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High Temperature Electron-Phonon and Magnon-Phonon Interactions
Get PDFComputational materials discovery and design has emerged in order to meet the surge in demand for new materials for applications ranging from clean alternative energy to human welfare. This acceleration of materials discovery is exhilarating, but the applications of new advanced materials can be limited by their thermodynamic stability. Accurate calculations of the Gibbs free energy, a measure of thermodynamic stability, require a deep understanding of atomic vibrations, a main source of entropy in materials. This deep understanding of atomic vibrations requires us to treat phonons (quantized lattice vibrations) beyond the harmonic model by considering their interactions with various excitations. In this thesis, I present the effects of high temperature interactions of phonons with electrons and magnetic excitations on the thermodynamics of FeTi, vanadium, and Pd3Fe.
A combination of ab initio calculations, inelastic neutron scattering (INS), and nuclear resonant inelastic x-ray scattering (NRIXS) showed an anomalous thermal softening of the M5− phonon mode in B2-ordered FeTi and a thermal stiffening of the longitudinal acoustic N phonon mode in body-centered-cubic vanadium. Computational investigations involving electronic band unfolding were performed to identify the nesting features on Fermi surfaces crucial to high temperature electron-phonon interactions in FeTi and vanadium. These investigations showed that the Fermi surface of FeTi undergoes a novel thermally driven electronic topological transition (ETT), in which new features of the Fermi surface arise at elevated temperatures. This ETT was also observed in vanadium, but the effects were overtaken by the thermal smearing of the Fermi surface that decreased the rate of electron-phonon scattering.
Iron phonon partial densities of states of Pd3Fe were measured with NRIXS from room temperature through the Curie transition at 500 K. The experimental results were compared to ab initio spin-polarized calculations that modeled the finite-temperature thermodynamic properties of Pd3Fe with magnetic special quasirandom structures (SQSs) of magnetic moments. The scattering measurements and first-principles calculations showed that the iron partial vibrational entropy is close to what is predicted by the quasiharmonic approximation owing to a cancellation of effects: phonon-phonon and magnon-phonon interactions approximately cancel a ferromagnetic optical phonon stiffening.</p
Spatio-Temporal Response of a Compliant-Wall, Turbulent Boundary Layer System to Dynamic Roughness Forcing
Get PDFThis thesis investigates the interaction between an elastic compliant surface and a turbulent boundary layer exposed to dynamic roughness forcing. The goals are to explore a unique perspective of this fluid-structural problem through narrow-band forcing, and to further develop the understanding of dynamic roughness. Water tunnel experiments are designed with flow and surface measurements, both phase-locked to the roughness actuation. This enables a phase-averaged analysis, which leverages the deterministic input to isolate the temporally correlated components of the flow and surface response. Identifying the directly interacting velocity and deformation modes allows the complex, fluid-structural system to be studied in a more tractable, input-output manner.
The first experiment is conducted with a smooth-wall turbulent boundary layer forced by dynamic roughness, and contributes to the knowledge of this type of forcing through structure-resolved particle image velocimetry. This allows for the streamwise-spatial nature and the wall-normal velocity component (v) of the roughness-forced flow to be explored, which had not been previously studied. A spatial amplitude modulation is observed in the synthetic structure and investigated directly through the spatial spectra. Through a parametric study and an empirical fit, the forcing frequency may now be selected to target a particular streamwise length scale.
The second experiment implements a gelatin sample subject to an unforced turbulent boundary layer. The surface response is characterized and serves as a base case with which to identify the roughness-forced component of the deformations. This naturally leads to the third experiment, where the full compliant-wall, dynamic-roughness-forced turbulent boundary layer system is considered. The surface response to the synthetic flow structure is confirmed, which sets the stage for a comparison between the smooth-wall and compliant-wall data to study the effect of the compliant surface.
The smooth/compliant comparison is guided by a resolvent analysis, which predicts a virtual wall feature in the v velocity mode for the elastic material under consideration. Using this prediction to inform a conditional average, the virtual wall is revealed in the experimental data. Thus, the action of the elastic surface is interpreted as opposing the v velocity near the wall, in a manner similar to wall-jet opposition control.
