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Formation and Migration Histories of Giant Exoplanets in Multi-stellar Systems
Get PDFThe first planets discovered outside of our solar system were very different from the solar system planets. These discoveries raised new challenges to planet formation models, which were designed to explain the origin of the solar system planets. One particularly intriguing population, the "hot Jupiters" were some of the first planets discovered. These gas giant planets have masses similar to Jupiter and Saturn, however, they were found on orbits 100 times closer to their star than Jupiter is to the sun. Proposed formation scenarios involve models that argue for formation at presently observed locations, but these are challenged by the lack of planet-building materials so close to the host star. Other models assume these planets form at more moderate locations, perhaps in a manner similar to Jupiter and Saturn, followed by inward migration via some other mechanism. These models are challenged by the lack of a known migration mechanism.
This dissertation compiles three studies conducted over the past five years to investigate the formation and migration histories of gas giant exoplanets. After the discovery of the first hot Jupiter, additional discoveries revealed some population characteristics that could provide evidence for certain formation or migration scenarios. A large fraction of hot Jupiters were found to have eccentric orbits and/or misaligned orbits relative to the star's spin axis. These properties suggest that a gravitational interaction with an additional massive object may have played a role in the dynamical history of these hot Jupiters. Studies of stellar multiplicity for nearby, sun-like stars have also revealed that multi-stellar systems are common.
The studies presented in this dissertation investigate whether stellar companions to giant planet systems influence the planets. In the first and second study, we conduct a survey for stellar companions around stars that host hot Jupiters detected by the transiting method. The first study examines whether stars hosting misaligned planets are more likely to host a companion star. We found no such correlation, suggesting that stellar companions do not play a dominant role in causing planetary misalignment. In the second study, we look at the population of stellar companions as a whole to quantify the fraction of hot Jupiters that might have migrated due to stellar interactions. We find that less than 20% of hot Jupiters might have experienced this migration scenario. However, we do find that hot Jupiters are three times more likely to be in a wide multi-stellar system compared to nearby stars that do not host hot Jupiters, suggesting some other connection between the companion star and the giant planet.
In the third study, we search for stellar companions around stars that host giant planets over a wide range of separations, from the close-in hot Jupiters to giant planets as far away as Jupiter is to our sun. These planets were found via the radial velocity method. We compare the giant planets' orbital properties for single- and multi-stellar systems to determine whether planets in multi-stellar systems show some evidence for star-planet interactions. With the current dataset, we find no evidence to support the hypothesis that planets in multi-stellar systems have a different set of orbital properties.
Finally, we present preliminary results of an ongoing survey to understand giant planet formation on the other extreme end. Instead of hot Jupiters on close-in orbits, this survey seeks to explain the origin of the very distant giant planetary mass objects found by direct imaging surveys. These objects are often found on separations that are ten to one hundred times farther away than Neptune is to our sun. Due to their distance and size, it's not certain if these objects are some of the biggest planets in existence or if they are the smallest stars. This new survey will search for planets to serve as the link between known giant exoplanets and these unknown directly imaged objects.</p
Biophysical Studies of Ligand-gated Ion Channels
Get PDFThis dissertation describes building a methodology for and the biophysical studies of ligand-gated ion channels (LGICs).
The primary focus of the first half of this dissertation is on developing a fluorescence-based assay to broadly study LGICs. Chapter 2 describes the site-selective incorporation of a turn-on fluorophore via unnatural amino acid mutagenesis on the mouse muscle-type nicotinic acetylcholine receptor (nAChR) in Xenopus oocytes as a proof-of-principle study. This method has proven to yield very low levels of undesired fluorescent background, which was a problem for previous incorporation techniques. Chapter 3 describes efforts towards imaging this in vivo system using lifetime imaging with efforts hampered by the inability to detect a clear signal. Chapter 4 describes efforts to apply the lifetime imaging approach towards a different system involving 5-HT3 proteins fused to fluorescent proteins in COS-7 cells.
