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Peak-Seeking Controller for Real-Time Mobile Satellite Tracking
Get PDFIncreasingly tightened restrictions on antenna beam-width force the use of higher performance hardware in gimbaled satellite communication transceivers. The need for more precise hardware is forcing the price of gimbal-mounted satellites antennas higher. In addition to the increased cost, as more satellites are launched every year, the demand for antenna systems which can receive data from the new satellites grows. Although algorithms capable of tracking a satellite with a mobile antenna have been developed and characterized in detail, instabilities in the system and cross-axis eects degrade the performance. Since an increase in tracking capability would be most benecial if it did not require extensive hardware changes, this project focuses on improvements to the conical scanning algorithm. An algorithm which is one of the oldest, and most common mobile satellite tracking system implementations. Initial work was done on developing and characterizing a new estimator which could be used while continuing to scan the antenna with as few software modications as possible. After successful development, work was done to eliminate the induced scanning motion and gain observability in the system using nothing but the noise inherent in the system
Ladder Studies of Gapless Quantum Spin Liquids: Spin Bose-metal and SU(2)-invariant Majorana Spin Liquids
Get PDFThe recent experimental realizations of spin-1/2 gapless quantum spin liquids in two-dimensional triangular lattice organic compounds EtMe3Sb[Pd(dmit)2]2 and κ-(ET)2Cu2(CN)3 have stimulated the investigation of the gapless spin liquid theories. The models in dimensions greater than one (D>1) usually involve multispin interactions, such as ring exchange interactions, that are difficult to study, while effective gauge theory descriptions are not well-controlled to give reliable physics information. Driven by the need for a systematic and controlled analysis of such phase, such models on ladders are seriously studied. This thesis first focuses on such ladder models. We propose that the gapless spin liquid phase can be accessed from a two-band interacting electron model by metal-Mott insulator phase transition. We use Bosonization analysis and weak-coupling Renormalization Group to further study the gapless spin liquid state in the presence of Zeeman magnetic fields or orbital magnetic fields. Several new exotic gapless spin liquids with dominant spin nematic correlations are predicted. In such a ladder spin liquid, we also consider the impurity effects. We conclude that the local energy textures and oscillating spin susceptibilities around the impurities are nontrivial and can be observed in the experiments. We then shift our focus to another theoretical candidate, an SU(2)-invariant spin liquid with Majorana excitations, which can also qualitatively explain the experimental phenomenology. We construct an exactly solvable Kitaev-type model realizing the long-wavelength Majorana spin liquid state and study its properties. We find that the state has equal power-law spin and spin-nematic correlations and behaves nontrivially in the presence of Zeeman magnetic fields. Finally, we realize such Majorana spin liquid states on a two-leg ladder and further explore their stability. We conclude the states can be stable against short-range interactions and gauge field fluctuations.</p
Orbits and Interiors of Planets
Get PDFThe focus of this thesis is a collection of problems of timely interest in orbital dynamics and interior structure of planetary bodies.
The first three chapters are dedicated to understanding the interior structure of close-in, gaseous extrasolar planets (hot Jupiters). In order to resolve a long-standing problem of anomalously large hot Jupiter radii, we proposed a novel magnetohydrodynamic mechanism responsible for inflation. The mechanism relies on the electro-magnetic interactions between fast atmospheric flows and the planetary magnetic field in a thermally ionized atmosphere, to induce electrical currents that flow throughout the planet. The resulting Ohmic dissipation acts to maintain the interior entropies, and by extension the radii of hot Jupiters at an enhanced level. Using self-consistent calculations of thermal evolution of hot Jupiters under Ohmic dissipation, we demonstrated a clear tendency towards inflated radii for effective temperatures that give rise to significant ionization of K and Na in the atmosphere, a trend fully consistent with the observational data. Furthermore, we found that in absence of massive cores, low-mass hot Jupiters can over-flow their Roche-lobes and evaporate on Gyr time-scales, possibly leaving behind small rocky cores. In systems where a transiting hot Jupiter is perturbed by a long-period companion, apsidal precession of the hot Jupiter that results from its tidal bulge plays an important, and often dominant role in determining the nature of the dynamical state onto which the system settles. This precession is in turn a strong function of the planet's degree of central concentration and is characterized by the planetary Love number. Utilizing this connection, we have shown that in tidally relaxed systems, measurement of the hot Jupiter's eccentricity directly yields the planetary Love number, which can then be used to place meaningful constraints on the physical structure of the planet with the aid of thermal evolution calculations.
