Darrigolen gramatikaz

Published in 2008.

Distributed optimization in power networks and general multi-agent systems

<p>The dissertation studies the general area of complex networked systems that consist of interconnected and active heterogeneous components and usually operate in uncertain environments and with incomplete information. Problems associated with those systems are typically large-scale and computationally intractable, yet they are also very well-structured and have features that can be exploited by appropriate modeling and computational methods. The goal of this thesis is to develop foundational theories and tools to exploit those structures that can lead to computationally-efficient and distributed solutions, and apply them to improve systems operations and architecture.</p> <p>Specifically, the thesis focuses on two concrete areas. The first one is to design distributed rules to manage distributed energy resources in the power network. The power network is undergoing a fundamental transformation. The future smart grid, especially on the distribution system, will be a large-scale network of distributed energy resources (DERs), each introducing random and rapid fluctuations in power supply, demand, voltage and frequency. These DERs provide a tremendous opportunity for sustainability, efficiency, and power reliability. However, there are daunting technical challenges in managing these DERs and optimizing their operation. The focus of this dissertation is to develop scalable, distributed, and real-time control and optimization to achieve system-wide efficiency, reliability, and robustness for the future power grid. In particular, we will present how to explore the power network structure to design efficient and distributed market and algorithms for the energy management. We will also show how to connect the algorithms with physical dynamics and existing control mechanisms for real-time control in power networks.</p> <p>The second focus is to develop distributed optimization rules for general multi-agent engineering systems. A central goal in multiagent systems is to design local control laws for the individual agents to ensure that the emergent global behavior is desirable with respect to the given system level objective. Ideally, a system designer seeks to satisfy this goal while conditioning each agent’s control on the least amount of information possible. Our work focused on achieving this goal using the framework of game theory. In particular, we derived a systematic methodology for designing local agent objective functions that guarantees (i) an equivalence between the resulting game-theoretic equilibria and the system level design objective and (ii) that the resulting game possesses an inherent structure that can be exploited for distributed learning, e.g., potential games. The control design can then be completed by applying any distributed learning algorithm that guarantees convergence to the game-theoretic equilibrium. One main advantage of this game theoretic approach is that it provides a hierarchical decomposition between the decomposition of the systemic objective (game design) and the specific local decision rules (distributed learning algorithms). This decomposition provides the system designer with tremendous flexibility to meet the design objectives and constraints inherent in a broad class of multiagent systems. Furthermore, in many settings the resulting controllers will be inherently robust to a host of uncertainties including asynchronous clock rates, delays in information, and component failures.</p>

The optoelectronic swept-frequency laser and its applications in ranging, three-dimensional imaging, and coherent beam combining of chirped-seed amplifiers

<p>This thesis explores the design, construction, and applications of the optoelectronic swept-frequency laser (SFL). The optoelectronic SFL is a feedback loop designed around a swept-frequency (chirped) semiconductor laser (SCL) to control its instantaneous optical frequency, such that the chirp characteristics are determined solely by a reference electronic oscillator. The resultant system generates precisely controlled optical frequency sweeps. In particular, we focus on linear chirps because of their numerous applications. We demonstrate optoelectronic SFLs based on vertical-cavity surface-emitting lasers (VCSELs) and distributed-feedback lasers (DFBs) at wavelengths of 1550 nm and 1060 nm. We develop an iterative bias current predistortion procedure that enables SFL operation at very high chirp rates, up to 10^16 Hz/sec. We describe commercialization efforts and implementation of the predistortion algorithm in a stand-alone embedded environment, undertaken as part of our collaboration with Telaris, Inc. We demonstrate frequency-modulated continuous-wave (FMCW) ranging and three-dimensional (3-D) imaging using a 1550 nm optoelectronic SFL.</p> <p>We develop the technique of multiple source FMCW (MS-FMCW) reflectometry, in which the frequency sweeps of multiple SFLs are "stitched" together in order to increase the optical bandwidth, and hence improve the axial resolution, of an FMCW ranging measurement. We demonstrate computer-aided stitching of DFB and VCSEL sweeps at 1550 nm. We also develop and demonstrate hardware stitching, which enables MS-FMCW ranging without additional signal processing. The culmination of this work is the hardware stitching of four VCSELs at 1550 nm for a total optical bandwidth of 2 THz, and a free-space axial resolution of 75 microns.</p> <p>We describe our work on the tomographic imaging camera (TomICam), a 3-D imaging system based on FMCW ranging that features non-mechanical acquisition of transverse pixels. Our approach uses a combination of electronically tuned optical sources and low-cost full-field detector arrays, completely eliminating the need for moving parts traditionally employed in 3-D imaging. We describe the basic TomICam principle, and demonstrate single-pixel TomICam ranging in a proof-of-concept experiment. We also discuss the application of compressive sensing (CS) to the TomICam platform, and perform a series of numerical simulations. These simulations show that tenfold compression is feasible in CS TomICam, which effectively improves the volume acquisition speed by a factor ten.</p> <p>We develop chirped-wave phase-locking techniques, and apply them to coherent beam combining (CBC) of chirped-seed amplifiers (CSAs) in a master oscillator power amplifier configuration. The precise chirp linearity of the optoelectronic SFL enables non-mechanical compensation of optical delays using acousto-optic frequency shifters, and its high chirp rate simultaneously increases the stimulated Brillouin scattering (SBS) threshold of the active fiber. We characterize a 1550 nm chirped-seed amplifier coherent-combining system. We use a chirp rate of 5*10^14 Hz/sec to increase the amplifier SBS threshold threefold, when compared to a single-frequency seed. We demonstrate efficient phase-locking and electronic beam steering of two 3 W erbium-doped fiber amplifier channels, achieving temporal phase noise levels corresponding to interferometric fringe visibilities exceeding 98%.</p>