The second half of this dissertation focuses on studies of menthol, a flavorant added to cigarettes that contributes to smoking addiction, as a negative allosteric modulator of the αβ42 nAChR. Chapter 5 reveals the stereochemical effects, or rather lack of, of menthol on the two stoichiometries of the αβ42 receptor. Chapter 6 seeks to identify the residue interactions with menthol of the αβ42 receptor using a combination of computational and experimental studies.</p
Essays on Information Collection
Get PDFThis thesis is devoted to the problem of information collection from theoretical and experimental perspectives.
In Chapter 2, I characterize the unique optimal learning strategy when there are two information sources, three possible states of the world, and learning is modeled as a search process. The optimal strategy consists of two phases. During the first phase, only beliefs about the state and the quality of information sources matter for the optimal choice between these sources. During the second phase, this choice also depends on how much the agent values different types of information. The information sources are substitutes when each individual source is likely to reveal the state eventually, and they are complements otherwise.
In Chapter 3, co-authored with Li Song, we conducted an experiment which demonstrates that even in a simple four person circle network people appear to fail to account for possible repetition of information they receive. Moreover, we show that this phenomenon can be partially attributed to rational considerations, which take into account other people’s deviations from optimal behavior.
In Chapter 4, co-authored with Marcelo A. Fernández,we model overconfidence as if a decision maker perceives information as being more precise than it actually is. We show that the effect of overconfidence on the quality of the final decision is shaped by three forces, overestimating the precision of future information, overestimating the precision of past information and overestimating the amount of information to be collected in the future. The first force pushes an overconfident decision maker to collect more information, while the second and the third forces work in the other direction.</p
Unveiling the Structure of Active Galactic Nuclei with Hard X-ray Spectroscopy
Get PDFDespite the long history of studies of active galactic nuclei (AGN), details of the structure of the accretion flow onto supermassive black holes are far from clear. Work presented in this thesis is directed at unveiling properties of AGN structure through broadband X-ray spectroscopy, with particular emphasis on the hard X-ray band (photon energies above 10 keV). With its unprecedented sensitivity in this energy band, the NuSTAR telescope provides the key observational diagnostics of the properties of the AGN X-ray source, the corona, and the surrounding gas in the accretion disk, the broad-line region, and the torus.
The first study presented in this thesis focuses on measurements of the optical depth and the temperature of the plasma in the corona of an obscured AGN. Fitting theoretical spectral models for coronal emission to the NuSTAR data constrained these two basic physical parameters under the assumption of either spherical or disk-like geometry for the corona.
The remainder of the thesis is dedicated to studies of the anisotropic obscuring structure broadly referred to as the torus. One of them is a case study of three heavily obscured AGN with spectra dominated by the X-ray light scattered and reprocessed in the torus, where it is possible to constrain one of the basic torus properties -- its globally averaged column density. The following study presents the calculation of a new spectral model for reprocessing of the intrinsic X-ray continuum within the torus. Its added flexibility compared to previously available models allows for both the average column density of the torus and its covering factor to be constrained from broadband X-ray spectra of a wide variety of AGN.
The final part of the thesis in based on a large survey of the local obscured AGN population performed with NuSTAR. Spectral modeling of more than a hundred individual AGN, including both old and new spectral models, is presented. From analyses of the X-ray data for a large and representative AGN sample, for the first time, it is found that their tori preferentially have high covering factors and average column densities close to unity optical depth for Compton scattering.</p
Photonic Crystal Waveguides for Integration into an Atomic Physics Experiment
Get PDFStrongly interacting systems of atoms and photons are an important resource in many active areas of research, including quantum information science, quantum simulation, and metrology. Frequently, the strength of these interactions is enhanced by using an optical resonator to confine light to a small volume. In recent years, there have been efforts to replace traditional Fabry–Pérot resonators, formed from macroscopic mirrors, with micro- and nano-fabricated systems, leveraging techniques and infrastructure from semiconductor manufacture to scalably produce high-quality, small mode volume waveguides and resonators. Of particular interest are nano-fabricated photonic crystals, in which very fine control over modal and dispersion properties is possible. Here I describe our efforts to reliably produce photonic crystal waveguides with guided modes designed to trap and interrogate an array of ultracold cesium atoms. Specifically, I present models capturing band placement, modal structure, finite photonic crystal effects, and waveguide input and output coupling; I discuss the techniques we use to fabricate our photonic crystal waveguides; and I describe our characterization capabilities and the packaging and installation of the waveguides into the atomic physics system.</p
