complexes with the amine group generated high molecular weight ES copolymers along with an atactic polystyrene (aPS) byproduct. The molecular weight of the ES copolymers produced by a coordination mechanism was found to coincide with that of the aPS produced by a radical polymerization mechanism. A method to separate these two components was developed by the addition of a catalytic chain-transfer agent, cobalt tetraphenylporphyrin, successfully decreasing the molecular weight of the radically-produced aPS and offering expedient separation of the ES copolymer from the aPS. Chapter 6 describes a series of new mono-, bi-, and trimetallic complexes based on the dinucleating ligand, N, N'-bis[2-(diphenylphosphino)phenyl] formamidine (PNNP), which provides two binding sites suitable for accommodating Pd, Ni, Co, Fe, and Cu. Definitive evidence for the structures of all complexes were given by X-ray crystal structures. The synthesis, characterization and crystal structure of each complex are discussed.

Keywords: Chemistry
Advisor: Waymouth Robert M. primary advisor. Thesis advisor
Du Bois Justin advisor. Thesis advisor
Frank C. W. advisor. Thesis advisor
Oscillations, waves, and symmetry breaking in cell motility [electronic resource]

Actin-based cell migration depends on the temporal and spatial integration of multiple force-generating systems. Polymerization of the actin network drives protrusion of the cell membrane, and the stretched membrane, in turn, exerts force on the actin network. Myosin contraction of the viscoelastic actin network is balanced by cell-substrate adhesion. The molecular components that contribute to each of these forces - actin-based protrusion, membrane tension, myosin-mediated contraction, and adhesion - have been extensively characterized, but the manner in which they are integrated in vivo to give rise to large-scale emergent properties such as cell shape and movement is not well understood. This thesis describes the role of cell-substrate adhesion in large-scale actin network organization and dynamic cell shape determination. Keratocytes exhibit several non-steady-state behaviors, including oscillatory retraction of the trailing edge, waves of protrusion at the leading edge, and symmetry breaking and motility initiation. I have shown that the mechanical and biochemical properties of adhesions contribute to each of these dynamic behaviors. Oscillatory retraction of the trailing edge emerges in fast-moving, fan-shaped keratocytes and I present evidence consistent with a mechanical model in which elastic coupling between the front of the cell and adhesions in the rear drives oscillations. In contrast, I have found that protrusion waves at the leading edge are likely the result of the biochemical, rather than mechanical, properties of adhesions. Traveling waves emerge at high adhesion strengths and adhesion maturation is required for waving. Mature adhesions have been shown previously to bind several components that contribute to leading edge protrusion, including VASP, a protein that promotes actin polymerization by preventing barbed end capping. Dynamic localization of VASP to the leading edge in waving keratocytes is consistent with a reaction-diffusion model in which global depletion of VASP by mature adhesion, in conjunction with local depletion by the polymerizing actin network, results in lateral propagation of protrusion waves. Finally, I present evidence that suggests that balance between cell-substrate adhesion and myosin contraction sets the mechanical instability threshold above which stationary, radially symmetric keratocytes break symmetry and begin to move. On the whole, the work described here represents significant progress towards elucidating the self-organization principles that underly whole cell migration.

Keywords: Biochemistry
Advisor: Theriot Julie primary advisor. Thesis advisor
Spudich James A.
Straight Aaron
Palladium and platinum complexes for the oxidation of small molecules [electronic resource]

