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Polarization-Based Navigation in Drosophila
Get PDFInsects maintain a constant bearing across a wide range of spatial scales. Monarch butterflies and locusts traverse continents (Williams, 1957; Wehner, 1984), and foraging bees and ants travel hundreds of meters to return to their nests (Dyer, 1996; Wehner, 1984, 2003), whereas many other insects fly straight for only a few centimeters before changing direction. Despite this variation in spatial scale, the brain region thought to underlie long-distance navigation is remarkably conserved (Loesel et al., 2002; Homberg, 2008), suggesting that the use of a celestial compass is a general and perhaps ancient capability of insects. Laboratory studies of Drosophila have identified a local search mode in which short, straight segments are interspersed with rapid turns (Mayer et al., 1988; Bender and Dickinson, 2006). However, this flight mode is inconsistent with measured gene flow between geographically separated populations (Jones et al., 1981; Slatkin, 1985; Turelli and Hoffmann, 1991), and individual Drosophila can travel 10 km in a single night (Yerington, 1961; Jones et al., 1981; Coyne et al., 1982, 1987) -- a feat that would be impossible without prolonged periods of straight flight. One well-known cue relevant to orientation and navigation is the pattern of polarization of skylight. To study possible mechanisms of orientation to skylight polarization, we built an arena in which we could observe individual flight responses to rotating the angle of polarized light in the laboratory. We found that flies robustly steer in response to changes in the polarization angle of light. Individual flies also stabilize a particular polarization plane when they are given closed-loop control of such a stimulus. To directly examine orientation behavior under outdoor conditions, we built two portable flight arenas in which a fly viewed the natural sky through a clear aperture. In the first we examined the ability of flies to compensate for external rotations with or without the aid of skylight polarization. The second arena contained a liquid crystal device that could experimentally rotate the polarization angle of the skylight. In both outdoor arenas we tracked fly orientation using a digital video camera and custom computer vision system. Our findings indicate that Drosophila actively orient using the sky's natural polarization pattern.</p
Si Microwire Array Photoanodes for Artificial Photosynthetic Devices
Get PDFTo realize the large-scale deployment of solar power, new materials and strategies must be developed for the fabrication of economical and sustainable artificial photosynthetic devices. These systems have multiple constraints, which are typically met by employing expensive, multi-junction solar cells coupled to noble metal catalysts. However, to supply and store power on a global, terawatt scale, these technologies must shift towards utilizing abundant elements and low-cost deposition techniques, while maintaining device efficiency. Driven by these challenges, this thesis presents achievements in Si microwire arrays to realize cost competitive and sustainable artificial photosynthetic devices.
The device performance of Si microwire arrays, a thin-film photovoltaic technology, was investigated using photoelectrochemical methods. Both n-type and lightly doped Si microwire arrays demonstrated improved performance as photoanodes, and may be used in an artificial photosynthetic device to perform oxidative reactions. In addition, lightly doped Si microwire arrays operating under high-level injection conditions achieved performance comparable to that of optimally doped p-type Si microwire array photocathodes, with Voc values exceeding 450 mV and carrier collection efficiencies of ~ 0.85. A model of these devices operating under high-level injection conditions was developed, using finite-element device physics simulations. These simulations predicted that the carrier collection efficiencies of the devices should deviate from unity, even for minority-carrier diffusion lengths greater than the radius. Such behavior was confirmed by experimental internal quantum yield measurements, reaffirming that these devices are limited by axial transport of carriers along the length of the wire. However, optimized arrays have the potential to generate voltages that exceed those generated by arrays operating under low-level injection conditions. Such studies offer increased understanding of the performance of structured, concentrator photovoltaics and considerations for structuring lightly doped materials on the nano- and microscale.</p
Aerosols and Chemistry in the Planetary Atmospheres
Get PDFThis dissertation is devoted to studying aerosols and their roles in regulating chemistry, radiation, and dynamics of planetary atmospheres. In chapter I, we provided a fundamental mathematical basis for the quasi-equilibrium growth assumption, a well-accepted approach to representing formation of secondary organic aerosols (SOAs) in microphysical simulations in the Earth’s atmosphere. Our analytical work not only explains the quasi-equilibrium growth, which emerges as a limiting case in our theory, but also predicts the other types of condensational growth, confirmed by the recent laboratory and field experiments. In chapter II, we presented a new photochemical mechanism in which the evaporation of the aerosols composed of sulfuric acid or polysulfur on the nightside of Venus could provide a sulfur source above 90 km. Our model results imply the enhancements of sulfur oxides such as SO, SO2, and SO3. This is inconsistent with the previous model results but in agreement with the recent ground-based and spacecraft observations. In chapters III and IV, we