Where Tori fear to tread : hypermassive neutron star remnants and absolute event horizons Or topics in computational general relativity

Computational general relativity is a field of study which has reached maturity only within the last decade. This thesis details several studies that elucidate phenomena related to the coalescence of compact object binaries. Chapters 2 and 3 recounts work towards developing new analytical tools for visualizing and reasoning about dynamics in strongly curved spacetimes. In both studies, the results employ analogies with the classical theory of electricity and magnitism, first (Ch. 2) in the post-Newtonian approximation to general relativity and then (Ch. 3) in full general relativity though in the absence of matter sources. In Chapter 4, we examine the topological structure of absolute event horizons during binary black hole merger simulations conducted with the SpEC code. Chapter 6 reports on the progress of the SpEC code in simulating the coalescence of neutron star-neutron star binaries, while Chapter 7 tests the effects of various numerical gauge conditions on the robustness of black hole formation from stellar collapse in SpEC. In Chapter 5, we examine the nature of pseudospectral expansions of non-smooth functions motivated by the need to simulate the stellar surface in Chapters 6 and 7. In Chapter 8, we study how thermal effects in the nuclear equation of state effect the equilibria and stability of hypermassive neutron stars. Chapter 9 presents supplements to the work in Chapter 8, including an examination of the stability question raised in Chapter 8 in greater mathematical detail.

Revealing, illuminating, and modifying proteins in human diseases using noncanonical amino acids

<p>To better understand human diseases, much recent work has focused on proteins to either identify disease targets through proteomics or produce therapeutics via protein engineering. Noncanonical amino acids (ncAAs) are tools for altering the chemical and physical properties of proteins, providing a facile strategy not only to label proteins but also to engineer proteins with novel properties. My thesis research has focused on the development and applications of noncanonical amino acids in identifying, imaging, and engineering proteins for studying human diseases. Chapter 1 introduces the concept of ncAAs and reveals insights to how I chose my thesis projects.</p> <p>ncAAs have been incorporated to tag and enrich newly synthesized proteins for mass spectrometry through a method termed BONCAT, or bioorthogonal noncanonical amino acid tagging. Chapter 2 describes the investigation of the proteomic response of human breast cancer cells to induced expression of tumor suppressor microRNA miR-126 by combining BONCAT with another proteomic method, SILAC or stable isotope labeling by amino acids in cell culture. This proteomic analysis led to the discovery of a direct target of miR-126, shedding new light on its role in suppressing cancer metastasis.</p> <p>In addition to mass spectrometry, ncAAs can also be utilized to fluorescently label proteins. Chapter 3 details the synthesis of a set of cell-permeant cyclooctyne probes and demonstration of selective labeling of newly synthesized proteins in live mammalian cells using azidohomoalanine. Similar to live cell imaging, the ability to selectively label a particular cell type within a mixed cell population is important to interrogating many biological systems, such as tumor microenvironments. By taking advantage of the metabolic differences between cancer and normal cells, Chapter 5 discusses efforts to develop selective labeling of cancer cells using a glutamine analogue.</p> <p>Furthermore, Chapter 4 describes the first demonstration of global replacement at polar amino acid positions and its application in developing an alternative PEGylation strategy for therapeutic proteins. Polar amino acids typically occupy solvent-exposed positions on the protein surface, and incorporation of noncanonical amino acids at these positions should allow easier modification and cause less perturbation compared to replacements at the interior positions of proteins.</p>

Multiplexed DNA-mediated electrochemistry

<p>The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of π-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the π-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA π-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.</p> <p>First, Methylene Blue (MB′) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB′ was reduced through DNA-mediated charge transport. The redox signal intensity for MB′-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB′ on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.</p> <p>Next, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening π-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA. Further gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.</p> <p>Finally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.</p>