Previous experimental studies of viscoelastic compliant surfaces have demonstrated the potential for turbulent drag reduction, though either indirectly via the turbulence intensities or with relatively high skin friction measurement error. A common observation in these studies was the importance of the interaction between the surface and the coherent structures in the flow. To that end, this study has isolated and modeled the behavior of the fluid-structural system with a single spatio-temporal scale generated by dynamic roughness forcing. The results provide a physical interpretation of the effect of an elastic surface on turbulent boundary layer flow structures and informs the ongoing development of a reduced-order modeling tool in the resolvent analysis.</p
Reaction Development for the Total Syntheses of the Terpenoid Natural Products (+)-Psiguadial B, (+)-Rumphellaone A, and (–)-Isodocarpin
Get PDFThe de novo synthesis of bioactive natural products provides an opportunity to learn more about the mechanism of bioactivity and to develop novel chemistry that is of interest to the synthetic community. Herein, we describe our strategy for the total synthesis of the trans-fused cyclobutane containing meroterpenoid (+)-psiguadial B. Key to this strategy was the development of a photochemical Wolff Rearrangement with asymmetric ketene aminolysis. A palladium-catalyzed C–H alkenylation is used to build structural complexity, and we use two different epimerization strategies to perform an enantiodivergent synthesis of (+)-psiguadial B.
This strategy was explored further and applied to the synthesis of chiral cyclobutanes through a 1,2-difunctionalization strategy, wherein a C–H arylation forges one carbon-carbon bond and a subsequent decarboxylative cross-coupling enables functionalization at the adjacent carbon. This strategy enabled the asymmetric total synthesis of (+)-rumphellaone A in 9 steps.
This report also highlights the work we have conducted in the development of a unified strategy for the enmein-type ent-kauranoid natural product, (–)-isodocarpin. We detail our investigation of a convergent cross-electrophile coupling as a means to build the core of (–)-isodocarpin. We also discuss our development of a 1,2-addition/semi-Pinacol rearrangement strategy for the preparation of all-carbon quaternary centers, which can be elaborated to enmein-type ent-kauranoid natural product scaffolds.</p
How Single Cells Sense Smad3 Signal
Get PDFAnimal cells possess the remarkable ability to send, receive, and respond to molecular signals. Accurate processing of these signals is essential for the development and maintenance of complex cell fates and organization. The regulation of cell behavior in response to signal is mediated by signal transduction pathways, which are highly conserved protein-protein interaction networks. Recent work has shown that the activation of biomolecular networks is highly sensitive to natural cellular variation in protein levels, making it unclear how these pathways accurately and reliably transmit signals in single cells. In this thesis, I address this question in the Transforming Growth Factor-β (Tgf-β) pathway, a major intercellular signaling pathway in animal cells. First, we asked whether extracellular signal is accurately transduced into pathway activation in single cells. Examining pathway dynamics in live reporter cells, we found evidence for fold-change detection. Although the level of nuclear Smad3 varied across cells, the fold change in the level of nuclear Smad3 was a more precise outcome of ligand stimulation. Indeed, by measuring Smad3 dynamics and gene expression in the same cells, we confirm that the fold-change in Smad3 carries signal in the pathway. These findings suggest that cells encode Tgf-β signal in a precise Smad3 fold-change as a strategy for coping with cellular noise. Second, we brought two significant advancements, which enabled us to ask how tightly signaling dynamics dictates target gene expression. By imaging endogenous dynamics of both signaling and gene expression in clonal cells, and correlating the full dynamics with a non-manifold learning approach, we show that knowing the full dynamics of Smad3 is necessary but not sufficient to predict the full dynamics of target gene expression. Indeed, we find evidence for the role of mTOR, MEK5, and cell cycle as cell-specific variables that influence how a cell responds to Smad3. This demonstrates the extent to which, even across clonal cells, response to signal considerably varies, as each cell computes decisions based on its own internal state
Genetic Determinants of Growth Arrest Survival in the Bacterial Pathogen Pseudomonas aeruginosa and the Role of Proteases
Get PDFGrowth arrest is the dominant mode of microbial existence on the planet, yet the molecular mechanisms that underpin survival during growth arrest remain far less studied than other growth states. A better understanding of these mechanisms would provide valuable insight into the activity of microbial communities in both biogeochemical and clinical contexts, including the treatment of chronic infections. This thesis investigates the genetic requirements for survival of the bacterium Pseudomonas aeruginosa, a metabolically versatile opportunistic pathogen that thrives in diverse environments in which growth arrest is often caused by energy limitation. After reviewing our current knowledge of the strategies used by growth-arrested bacteria to adjust metabolism, regulate transcription and translation, and maintain the chromosome, I perform a functional genomic screen to identify genes that promote fitness of P. aeruginosa during growth arrest caused by carbon or oxygen starvation. I find that P. aeruginosa can survive for days to weeks in these energy-starved conditions by maintaining a reduced steady-state level of ATP, and