Chapters four through six focus on the improvement and implications of a model for orbital evolution of the solar system, driven by dynamical instability (termed the ``Nice" model). Hydrodynamical studies of the orbital evolution of planets embedded in protoplanetary disks suggest that giant planets have a tendency to assemble into multi-resonant configurations. Following this argument, we used analytical methods as well as self-consistent numerical N-body simulations to identify fully-resonant primordial states of the outer solar system, whose dynamical evolutions give rise to orbital architectures that resemble the current solar system. We found a total of only eight such initial conditions, providing independent constraints for the solar system's birth environment. Next, we addressed a significant drawback of the original Nice model, namely its inability to create the physically unique, cold classical population of the Kuiper Belt. Specifically, we showed that a locally-formed cold belt can survive the transient instability, and its relatively calm dynamical structure can be reproduced. We developed a simple analytical model for dynamical excitation in the cold classical region and showed that comparatively fast apsidal precession and nodal recession of Neptune, during its eccentric phase, are essential for preservation of an unexcited state. Subsequently, we confirmed our findings with self-consistent N-body simulations, suggesting that the cold classical Kuiper belt's unique physical characteristics are a result of its remote formation site. Finally, we showed that the solar system may have initially hosted an additional ice-giant planet, that was ejected from the system during the transient phase of instability. Namely, we demonstrated that a large array of 5-planet (2 gas giants + 3 ice giants) multi-resonant initial states can lead to an adequate formation of the outer solar system, deeming the construction of a unique model of solar system's early dynamical evolution impossible.
The last four chapters of this thesis address various aspects and consequences of dynamical relaxation of planetary orbits through dissipative effects as well as the formation of planets in binary stellar systems. Using octopole-order secular perturbation theory, we demonstrated that in multi-planet systems, tidal dissipation often drives orbits onto dynamical ``fixed points," characterized by apsidal alignment and lack of periodic variations in eccentricities. We applied this formalism towards investigating the possibility that the large orbital eccentricity of the transiting Neptune-mass planet Gliese 436b is maintained in the face of tidal dissipation by a second planet in the system and computed a locus of possible orbits for the putative perturber. Following up along similar lines, we used various permutations of secular theory to show that when applied specifically to close-in low-mass planetary systems, various terms in the perturbation equations become separable, and the true masses of the planets can be solved for algebraically. In practice, this means that precise knowledge of the system's orbital state can resolve the sin(i) degeneracy inherent to non-transiting planets. Subsequently, we investigated the onset of chaotic motion in dissipative planetary systems. We worked in the context of classical secular perturbation theory, and showed that planetary systems approach chaos via the so-called period-doubling route. Furthermore, we demonstrated that chaotic strange attractors can exist in mildly damped systems, such as photo-evaporating nebulae that host multiple planets. Finally, we considered planetary formation in highly inclined binary systems, where orbital excitation due to the Kozai resonance apparently implies destructive collisions among planetesimals. Through a proper account of gravitational interactions within the protoplanetary disk, we showed that fast apsidal recession induced by disk self-gravity tends to erase the Kozai effect, and ensure that the disk's unwarped, rigid structure is maintained, resolving the difficulty in planet-formation. We also showed that the Kozai effect can continue to be wiped out as a result of apsidal precession, arising from planet-planet interactions in a mature planetary system. However, if such a system undergoes a dynamical instability, its architecture may change in such a way that the Kozai effect becomes operative, giving rise to the near-unity eccentricities, observed in some extrasolar planetary systems.</p
Protein Folding and Macromolecular Dynamics: Fundamental Limits of Length and Time Scales
Get PDFIn this thesis, physics-based models of protein folding at the secondary and tertiary level are developed to resolve long-standing issues of protein folding kinetics. As discussed in the Introduction, the main objective is to provide fundamental limits on the length and time scales involved in protein folding. Protein folding is also placed within the broader context of macromolecular dynamics, which is extensively studied in the unfolded, folded, and unfolding regimes for the key molecular motifs of cellular biochemistry, including lipids, nucleic acids, and proteins. The effect of the water hydration and temperature are systematically probed to elucidate the crucial role of the environment in macromolecular stability and dynamics. For a wide range of bio-molecular phenomena, the observed collective behavior is shown to arise directly from first principles. Throughout, the emphasis is on analytic results free of tunable parameters, supported by ensemble-converging computational simulations, and corroborated by experimental evidence
Clefted Equilibrium Shapes of Superpressure Balloon Structures
Get PDFThis thesis presents a numerical and analytical study of the clefted equilibrium shape of superpressure balloon structures. Lobed superpressure balloons have shown a tendency to deploy into unexpected asymmetric shapes, hence their design has to strike a balance between the lower stresses achieved by increasing lobing and the risk of incomplete deployment. Extensive clefting is a regular feature of balloons that are incompletely inflated, and is regularly seen during launch and ascent. Our particular interest in the research is in clefts that remain once a balloon has reached its float altitude and is fully pressurized.
