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Atmospheric and Ocean Dynamics of Water Worlds
Get PDFThis dissertation explores the fundamental dynamics that control atmospheric and ocean circulation on water worlds. These planets are defined by the presence of liquid water, which is a minimum requirement for life as we know it, making them compelling targets in the search for extraterrestrial life. This work begins by examining the atmospheric features and surface climates of Earth-like planets with surface liquid water (Chapters I-III). These atmospheres are driven by top-of-atmosphere radiative imbalance. To further our understanding of planetary climate and of the atmosphere’s dynamical controls, particularly with regards to seasonal behavior, we examine the circulation, energy budget, and hydrological cycle responses to changes in shortwave and longwave radiative forcings. This dissertation also explores icy worlds (Chapters IV-V), a type of water world where a liquid water ocean hides beneath a substantial icy shell. Processes occurring at the ocean boundaries can shape the circulation dynamics, stratification, and subsequent heat and salt distributions in the ocean interior. This work presents a new model for exploring these oceans, focusing on ocean-ice interactions and freshwater forcings on Enceladus.</p
Deciphering Regulation in Escherichia coli: From Genes to Genomes
Get PDFAdvances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈ 65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively-parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than 100 E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.</p
Mechanistic Studies of Tail-Anchored Membrane Protein Targeting to the ER
Get PDFThe successful biogenesis – synthesis, delivery, and insertion into designated membranes – of membrane proteins is a crucial cellular process. One particular class of membrane proteins, tail-anchored (TA) proteins have a single transmembrane domain (TMD) that this located at their C-termini and are targeted to membranes post-translationally. Multiple pathways have been identified to target TA proteins to the ER membranes, but designated pathways for targeting TA proteins to the mitochondria remain elusive. The most well understood ER TA protein pathway is the Guided Entry of Tail-anchored proteins (GET) pathway, consisting of six (fungal) or seven (metazoans) proteins, SGTA, Get1-5, and Bag6 (metazoans only), has nearly been studied exclusively in Opisthokants (fungi and metazoans). Here we employed a combination of x-ray crystallography, cryo-electron microscopy, computational modeling, cellular biology, fluorescent imaging, and bioinformatics in order to understand the underlying factors that regulate the targeting of these TA proteins to their correct membranes. Our work reveals that ER-bound TA proteins tend to have a hydrophobic face whereas mitochondria-bound TA proteins contain a charge following their TMD. This finding corroborates our observation that the first component of the GET pathway to interact with TA proteins, SGTA, falls in a category of other hydrophobic segment binding domains, dubbed STI1-domains. Structures presented here demonstrate that the overall structure of Get3 is conserved in organisms as distant as Excavats and Opistokonts, and slight conformational changes in the ATPase allows the described chaperone cascade of the GET pathway to progress. Together these results refine the model for TA protein targeting to the ER membrane.</p
Remodeling Jellyfish
Get PDFWhy are jellyfish round? Circularity facilitates many physiological functions in jellyfish like the moon jelly Aurelia aurita, including swimming and feeding. Previous work suggests that Aurelia might maintain its circularity through its muscle contractions. We use grafting experiments to investigate how these muscle contractions regulate shape in Aurelia and find that the same mechanism Aurelia uses to quickly recover circularity after it is injured can also produce square, oval, and triangular jellyfish. We then turn to modeling to ask what characteristics of the jellyfish muscle contractions and body materials give Aurelia the capability to reorganize its shape. Our simulations suggest that Aurelia body shape is a dynamic equilibrium that is not only reorganized by periodic muscle contractions when it is disrupted, but is also reinforced by the same muscle contractions over the course of normal physiological function.</p
Felt, Imagined, and Seen Touch Share a Substrate in Human Posterior Parietal Cortex
Get PDFOne of the most remarkable aspects of human cognition is its flexibility. We can think new thoughts, infer meaning, plan actions, predict, extrapolate, and so much more. How do our brains enable this versatility? A growing ability to simultaneously record from large populations of single neurons in human cortex has begun to provide insight. Recent studies have identified that shared populations of neurons in posterior parietal cortex (PPC) of a human subject (involved in a brain-machine interface (BMI) clinical trial) encode many aspects of motor cognition: attempted and imagined actions, observed actions and the semantic processing of action verbs. Individual units are complex, but population representations manifest rich associations across neurons, supporting diverse behavioral contexts. Here, in novel work, we establish that the same PPC substrate also encodes aspects of sensory cognition, and unpack the functional organization of information that enables this versatility. We record populations of neurons in PPC of the same human subject, a tetraplegic trial participant implanted with a 4x4 mm microelectrode array. In a series of novel results, we first establish that neurons in this PPC substrate encode actual (or felt) touch to oneself, at short latency, with bilateral receptive fields, organized by body-part. We show that imagined touch to oneself and observed touch to others engage the same substrate. To understand coding mechanisms further, we manipulated the touch location (cheek, shoulder), and the touch type (pinch, press, rub, tap). As in the motor domain, individual neurons exhibit highly variable responses. At the population-level, however, we find that the diverse touch conditions are explained by a small number of subspaces (meaningful groupings of neurons) that encode basic-level, elemental information such as touch location, and touch type. This suggests a compositional basis in PPC, such that various touch conditions are encoded through diverse combinations of common primitive elements. Moreover, these subspaces are generalizable, able to explain novel (held out) data. These principles of compositionality and generalizability suggest a basis by which PPC may support cognitive behaviors such as comprehension, in situations that extend beyond our experiences. In support of this interpretation, we show finally that this PPC substrate encodes seen touch universally – not only to insensate arm regions on the tetraplegic human subject, and to other human individuals, but also to a wide sampling of inanimate objects. As predicted, neural information combines and generalizes across conditions such that touch to objects with more similar features, is more similarly encoded. Taken together, our work is a novel, neuron-level characterization of how high-level cortex in humans may support diverse sensory, motor, and cognitive behaviors. We speculate that populations of neurons in PPC encode rich internal models of the world that can be flexibly repurposed for diverse (and novel) behavioral contexts
Dwarf Galaxies in the Local Universe as Probes of Stellar and Galactic Evolution
Get PDFLow-mass "dwarf" galaxies are numerous, diverse, and relatively simple, making them excellent laboratories for understanding both stellar and galactic evolution. Dwarf galaxies (galaxies with stellar masses 107-109 solar masses) in the nearby universe (out to distances of ~10 Mpc from our own Milky Way, or redshifts z ≾ 0.01), are a particularly interesting population due to their proximity, which allows us to study them in detail on both spatially-resolved and global scales. In this thesis, I present a variety of observational studies investigating star formation and chemical enrichment within nearby dwarf galaxies.
I first use the chemical abundances of individual stars within Local Group dwarf spheroidal galaxies (dSphs) to understand how past stars lived and died. I use this "galactic archaeology" approach to test theoretical models of Type Ia supernovae by investigating the nucleosynthetic products of these supernovae. For example, using medium-resolution spectra from DEIMOS, I measure manganese abundances that place observational constraints on the masses of Type Ia progenitors. I also describe a novel method to measure the delay-time distribution of Type Ia SNe in an individual dSph, which probes the number of white dwarfs involved in Type Ia SNe. Finally, I show how galactic archaeology can also be used to trace star formation using a simple chemical evolution model.
For more distant galaxies, in which individual stars cannot be resolved, galaxy properties can be measured on larger scales. Using the integral field spectrograph KCWI, I produce spatially-resolved maps of dwarf galaxies located in extremely under-dense regions called cosmic voids. The dynamical properties of these galaxies provide insight into the formation of dwarf galaxies in the absence of large-scale environmental effects. On even larger spatial scales, I use photometry to measure the global properties of galaxies and understand the physical processes that drive star formation on galaxy-wide scales.
These studies pave the way for future work with ongoing and upcoming surveys that will map out our local universe---and the dwarf galaxies around us---in unprecedented detail.</p
The Irradiation-Driven Evolution of Gas-Giant Exoplanets
Get PDFNearly thirty years after their initial discovery, we now know of over five thousand extrasolar planets. Intensive efforts have been made to characterize the sizes, masses, orbits, and compositions of these new worlds, and the resulting population challenges our intuition from the Solar System. One striking feature of the exoplanet census is that the vast majority of known planets reside quite close to their host stars, with orbital periods of less than a hundred days. Our galaxy is replete with hot Jupiters, sub-Neptunes, and super-Earths orbiting their stars more quickly than Mercury orbits the Sun. These close-in planets are bombarded by high-energy stellar radiation, which heats their upper atmospheres and triggers mass loss via hydrodynamic escape. This means that planetary sizes, masses, and compositions can be substantially altered from their values at formation. This thesis presents five studies aimed at elucidating the irradiation-driven evolution of close-in extrasolar planets
Singularity Formation in Incompressible Fluids and Related Models
Get PDFWhether the three-dimensional (3D) incompressible Euler equations can develop a finite-time singularity from smooth initial data with finite energy is a major open problem in partial differential equations. A few years ago, Tom Hou and Guo Luo obtained strong numerical evidence of a potential finite time singularity of the 3D axisymmetric Euler equations with boundary from smooth initial data. So far, there is no rigorous justification. In this thesis, we develop a framework to study the Hou-Luo blowup scenario and singularity formation in related equations and models. In addition, we analyze the obstacle to singularity formation.
In the first part, we propose a novel framework of analysis based on the dynamic rescaling formulation to study singularity formation. Our strategy is to reformulate the problem of proving finite time blowup into the problem of establishing the nonlinear stability of an approximate self-similar blowup profile using the dynamic rescaling equations. Then we prove finite time blowup of the 2D Boussinesq and the 3D Euler equations with C1,α velocity and boundary. This result provides the first rigorous justification of the Hou-Luo scenario using C1,α velocity.