developed a nonlinear optimization approach to retrieve the aerosol and cloud structure on Jupiter from the visible and ultraviolet images acquired by the Cassini spacecraft, combined with the ground-based near-infrared observations. We produced the first realistic spatial distribution of Jovian stratospheric aerosols in latitudes and altitudes. We also retrieved the stratospheric temperature and hydrocarbon species based on the mid-infrared spectra from the Cassini and Voyager spacecrafts. Based on the above information, the accurate and detailed maps of the instantaneous radiative forcing in Jovian stratosphere are obtained, revealing a significant heating effect from the polar dark aerosols in the high latitude region and therefore a strong modulation on the global meridional circulation in the stratosphere of Jupiter. In chapter V, we study the transport of passive tracers, such as aerosols, acetylene (C2H2) and ethane (C2H6) in the Jovian stratosphere, using both analytical and numerical approaches. We established several benchmark analytical solutions for the coupled photochemical-advective-diffusive system to understand its basic behaviors under different assumptions. A numerical two-dimensional chemical transport model is applied to Jupiter, and the effects of eddy mixing process and meridional circulation on the distributions of stratospheric species are discussed
Thermodynamic Properties of Organometallic Dihydrogen Complexes for Hydrogen Storage Applications
Get PDFThe mechanism and thermodynamic properties of hydrogen binding to the solid-state complexes [M(CO)dppe2][BArF24] (M = Mn, Re, Tc) and [M'Hdppe2][NTf2] (M' = Fe, Ru, Os) were investigated experimentally and computationally over the temperature range 298K-373K and pressure range 0-2800 torr, based on the Sieverts method. The bulk absorption behavior was found to be accurately described by Langmuir isotherms. Enthalpy and entropy values of ΔH° = -52.2 kJ/mol and ΔS° = -99.6 J/mol-K were obtained experimentally for hydrogen absorption onto [Mn(CO)dppe2][BArF24] from the Langmuir equilibrium constant, and values obtained from electronic structure calculations using the LANL2DZ-ECP basis set were found to successfully reproduce both the pressure-temperature-composition behavior and the thermodynamic values to within 5% of those obtained through experiment. Results from simulations for all complexes yielded large enthalpy values similar to metal hydride formation enthalpies for all complexes studied, and the substitution of the metal center reproduced qualitative binding strength trends of 5d>3d>4d consistent with those previously reported for the group 6 metals.
X-ray diffraction patterns and Mössbauer spectra were taken to determine the thermal decomposition pathway for [FeH(η2-H2)dppe2][NTf2]. Simulations at the B3LYP/TZVP level of theory and experimental Mössbauer spectra confirmed the direct thermal decomposition from singlet-state [FeH(η2-H2)dppe2][NTf2] to triplet-state [FeHdppe2][NTf2] under vacuum conditions at 398K. Evaluation of the partial quadrupole splitting values of Q(H2) = -0.245 mm/s from Mössbauer spectroscopy significantly differ from typical values obtained for hydrides, indicating an underutilized mechanism for identification of dihydrogen ligands. Singlet-state thermodynamic values from simulation were consistent with experimental observations for Ru and Os, and ruthenium complexes were found to have thermodynamic properties within appropriate ranges for hydrogen storage applications. Simulated thermodynamic values for Fe complexes were found to significantly underestimate experimental behavior, demonstrating the importance of the magnetic spin state of the molecule to hydrogen binding properties.</p
Analysis and Optimization of Stress Wave Propagation in Two-Dimensional Granular Crystals with Defects
Get PDFGranular crystals are compact periodic assemblies of elastic particles in Hertzian contact whose dynamic response can be tuned from strongly nonlinear to linear by the addition of a static precompression force. This unique feature allows for a wide range of studies that include the investigation of new fundamental nonlinear phenomena in discrete systems such as solitary waves, shock waves, discrete breathers and other defect modes. In the absence of precompression, a particularly interesting property of these systems is their ability to support the formation and propagation of spatially localized soliton-like waves with highly tunable properties. The wealth of parameters one can modify (particle size, geometry and material properties, periodicity of the crystal, presence of a static force, type of excitation, etc.) makes them ideal candidates for the design of new materials for practical applications. This thesis describes several ways to optimally control and tailor the propagation of stress waves in granular crystals through the use of heterogeneities (interstitial defect particles and material heterogeneities) in otherwise perfectly ordered systems. We focus on uncompressed two-dimensional granular crystals with interstitial spherical intruders and composite hexagonal packings and study their dynamic response using a combination of experimental, numerical and analytical techniques. We first investigate the interaction of defect particles with a solitary wave and utilize this fundamental knowledge in the optimal design of novel composite wave guides, shock or vibration absorbers obtained using gradient-based optimization methods
Essays on Cooperation and Reciprocity
Get PDFThis dissertation comprises three essays that use theory-based experiments to gain understanding of how cooperation and efficiency is affected by certain variables and institutions in different types of strategic interactions prevalent in our society.