A simplified simulation technique for orthotropic viscoelastic membranes is presented in the thesis. Wrinkling is detected by a combined stress-strain criterion and an iterative scheme searches for the wrinkle angle using a pseudoelastic material stiffness matrix based on a nonlinear viscoelastic constitutive model. This simplified model has been implemented in ABAQUS/Explicit and is able to compute the behavior of a membrane structure by superposition of a small number of response increments. The model has been tested against a published solution for a time-independent isotropic membrane under simple shear and also against experimental results on StratoFilm 420 under simple shear.
A fully three-dimensional finite element model of balloon structures incorporating wrinkling and frictionless contact, able to simulate the shapes taken up by lobed superpressure balloons during the final stages of their ascent has been established. Two different methods have been considered to predict the clefts: (i) deflation and
inflation method and (ii) constraint shift method. In method (i), the starting configuration is obtained by deflating an initially symmetric balloon subject to uniform pressure. The deflation simulation is continued until the differential pressure at the bottom of the balloon has become negative, at which point the balloon is extensively clefted. The balloon is then inflated by increasing the bottom pressure while maintaining a uniform vertical ressure gradient, and the evolution of the shape and stress distribution of the balloon is studied. Two different designs of uperpressure balloons are investigated: a flat facet balloon and a ighly lobed balloon. It is found that the flat facet balloon follows essentially the same path during deflation and inflation, and hence will deploy into a unique, symmetric shape. For the lobed balloon it is found that it follows different paths during deflation and inflation, and deploys into an alternate, clefted equilibrium shape.
Compared to method (i), method (ii) is computationally a more efficient clefting test. The test consists in setting up the balloon in its symmetrically inflated configuration, then breaking the symmetry of this shape by artificially introducing a clefting imperfection, and finally determining the equilibrium shape of the balloon. The clefting imperfection is computed by shifting the constraint at the bottom of the balloon and removing the pressure in the bottom region, below the shifted constraint. The clefting test is applied successfully to three 27~m diameter superpressure balloons that have been tested indoors by NASA, of which one had remained clefted when it was inflated and the other two had deployed completely.
In addition to numerical simulations, formulation of a new cleft factor, employed as an indicator of tendency to S-cleft for superpressure balloons based on constant-stress design has been established through dimensional analysis. The cleft factor, defined as the ratio of clefted volume to cyclically symmetrical volume, is expressed in the form of power law relation of the dimensionless groups. An example illustrates how to calculate the coefficients of the analytical formula and analyze sensitivity of design parameters to clefting.</p
Plasma-Surface Interactions in Hollow Cathode Discharges for Electric Propulsion
Get PDFElectric thrusters generate high exhaust velocities and can achieve specific impulses in excess of 1000 s. The low thrust generation and high specific impulse make electric propulsion ideal for interplanetary missions, spacecraft station keeping, and orbit raising maneuvers. Consequently, these devices have been used on a variety of space missions including Deep Space 1, Dawn, and hundreds of commercial spacecraft in Earth orbit. In order to provide the required total impulses, thruster burn time can often exceed 10,000 hours, making thruster lifetime essential.
One of the main life-limiting components on ion engines is the hollow cathode, which serves as the electron source for ionization of the xenon propellant gas. Reactive contaminants such as oxygen can modify the cathode surface morphology and degrade the electron emission properties. Hollow cathodes that operate with reactive impurities in the propellant will experience higher operating temperatures, which increase evaporation of the emission materials and reduce cathode life. A deeper understanding of the mechanisms initiating cathode failure will improve thruster operation, increase lifetime, and ultimately reduce cost.