Palladium is a versatile metal used prominently in synthesis. The rapid growth of palladium oxidation chemistry in the past decade has spurred a number of new processes that allow for the selective oxidation of substrates under mild conditions. This growth, specifically in the field of aerobic alcohol oxidation, attracted our attention, with the hope that it would provide new catalysts for use in direct methanol fuel cells. Toward that goal we developed a new cationic palladium complex, [(neocuproine)Pd(OAc)]2[OTf]2, which shows unprecedented initial turnover frequencies for aerobic alcohol oxidation at room temperature. However, catalyst lifetimes are limited due to the generation of reactive partially reduced oxygen species that promote oxidation of the ligand and deactivation of the catalyst. The use of milder oxidant like benzoquinone extended catalyst lifetimes prompting a further exploration of the substrate scope. Oxidation of glycerol proceeds exclusively at the secondary alcohol to yield dihydroxyacetone. Other 1,2-diols also favors oxidation of the secondary alcohol. Methanol oxidation proceeds at a much slower rate, but yields methyl formate with selectivities greater than 90 %. The mechanism for this process was probed through the use of model studies and isotopic labels suggesting the transient generation and oxidation of methyl hemiformal. In a parallel effort toward the extension of catalyst lifetimes, a number of new oxidatively resistant ligands were synthesized and used toward the formation of palladium catalysts that exhibit extended catalyst lifetimes. Additional efforts have focused on the use of similar catalyst for the oxidative carbonylation of 1,2- and 1,3-diols to yield 5-membered and 6-membered cyclic carbonates in the presence of N-chlorosuccinimide, iodosylbenzene, or dichloroisocyanuric acid. Finally, a new platinum dimer containing a trimethylplatinum unit and bridging amides was synthesized and characterized. Its reactivity toward the reductive elimination of ethane of methanol derivatives was explored. Additional work with known platinum dimers suggests these species, upon addition of silver triflate, facilitates the C-H activation of a number of unactivated arenes and promotes the C-H functionalization of propargyl aryl ethers.

Keywords: Chemistry
Advisor: Waymouth Robert M. primary advisor. Thesis advisor
Kool Eric T. advisor. Thesis advisor
Trost Barry M. advisor. Thesis advisor
Paradigm and discourse in archaic greek poetry [electronic resource]

This dissertation is a study in the style of paradeigmata ([Greek word omitted], mytho- logical exempla, exemplary tales) in Archaic Greek poetry and wisdom discourse. Part One comprises two corpus-based studies of Homeric poetry in terms of three linguistic features (discourse markers, relative clauses, and register); each of these studies is fol- lowed by a comparative study in Hesiodic poetry. Here I suggest that genealogical cata- logue poetry known from the Hesiodic tradition is an important traditional resource for these narratives. Part Two makes an analogous study of non-hexameter poetry from the Archaic Period as well as wisdom discourse attributed to Aesop and the Seven Sages. In these chapters I emphasize two strategies in particular: the creation and 'mythologization' of authoritative personae, and the sociocultural import of the stylistic features of ge- nealogical catalogue in select Pindaric odes. Drawing on the findings of Part One and Part Two, the two studies in Part Three present readings of the Iliad and Odyssey through an analysis of how the linguistic features and themes of paradeigmata work at the level of poetic composition.

Keywords: Classics
Advisor: Martin Richard P. primary advisor. Thesis advisor
Peponi Anastasia-Erasmia primary advisor. Thesis advisor
Kurke Leslie advisor. Thesis advisor
Paradigms for virtualization based host security [electronic resource]

Virtualization has been one of the most potent forces reshaping the landscape of systems software in the last 10 years and has become ubiquitous in the realm of enterprise compute infrastructure and in the emerging field of cloud computing. This presents a variety of new opportunities when designing host based security architectures. We present several paradigms for enhancing host security leveraging the new capabilities afforded by virtualization. First, we present a virtualization based approach to trusted computing. This allows multiple virtual hosts with different assurance levels to run concurrently on the same platform using a novel "open box" and "closed box" model that allows the virtualized platform to present the best properties of traditional open and closed platforms on a single physical platform. Next, we present virtual machine introspection, an approach to enhancing the attack resistance intrusion detection and prevention systems by moving them "out of the box" i.e. out of the virtual host they are monitoring and into a seperate protection domain where they can inspect the host they are monitoring from a more protected vantage point. Finally, we present overshadow data protection, an approach for providing a last line of defense for application data even if the guest OS running an application has been compromised. We accomplish this by presenting two views of virtual memory, an encrypted view to the operating system and a plain text view to the application the owning that memory. This approach more generally illustrates the mechanisms necessary to introduce new orthogonal protection mechanisms into a Guest Operating system from the virtualization layer while maintaining backwards compatibility with existing operating systems and applications.

Advisor: Rosenblum Mendel primary advisor. Thesis advisor
Boneh Dan
Mitchell John C. advisor. Thesis advisor