Chapter 2 analyzes indefinite horizon two-person dynamic favor exchange games with private information in the laboratory. Using a novel experimental design to implement a dynamic game with a stochastic jump signal process, this study provides insights into a relation where cooperation is without immediate reciprocity. The primary finding is that favor provision under these conditions is considerably less than under the most efficient equilibrium. Also, individuals do not engage in exact score-keeping of net favors, rather, the time since the last favor was provided affects decisions to stop or restart providing favors.
Evidence from experiments in Cournot duopolies is presented in Chapter 3 where players indulge in a form of pre-play communication, termed as revision phase, before playing the one-shot game. During this revision phase individuals announce their tentative quantities, which are publicly observed, and revisions are costless. The payoffs are determined only by the quantities selected at the end under real time revision, whereas in a Poisson revision game, opportunities to revise arrive according to a synchronous Poisson process and the tentative quantity corresponding to the last revision opportunity is implemented. Contrasting results emerge. While real time revision of quantities results in choices that are more competitive than the static Cournot-Nash, significantly lower quantities are implemented in the Poisson revision games. This shows that partial cooperation can be sustained even when individuals interact only once.
Chapter 4 investigates the effect of varying the message space in a public good game with pre-play communication where player endowments are private information. We find that neither binary communication nor a larger finite numerical message space results in any efficiency gain relative to the situation without any form of communication. Payoffs and public good provision are higher only when participants are provided with a discussion period through unrestricted text chat.</p
Novel Roles of the SRP RNA in Co-Translational Protein Targeting
Get PDFThe signal recognition particle (SRP) and its receptor (SR) are universally conserved protein machineries that deliver nascent peptides to their proper destination. The SRP RNA is a universally conserved and essential component of SRP, which serves as the “catalyst” of the protein targeting cycle. The SRP RNA accelerates SRP-SR complex formation at the beginning of the protein targeting reaction, and triggers GTP hydrolysis and SRP-SR complex disassembly at the end. Here we combined biochemical and biophysical approaches to investigate the molecular mechanism of the functions of the SRP RNA. We found that two functional ends in the SRP RNA mediate distinct functions. The tetraloop end facilitates initial assembly of SRP and SR by mediating an electrostatic interaction with the Lys399 receptor, which ensures efficient and accurate substrate targeting. At the later stage of the SRP cycle, the SRP-SR complex relocalizes ~ 100 Angstrom to the 5’,3’-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. These results, combined with recent structural work, elucidate the functions of the SRP RNA during the protein targeting reaction
Essays on Economics Networks
Get PDFThis thesis belongs to the growing field of economic networks. In particular, we develop three essays in which we study the problem of bargaining, discrete choice representation, and pricing in the context of networked markets. Despite analyzing very different problems, the three essays share the common feature of making use of a network representation to describe the market of interest.
In Chapter 1 we present an analysis of bargaining in networked markets. We make two contributions. First, we characterize market equilibria in a bargaining model, and find that players' equilibrium payoffs coincide with their degree of centrality in the network, as measured by Bonacich's centrality measure. This characterization allows us to map, in a simple way, network structures into market equilibrium outcomes, so that payoffs dispersion in networked markets is driven by players' network positions. Second, we show that the market equilibrium for our model converges to the so called eigenvector centrality measure. We show that the economic condition for reaching convergence is that the players' discount factor goes to one. In particular, we show how the discount factor, the matching technology, and the network structure interact in a very particular way in order to see the eigenvector centrality as the limiting case of our market equilibrium.
We point out that the eigenvector approach is a way of finding the most central or relevant players in terms of the “global” structure of the network, and to pay less attention to patterns that are more “local”. Mathematically, the eigenvector centrality captures the relevance of players in the bargaining process, using the eigenvector associated to the largest eigenvalue of the adjacency matrix of a given network. Thus our result may be viewed as an economic justification of the eigenvector approach in the context of bargaining in networked markets.
As an application, we analyze the special case of seller-buyer networks, showing how our framework may be useful for analyzing price dispersion as a function of sellers and buyers' network positions.