DarwinDock and GAG-Dock: Methods and Applications for Small Molecule Docking
Get PDFComputational modeling is an effective tool in studying complex biological systems. Docking of small molecule ligands in particular is useful both in understanding the functioning of proteins as well as in the development of pharmaceuticals. Together with experiment, modeling can often provide a thorough picture of a given system. Computation can often provide details that are difficult or impossible to determine experimentally, while experiments provide guidance on what calculations are useful or interesting. Our goal is to extend computational modeling, specifically ligand docking, to systems not previously possible, such as the challenging glycosaminoglycan (GAG) systems. In order to do this it was first necessary to develop an automatic way of performing docking without extensive user input and experimental knowledge to narrow the list of candidate poses. DarwinDock represents our efforts in this respect. It is a method for small-molecule docking that separates pose generation and scoring into separate stages, which allows for complete binding site sampling followed by efficient, hierarchical sampling. Our convergence criteria for complete sampling allows for diverse systems to be studied without prior knowledge of how large a set of poses needs to be to span a given binding site, making the procedure more automatic. We also replace bulky, nonpolar residues with alanine, which we refer to as "alanization". This allows the ligand to interact more closely with polar sidechains, which help to orient the ligand. Additionally, alanization reduces the impact of incorrect sidechain placement on ligand placement, a concern that sometimes requires user intervention. With DarwinDock working for standard small molecules, it was then necessary to modify the procedure to work on challenging GAG ligands, which are large and have strong negative charges. A modification to DarwinDock – GAG-Dock – allows the method to be applied to GAGs and protein surface interactions. GAGs are large, linear polysaccharides with strong negative charge. They typically interact with the surfaces of proteins, rather than the cavities favored by most small-molecule drugs. GAG-Dock systematically samples the protein surface for unknown binding sites and modifies the pose generation to allow for large, surface-interacting ligands. GAG-Dock allowed us to study several systems important for neuronal development and answer interesting questions posed by experiment. Finally, we needed a way to validate our predictions for GAG binding sites. We used a systematic approach to identify sets of beneficial mutations to the GAG binding sites by building up from individual in silico mutations. Standard mutation experiments typically employ large mutations, such as arginine to alanine, which decrease or destroy binding. However, such information is not always definitive, as large mutations can have wide-ranging effects beyond direct protein-ligand interactions. Mutations that increase binding, however, are less ambiguous because they must form new interactions with the ligand in order to affect binding energies or affinity. Therefore, we have identified and proposed sets of mutations for our GAG predictions for PTPs, NgR1, NgR3, and EphB3. We encourage our experimentalist colleagues to try these mutations and validate our predictions.</p
Morphogenesis of the Arabidopsis Shoot Apical Meristem
Get PDFPhyllotaxis patterns in plants, or the arrangement of leaves and flowers radially around the shoot, have fascinated both biologists and mathematicians for centuries. The current model of this process involves the lateral transport of the hormone auxin through the first layer of cells in the shoot apical meristem via the auxin efflux carrier protein PIN1. Locations around the meristem with high auxin concentration are sites of organ formation and differentiation. Many of the molecular players in this process are well known and characterized. Computer models composed of all these components are able to produce many of the observed phyllotaxis patterns. To understand which parts of this model have a large effect on the phenotype I automated parameter testing and tried many different parameter combinations. Results of this showed that cell size and meristem size should have the largest effect on phyllotaxis. This lead to three questions: (1) How is cell geometry regulated? (2) Does cell size affect auxin distribution? (3) Does meristem size affect phyllotaxis? To answer the first question I tracked cell divisions