A significant amount of work has been done previously to understand the effects of oxygen poisoning on vacuum cathodes; however, the xenon plasma adds complexity, and its role during cathode poisoning is not completely understood. The work presented here represents the first attempt at understanding how oxygen impurities in the xenon discharge plasma alter the emitter surface and affect operation of a 4:1:1 BaO-CaO-Al2O3 hollow cathode.
A combination of experimentation and modeling was used to investigate how oxygen impurities in the discharge plasma alter the emitter surface and reduce the electron emission capability. The experimental effort involved operating a 4:1:1 hollow cathode at various conditions with oxygen impurities in the xenon flow. Since direct measurements of the emitter surface state cannot be obtained because of the cathode geometry and high particles fluxes, measurements of the emitter temperature using a two-color pyrometer were used to determine the oxygen surface coverage and characterize the rate processes that occur during poisoning.
A model describing the material transport in the plasma discharge was developed and is used to predict the barium and oxygen fluxes to the emitter surface during cathode operation by solving the species continuity and momentum equations. The dominant ionization process for molecular oxygen in the plasma gas is resonant charge exchange with xenon ions. Barium is effectively recycled in the plasma; however, BaO and O2 are not. The model shows that the oxygen flux to the surface is not diffusion limited.
Experimental results indicate that the oxygen poisoning rate is slow and that the oxygen poisoning coverage on the emitter surface is less than 3%. A time-dependent model of the reaction kinetics of oxygen and barium at the tungsten surface was developed using the experimental results.
The experiments and kinetics model indicate that the dominant processes at the emitter surface are dissociative adsorption of O2, sputtering of the O2 precursor, and desorption of O. Ion sputtering of the weakly bound O2 precursor state limits the poisoning rate and yields low oxygen coverage. Removal of chemisorbed atomic oxygen is dominated by thermal processes. Based on the low oxygen coverage and long poisoning transients, plasma cathodes appear to be able to withstand higher oxygen concentrations than vacuum cathodes.</p
Following Motion of Early Heart Development at the Cellular Level Using Confocal Microscopy in Transgenic Quail Embryos
Get PDFThe heart has fascinated scientists for centuries, from the days of Leonardo da Vinci to the modern scientist. As tools have developed over the years, we have begun to create a different perspective of how the heart develops and functions from original ideas. Genetics, molecular biology, and microscopes have allowed us to examine the heart with a level of detail that could not have been imagined by da Vinci.
The heart is a complex organ to study due to its innate nature of contracting and relaxing for the entire life of an organism. The motions of systole and diastole complicate any measurements and analysis that can be done. In general, most research has been done in either fixed tissue or dead organisms, neither being ideal for studying a live heart. But current research aims to change our knowledge of cardiogenesis through dynamic imaging of live tissue. With the progress made in the last few years, we have had to revise many of our assumptions about heart development and pumping mechanics. Now, we are at a new stage of research that requires the quantification of cardiogenesis to understand the requirements of heart development to prevent future diseases from occurring.
The following work divides the heart into three areas: 1-dimensional dynamic imaging and analysis of contractions and relaxation to achieve temporal resolution, 4-dimensional modeling of a beating heart during tube formation and early looping to observe individual cellular motion, and 4-dimensional fate mapping of the developing heart tube to visualize development with cellular resolution. With these three perspectives, we are able to quantify the movements of the myocardium and endocardium during development while the heart is beating. This novel approach will give us a wealth of information never seen before.
We use transgenic Japanese quail to highlight the nuclei of individual endothelial cells in the vasculature to analyze the inner tube of the heart, and another transgenic with a ubiquitous marker that fluoresces in every cell of the embryo. The quail heart is comparable to the human heart in that both have 4-chambered hearts, yet the quail is a much easier organism to study. The embryo is transparent and develops outside the mother. The quail embryo can be imaged ex ovo on inverted microscopes, allowing for ease of setup in a controlled environment.