In the second part, we further develop the framework for smooth data. The method in the first part relies crucially on the low regularity of the data, and there are several essential difficulties to generalize it to study the Hou-Luo scenario with smooth data. We demonstrate that some of the challenges can be overcome by proving the asymptotically self-similar blowup of the Hou-Luo model. Applying this framework, we establish the finite time blowup of the De Gregorio (DG) model on the real line (ℝ) with smooth data. Our result resolves the open problem on the regularity of this model on ℝ that has been open for quite a long time.
In the third part, we investigate the competition between advection and vortex stretching, an essential difficulty in studying the regularity of the 3D Euler equations. This competition can be modeled by the DG model on S1. We consider odd initial data with a specific sign property and show that the regularity of the initial data in this class determines the competition between advection and vortex stretching. For any 0 < α < 1, we construct a finite time blowup solution from some Cα initial data. On the other hand, we prove that the solution exists globally for C1 initial data. Our results resolve some conjecture on the finite time blowup of this model and imply that singularities developed in the DG model and the generalized Constantin-Lax-Majda model on S1 can be prevented by stronger advection.</p
Search for Beyond Standard Model Physics at BaBar
Get PDFThis thesis reports searches for beyond Standard Model physics in e+e− collisions in two directions.
We report the first search for a dark matter bound state. The existence of dark matter bound states could arise in a simple dark sector model in which a dark photon (A′) is light enough to generate an attractive force between dark fermions. We report herein a search for a JPC = 1 − − darkonium state, the ΥD, produced in the reaction e+e− → γΥD, ΥD → A′A′A′, where the dark photons subsequently decay into pairs of leptons or pions, using data collected with the BaBar detector. No significant signal is observed, and we derive limits on the γ − A′ kinetic mixing (ϵ) as a function of the dark sector coupling constant for 0.001 < mA′ < 3.16 GeV and 0.05 < mΥD < 9.5 GeV. Bounds on the mixing strength ϵ down to 5 × 10 − 5 − 10 − 3 are set for a large fraction of the parameter space.
We also report a measurement of R(D) = B(B → D̄τν̄τ)/B(B → D̄ℓν̄ℓ) and R(D*) = B(B → D̄*τν̄τ)/B(B → D̄*ℓν̄ℓ), where ℓ refers to either an electron or muon. We select samples by reconstructing tag-side B mesons in semileptonic decays and signal-side τ in a purely leptonic decay. Using data collected with the BaBar detector, we measure R(D) = 0.316 ± 0.062(stat) ± 0.019(syst) and R(D*) = 0.226 ± 0.022(stat) ± 0.012(syst), which agree with the Standard Model expectations by 0.26σ and 1.10σ, respectively. Taken together, the results are in agreement with the Standard Model within 1.51σ level.</p
Analytical Chemistry Investigations Toward Understanding the Mechanism of Nitrogenase from Azotobacter vinelandii and the Role of the 4Fe-4S Cluster of Dna2 from Saccharomyces cerevisiae
Get PDFIron sulfur clusters are ubiquitous metal cofactors that play a variety of roles in many enzymes important for health and the climate. The bacterial nitrogenase enzyme, which supports the growth of all organisms by converting atmospheric dinitrogen into ammonia, contains three different redox-active iron sulfur clusters that are central to its function. Dna2, found in all eukaryotes, is integral to genome maintenance and coordinates an iron sulfur cluster of unknown function. Many details of the nitrogenase mechanism are yet to be revealed and pursuits toward this goal will support human efforts to develop more sustainable solutions to nitrogen fixation, which is required for maintaining our food supply. Thorough characterization of the DNA-maintenance enzyme Dna2 will allow us to develop better technologies for cancer prevention and treatment. Development and optimization, as well as technical critique, of a variety of analytical chemistry techniques were performed toward the goal of increasing our understanding of these two important enzymes. Yeast Dna2 was successfully overexpressed and purified from E. coli and spectroscopic features of the 4Fe-4S cluster were characterized. Toward measuring the redox potential of the 4Fe-4S cluster of Dna2, the DNA-modified electrochemistry technique was evaluated leading to the discovery that the source of electrochemical signals proposed to be due to redox activity of 4Fe-4S clusters in DNA-binding proteins are actually due to the redox activity of Fe-EDTA complexes that form in the buffers of these proteins. These results will support future scientists in accurately interpreting the electrochemical signals from DNA-modified electrochemistry. The solvent isotope effect of nitrogenase reduction was investigated by measuring deuterium incorporation into nitrogenase products by GC-MS, FTIR and NMR, revealing that the enzyme exhibits modest preference for H vs. D in acetylene reduction to ethylene, but significant preference for H in the reduction of protons to dihydrogen. These results indicate that there are distinct mechanisms of H atom transfer in the reduction of these two substrates and the experimental design that we developed opens the door for a new avenue of nitrogenase research to reveal the solvent isotope effects of reduction of a variety of different substrates under different experimental conditions. Finally, a new ATPase assay using ion chromatography was developed to measure ATPase activity of the Fe protein, which provides a tool for future pursuits toward quantifying inorganic phosphate release by ATPases and led to our surprising result that the apo-form of the Fe protein is active in ATP hydrolysis.</p