Finally, in Chapter 3 we study the problem of price competition and free entry in networked markets subject to congestion effects. In many environments, such as communication networks in which network flows are allocated, or transportation networks in which traffic is directed through the underlying road architecture, congestion plays an important role. In particular, we consider a network with multiple origins and a common destination node, where each link is owned by a firm that sets prices in order to maximize profits, whereas users want to minimize the total cost they face, which is given by the congestion cost plus the prices set by firms. In this environment, we introduce the notion of Markovian traffic equilibrium to establish the existence and uniqueness of a pure strategy price equilibrium, without assuming that the demand functions are concave nor imposing particular functional forms for the latency functions. We derive explicit conditions to guarantee existence and uniqueness of equilibria. Given this existence and uniqueness result, we apply our framework to study entry decisions and welfare, and establish that in congested markets with free entry, the number of firms exceeds the social optimum. </p
Nonlinear Optics and Wavelength Translation Via Cavity-Optomechanics
Get PDFThe field of cavity-optomechanics explores the interaction of light with sound in an ever increasing array of devices. This interaction allows the mechanical system to be both sensed and controlled by the optical system, opening up a wide variety of experiments including the cooling of the mechanical resonator to its quantum mechanical ground state and the squeezing of the optical field upon interaction with the mechanical resonator, to name two.
In this work we explore two very different systems with different types of optomechanical coupling. The first system consists of two microdisk optical resonators stacked on top of each other and separated by a very small slot. The interaction of the disks causes their optical resonance frequencies to be extremely sensitive to the gap between the disks. By careful control of the gap between the disks, the optomechanical coupling can be made to be quadratic to first order which is uncommon in optomechanical systems. With this quadratic coupling the light field is now sensitive to the energy of the mechanical resonator and can directly control the potential energy trapping the mechanical motion. This ability to directly control the spring constant without modifying the energy of the mechanical system, unlike in linear optomechanical coupling, is explored.
Next, the bulk of this thesis deals with a high mechanical frequency optomechanical crystal which is used to coherently convert photons between different frequencies. This is accomplished via the engineered linear optomechanical coupling in these devices. Both classical and quantum systems utilize the interaction of light and matter across a wide range of energies. These systems are often not naturally compatible with one another and require a means of converting photons of dissimilar wavelengths to combine and exploit their different strengths. Here we theoretically propose and experimentally demonstrate coherent wavelength conversion of optical photons using photon-phonon translation in a cavity-optomechanical system. For an engineered silicon optomechanical crystal nanocavity supporting a 4 GHz localized phonon mode, optical signals in a 1.5 MHz bandwidth are coherently converted over a 11.2 THz frequency span between one cavity mode at wavelength 1460 nm and a second cavity mode at 1545 nm with a 93% internal (2% external) peak efficiency. The thermal and quantum limiting noise involved in the conversion process is also analyzed and, in terms of an equivalent photon number signal level, are found to correspond to an internal noise level of only 6 and 4 times 10x^-3 quanta, respectively.
We begin by developing the requisite theoretical background to describe the system. A significant amount of time is then spent describing the fabrication of these silicon nanobeams, with an emphasis on understanding the specifics and motivation. The experimental demonstration of wavelength conversion is then described and analyzed. It is determined that the method of getting photons into the cavity and collected from the cavity is a fundamental limiting factor in the overall efficiency. Finally, a new coupling scheme is designed, fabricated, and tested that provides a means of coupling greater than 90% of photons into and out of the cavity, addressing one of the largest obstacles with the initial wavelength conversion experiment.</p
Diagonal Forms, Linear Algebraic Methods and Ramsey-Type Problems
Get PDFThis thesis focuses mainly on linear algebraic aspects of combinatorics. Let N_t(H) be an incidence matrix with edges versus all subhypergraphs of a complete hypergraph that are isomorphic to H. Richard M. Wilson and the author find the general formula for the Smith normal form or diagonal form of N_t(H) for all simple graphs H and for a very general class of t-uniform hypergraphs H.
As a continuation, the author determines the formula for diagonal forms of integer matrices obtained from other combinatorial structures, including incidence matrices for subgraphs of a complete bipartite graph and inclusion matrices for multisets.
One major application of diagonal forms is in zero-sum Ramsey theory. For instance, Caro's results in zero-sum Ramsey numbers for graphs and Caro and Yuster's results in zero-sum bipartite Ramsey numbers can be reproduced. These results are further generalized to t-uniform hypergraphs. Other applications include signed bipartite graph designs.
Research results on some other problems are also included in this thesis, such as a Ramsey-type problem on equipartitions, Hartman's conjecture on large sets of designs and a matroid theory problem proposed by Welsh.</p