With the use of dynamic imaging and innovative computer software, we were able to reconstruct the live heart while it is beating and developing. By dynamically imaging the endocardium and myocardium, we were able to study the interactions between the two layers by offering unsurpassed visual access to the morphogenetic events of cardiogenesis. Questions that have remained elusive are now being answered with extensive analysis from the data collected. Quantification of cardiogenesis is possible and a detailed fate-map has been produced from this research.</p
Biochemical and Biophysical Characterizations of Immunoglobulin Superfamily Receptors Neogenin and L1
Get PDFImmunoglobulin (Ig) superfamily receptors function in a wide variety of developmental and metabolic processes. We are particularly interested to characterize two Ig superfamily receptors neogenin and L1. The first chapter of the thesis gives a brief review of the biological significance of neogenin and L1 and what has been learned in their functions. In Chapter 2, we described the localization of the hemojuvelin-binding epitope of neogenin to the membrane proximal fifth and sixth fibronectin type III (FNIII) domains, with the sixth FNIII domain contributing the majority of the binding. Chapter 3 presents the crystal structure of this hemojuvelin-binding fragment at 1.8 Å, revealing a nearly linear domain arrangement. Hemojuvelin binding sites have been mapped to one face of the sixth FNIII domain based on sequence alignment between neogenin and DCC (Deleted in Colorectal Cancer), a molecule related to neogenin but does not bind to hemojuvelin. These results should also be informative in understanding the interaction between neogenin and repulsive guidance molecule (RGM), the closest homologue of hemojuvelin. The interaction between neogenin and RGM is known to regulate neuronal survival. Chapter 4, the second part of the thesis, describes our studies of L1-mediated homophilic adhesion using biophysical approaches. We built a basis shape model to describe L1-mediated homophilic adhesion between L1-coated giant unilamellar vesicles and flat substrate. Using confocal microscopy techniques, we were able to reconstruct the three-dimensional shape of an adhered vesicle. We developed an algorithm in order to derive adhesion strength from the configurations of adhered vesicles based on our basis shape model using energy minimization approach
Technologies for Protein Analysis and Tissue Engineering, with Applications in Cancer
Get PDFThe first part of this thesis describes electrolyte transport through an array of 20 nm wide, 20 μm long SiO2 nanofluidic transistors. At sufficiently low ionic strength, the Debye screening length exceeds the channel width, and ion transport is limited by the negatively charged channel surfaces. At source-drain biases > 5 V, the current exhibits a sharp, nonlinear increase, with a 20 − 50-fold conductance enhancement. This behavior is attributed to a breakdown of the zero-slip condition. Implications for peptide sequencing as well as energy conversion devices are discussed.
The next part describes a technology for the detection of the highly aggressive brain cancer glioblastoma multiforme (GBM). In this study, we used an antibody-based microarray to compare plasma samples from glioblastoma patients and healthy controls with respect to the plasma levels of 35 different proteins known to be generally associated with tumor growth, survival, invasion, migration, and immune regulation. Average-linkage hierarchical clustering of the patient data stratified the two groups effectively, permitting accurate assignment of test samples into either GBM or healthy control groups with a sensitivity and specificity as high as 90 % and 94 %, respectively. Using the same 35-protein panel, we then analyzed plasma samples from GBM patients who were treated with the chemotherapeutic drug Avastin (Bevacizumab) and were able to effectively stratify patients based on treatment-responsiveness.
Finally, single-cell resolution patterning of tissue engineered structures is demonstrated. The proper functioning of engineered constructs for tissue and organ transplantation requires positioning different cell types in anatomically precise arrangements that mimic their configurations in native tissues. Toward this end, we have developed a technique that involves two microfluidic-patterning steps run perpendicularly to each other using “anchor” and “bridge” DNA oligomers to create dense arrays of DNA grids which can then be converted into cell arrays. As a proof-of-concept, both a neuron-astrocyte construct and a pancreatic islet construct containing 2 distinct islet cell types were patterned separately as a dense array of cell grids. Once fixed in a hydrogel matrix, layers of patterned cells were then stacked to form 3-D tissue engineered constructs.</p
Biophysics and Protein Engineering with Noncanonical Amino Acids
Get PDFNoncanonical amino acids are tools for expanding and altering the chemical functionalities available within proteins. Much recent work has focused on developing biosynthetic means for incorporating noncanonical amino acids into proteins, and applications of noncanonical amino acids to many problems in science and engineering are emerging. The first portion of this thesis describes established methods to incorporate noncanonical amino acids into proteins and efforts to exploit the properties of noncanonical amino acids in areas such as protein structure determination, protein and organism evolution, modulation of the immune system, and proteomics. Researchers’ creative and successful use of this growing toolkit suggests that noncanonical amino acids will continue to be a valuable asset for dissecting biological problems and imparting proteins with new chemical and physical properties.