Demographic studies of extrasolar planets

<p>Uncovering the demographics of extrasolar planets is crucial to understanding the processes of their formation and evolution. In this thesis, we present four studies that contribute to this end, three of which relate to NASA's Kepler mission, which has revolutionized the field of exoplanets in the last few years.</p> <p>In the pre-Kepler study, we investigate a sample of exoplanet spin-orbit measurements---measurements of the inclination of a planet's orbit relative to the spin axis of its host star---to determine whether a dominant planet migration channel can be identified, and at what confidence. Applying methods of Bayesian model comparison to distinguish between the predictions of several different migration models, we find that the data strongly favor a two-mode migration scenario combining planet-planet scattering and disk migration over a single-mode Kozai migration scenario. While we test only the predictions of particular Kozai and scattering migration models in this work, these methods may be used to test the predictions of any other spin-orbit misaligning mechanism.</p> <p>We then present two studies addressing astrophysical false positives in Kepler data. The Kepler mission has identified thousands of transiting planet candidates, and only relatively few have yet been dynamically confirmed as bona fide planets, with only a handful more even conceivably amenable to future dynamical confirmation. As a result, the ability to draw detailed conclusions about the diversity of exoplanet systems from Kepler detections relies critically on understanding the probability that any individual candidate might be a false positive. We show that a typical a priori false positive probability for a well-vetted Kepler candidate is only about 5-10%, enabling confidence in demographic studies that treat candidates as true planets. We also present a detailed procedure that can be used to securely and efficiently validate any individual transit candidate using detailed information of the signal's shape as well as follow-up observations, if available.</p> <p>Finally, we calculate an empirical, non-parametric estimate of the shape of the radius distribution of small planets with periods less than 90 days orbiting cool (less than 4000K) dwarf stars in the Kepler catalog. This effort reveals several notable features of the distribution, in particular a maximum in the radius function around 1-1.25 Earth radii and a steep drop-off in the distribution larger than 2 Earth radii. Even more importantly, the methods presented in this work can be applied to a broader subsample of Kepler targets to understand how the radius function of planets changes across different types of host stars.</p>

Market Instruments and CO2 Mitigation: A General Equilibrium Analysis for Spain

25 p.

Cooperative and market-based solutions to pollution abatement problems

<p>This work concerns itself with the possibility of solutions, both cooperative and market based, to pollution abatement problems. In particular, we are interested in pollutant emissions in Southern California and possible solutions to the abatement problems enumerated in the 1990 Clean Air Act. A tradable pollution permit program has been implemented to reduce emissions, creating property rights associated with various pollutants. </p> <p>Before we discuss the performance of market-based solutions to LA's pollution woes, we consider the existence of cooperative solutions. In Chapter 2, we examine pollutant emissions as a trans boundary public bad. We show that for a class of environments in which pollution moves in a bi-directional, acyclic manner, there exists a sustainable coalition structure and associated levels of emissions. We do so via a new core concept, one more appropriate to modeling cooperative emissions agreements (and potential defection from them) than the standard definitions. </p> <p>However, this leaves the question of implementing pollution abatement programs unanswered. While the existence of a cost-effective permit market equilibrium has long been understood, the implementation of such programs has been difficult. The design of Los Angeles' REgional CLean Air Incentives Market (RECLAIM) alleviated some of the implementation problems, and in part exacerbated them. For example, it created two overlapping cycles of permits and two zones of permits for different geographic regions. While these design features create a market that allows some measure of regulatory control, they establish a very difficult trading environment with the potential for inefficiency arising from the transactions costs enumerated above and the illiquidity induced by the myriad assets and relatively few participants in this market. </p> <p>It was with these concerns in mind that the ACE market (Automated Credit Exchange) was designed. The ACE market utilizes an iterated combined-value call market (CV Market). Before discussing the performance of the RECLAIM program in general and the ACE mechanism in particular, we test experimentally whether a portfolio trading mechanism can overcome market illiquidity. Chapter 3 experimentally demonstrates the ability of a portfolio trading mechanism to overcome portfolio rebalancing problems, thereby inducing sufficient liquidity for markets to fully equilibrate. </p> <p>With experimental evidence in hand, we consider the CV Market's performance in the real world. We find that as the allocation of permits reduces to the level of historical emissions, prices are increasing. As of April of this year, prices are roughly equal to the cost of the Best Available Control Technology (BACT). This took longer than expected, due both to tendencies to mis-report emissions under the old regime, and abatement technology advances encouraged by the program. Vve also find that the ACE market provides liquidity where needed to encourage long-term planning on behalf of polluting facilities. </p>