in live meristems and quantified the geometry of the cells and the division planes using advanced image processing techniques. The results show that cell shape is maintained by minimizing the length of the new wall and by minimizing the difference in area of the daughter cells. To answer the second question I observed auxin patterning in the meristem, shoot, leaves, and roots of Arabidopsis mutants with larger and smaller cell sizes. In the meristem and shoot, cell size plays an important role in determining the distribution of auxin. Observations of auxin in the root and leaves are less definitive. To answer the third question I measured meristem sizes and phyllotaxis patterns in mutants with altered meristem sizes. These results show that there is no correlation between meristem size and average divergence angle. But in an extreme case, making the meristem very small does lead to a switch on observed phyllotaxis in accordance with the model
Understanding Co-Translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models
Get PDFWe describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth
Investigating the Death of the Early Paleozoic Moyero River Geomagnetic Superchron: Middle Ordovician Paleomagnetism from Estonia
Get PDFFlat-lying Early and Middle Ordovician limestones exposed on the North margin of Estonia provide key insights into the early Paleozoic biosphere and climatic history of the Baltic Platform, and potentially offer a site for calibrating the duration of the proposed Moyero River Reversed Superchron. Past paleomagnetic analyses on these rocks have been focused primarily on determining paleomagnetic pole positions and have been hampered by relatively weak remanent magnetizations. We therefore applied techniques of the Rock and Paleomagnetic Instrument Development (RAPID) consortium using thin-walled, low-noise quartz glass sample holders on an automatic system to enhance magnetostratigraphic resolution. Our results, based on over 300 oriented core samples spanning the stratigraphic interval from the Volkhov stage, up through the Lasnamägi stage, confirm previous work isolating a stable characteristic magnetization of reversed polarity, and furthermore confirm the presence of an interval of magnetically Reversed polarity spanning an interval of at least 15 million year duration. In addition, we recognize a magnetic overprint of presumed Normal polarity held in antiferromagnetic phases, of presumed Permian age, based on the apparent polar wander path given by (Plado et al., 2010)
Design and Applications of a Decade-Spanning Terahertz Frequency Comb Spectrometer: Doppler-limited Rotational Spectroscopy of Methanol and Methanol-OD
Get PDFThis thesis details the design and applications of a terahertz (THz) frequency comb spectrometer. The spectrometer employs two offset locked Ti:Sapphire femtosecond oscillators with repetition rates of approximately 80 MHz, offset locked at 100 Hz to continuously sample a time delay of 12.5 ns at a maximum time delay resolution of 15.6 fs. These oscillators emit continuous pulse trains, allowing the generation of a THz pulse train by the master, or pump, oscillator and the sampling of this THz pulse train by the slave, or probe, oscillator via the electro-optic effect. Collecting a train of 16 consecutive THz pulses and taking the Fourier transform of this pulse train produces a decade-spanning frequency comb, from 0.25 to 2.5 THz, with a comb tooth width of 5 MHz and a comb tooth spacing of ~80 MHz. This frequency comb is suitable for Doppler-limited rotational spectroscopy of small molecules. Here, the data from 68 individual scans at slightly different pump oscillator repetition rates were combined, producing an interleaved THz frequency comb spectrum, with a maximum interval between comb teeth of 1.4 MHz, enabling THz frequency comb spectroscopy.
The accuracy of the THz frequency comb spectrometer was tested, achieving a root mean square error of 92 kHz measuring selected absorption center frequencies of water vapor at 10 mTorr, and a root mean square error of 150 kHz in measurements of a K-stack of acetonitrile. This accuracy is sufficient for fitting of measured transitions to a model Hamiltonian to generate a predicted spectrum for molecules of interest in the fields of astronomy and physical chemistry. As such, the rotational spectra of methanol and methanol-OD were acquired by the spectrometer. Absorptions from 1.3 THz to 2.0 THz were compared to JPL catalog data for methanol and the spectrometer achieved an RMS error of 402 kHz, improving to 303 kHz when excluding low signal-to-noise absorptions. This level of accuracy compares favorably with the ~100 kHz accuracy achieved by JPL frequency multiplier submillimeter spectrometers. Additionally, the relative intensity performance of the THz frequency comb spectrometer is linear across the entire decade-spanning bandwidth, making it the preferred instrument for recovering lineshapes and taking absolute intensity measurements in the THz region. The data acquired by the Terahertz Frequency Comb Spectrometer for methanol-OD is of comparable accuracy to the methanol data and may be used to refine the fit parameters for the predicted spectrum of methanol-OD.</p