Biophysical studies with noncanonical amino acids provide a platform for studying the effects of atom-by-atom manipulations of amino acid side chains on protein properties. The middle portions of this thesis describe work to better understand how protein properties are affected by subtle amino acid side chain manipulations. This work was aided greatly by the establishment of homoisoleucine as a translationally active analog of leucine in bacterial cells. The small side chain differences between leucine, homoisoleucine, and the fluorinated amino acid trifluoroleucine allow for detailed studies on how amino acid side chain size and fluorination affect protein stability and hydration dynamics. Replacement of leucine by homoisoleucine in coiled-coil peptides stabilizes these proteins, as shown by elevation of the coiled coil thermal denaturation temperature. The stabilization observed when homoisoleucine replaces leucine in the peptides is greater than when trifluoroleucine replaces leucine, suggesting that expansion of side chain volume may play a role in protein stabilization irrespective of hydrocarbon or fluorocarbon character.
Studies of water-protein interactions using designed coiled coils containing surface-exposed leucine, homoisoleucine, or trifluoroleucine residues enabled systematic examination of the roles that side chain size and fluorination play in dictating solvation dynamics. Fluorinated side chains appear to exert a large electrostatic drag on nearby water molecules. These results have important implications for the design and engineering of fluorinated proteins due to the critical role water-protein interactions play in many protein properties and functions.
The final portion of this thesis details efforts to engineer the binding properties and chemical reactivity of antibody fragments with noncanonical amino acids. The properties of the single chain variable fragment form of a model anti-digoxin antibody have been studied after replacement of the protein’s methionine residues with methionine analogs containing alkyne, azide, and aliphatic side chains. Experiments with antibody fragments displayed on the surface of Escherichia coli cells revealed that replacement of the methionine residues of the fragment with an analog containing an alkyne side chain reduced the fluorescence levels of cells treated with a fluorescently labeled antigen to background levels, indicating loss of binding function. Replacement of methionine with analogs containing aliphatic and azide side chains left the fluorescence of cells unchanged and reduced by a factor of 0.6, respectively. Fluorescence-activated cell sorting of libraries of cell surface-displayed antibody fragments enabled the isolation of clones functional in multiple amino acid contexts. Cells displaying variants containing alkyne, azide, and aliphatic analogs and treated with fluorescently labeled antigen were more fluorescent than cells displaying the methionine form of the parent antibody fragment by factors of roughly 1.7, 3.5, and 1.3, respectively. Furthermore, the amino acid context used during high-throughput screening experiments appears to affect the frequencies of mutations occurring at various positions within the antibody fragment construct. High-throughput sequencing revealed that populations isolated in different amino acid contexts exhibit mutational rates differing by greater than twenty percent at some residues in the protein.
Characterization of soluble fragments indicated that each noncanonical amino acid used in this study modulates the binding kinetics of antibody fragments in a distinct fashion. Perhaps most interestingly, fragments containing the azide-containing analog azidohomoalanine exhibit improved binding kinetics relative to their methionine-containing counterparts. Replacement of methionine by azidohomoalanine in several variants lowers the dissociation constant of the fragment by up to a factor of two. Chemical conjugation of azide-containing fragments to fluorescent dyes and biotin proved facile with strain-promoted cycloaddition reactions. Quantifications of the extent of reaction using fluorescent dyes revealed that approximately 0.4 dyes had been conjugated per protein, and the resulting conjugates were found to retain their binding function in kinetic and Western blotting assays. Experiments in which azide-containing fragments were displayed on the surface of Escherichia coli cells and subjected to strain-promoted cycloadditions demonstrated that the extent of chemical modification and antigen binding can be monitored simultaneously and used to isolate cells displaying functional, modified proteins. These experiments demonstrate how noncanonical amino acids can be used to modulate multiple properties of antibody fragments and illustrate the feasibility of developing and screening libraries of chemically modified proteins. Evolved, functional bioconjugates may be applicable to a variety of outstanding diagnostic and therapeutic problems.</p