that many functional classes of genes are required for fitness. Intriguingly, a majority of genetic fitness determinants differ between carbon and oxygen starvation, despite the common endpoint of reduced ATP levels in these two conditions. Among the few genes generally required for fitness are the stress response sigma factor encoded by rpoS and the heat shock protease encoded by ftsH. Using independently-generated deletion strains, I show that mutants in distinct functional categories exhibit temporal fitness dynamics during oxygen starvation: regulatory genes generally manifest a phenotype early during growth arrest, whereas genes involved in cell wall metabolism are required later. Building on these findings, I investigate the functional role of FtsH during growth arrest more deeply and find a surprising negative genetic interaction between ftsH and rpoS, with mutations in rpoS alleviating the fitness defects of ΔftsH during growth arrest. I also find that FtsH functions coordinately with the other conserved heat shock proteases to maintain cellular integrity and delay aging of P. aeruginosa during growth arrest. Finally, I investigate the role of FtsH and the other heat shock proteases in a novel N-terminal protein degradation pathway and find that the molecular details of this pathway likely differ between E. coli and P. aeruginosa. Together, these findings uncover essential molecular processes that promote fitness of an important bacterial pathogen during growth and survival.</p
Data: Implications for Markets and for Society
Get PDFEvery day, massive amounts of data are gathered, exchanged, and used to run statistical computations, train machine learning algorithms, and inform decisions on individuals and populations. The quick rise of data, the need to exchange and process it, to take data privacy concerns into account, and to understand how it affects decision-making, introduce many new and interesting economic, game theoretic, and algorithmic challenges.
The goal of this thesis is to provide theoretical foundations to approach these challenges. The first part of this thesis focuses on the design of mechanisms that purchase then aggregate data from many sources, in order to perform statistical tasks. The second part of this thesis revolves around the societal concerns associated with the use of individuals' data. The first such concern we examine is that of privacy, when using sensitive data about individuals in statistical computations; we focus our attention on how privacy constraints interact with the task of designing mechanisms for acquisition and aggregation of sensitive data. The second concern we focus on is that of fairness in decision-making: we aim to provide tools to society that help prevent discrimination against individuals and populations based on sensitive attributes in their data, when making important decisions about them. Finally, we end this thesis on a study of the interactions between data and strategic behavior. There, we see data as a source of information that informs and affects agents' incentives; we study how information revelation impacts agent behavior in auctions, and in turn how a seller should design auctions that take such information revelation into account.</p
Effects of Branching on Conformation, Crystallization, and Self-Assembly of Polymers
Get PDFThe central feature of bottlebrush polymers is the stiffening of the main-chain (MC) due to side-chain side-chain (SC-SC) repulsion, amplified by densely grafting long SCs, particularly in good solvent conditions. The expectation of stiffening has led most prior studies to refer to bottlebrush polymers as "worm-like," "cylindrical" or a "self-avoiding walk (SAW) of superblobs". However, there is no direct evidence of stiffening of the main-chain and measurements of the overall segment distribution of the whole molecule have failed to discriminate between competing models. Here, we provide a set of measurements of the main-chain conformation (neutron scattering in a solvent that is contrast matched to the side chains) together with the overall conformation of the bottlebrush as a whole (light, X-ray, and neutron scattering) under conditions that highlight SC-SC repulsion: the side-chains are relatively long compared to prior literature, the concentration of bottlebrushes is low, and the solvent quality is good. Surprisingly, the main-chain has a conformation that does not conform to any prior models: all three main-chain lengths examined showed a window of length scales in which the scattering power increased less than linearly with length scale. In particular, the MC conformation is not worm-like. Direct observation of the main-chain conformation and the overall conformation discriminates among models more powerfully than the overall conformation alone. Inspired by the Paturej-Rubinstein tension blob model, we examined a conceptual model in which tension of the MC accumulates with distance from the ends of the MC and found that it can capture the salient features of both the MC- and whole bottlebrush scattering more gradually than previous theoretical models predicted. The conceptual model also explains our observation of a substantial increase in anisometry with increasing MC length, opposite to a worm-like chain. The results indicate that synthetically accessible bottlebrushes are not fractals; they cannot have self-similar (fractal) conformation because each increase in main-chain length accesses greater side-chain crowding than any of its shorter siblings. We expanded the work to understand the behavior in θ conditions and shorter side-chains expected to have reduced tension as well as the behavior at different concentrations.
In addition, we characterized the interplay of self-assembly and polymer crystallization through analysis of three representative bottlebrush copolymer systems. Our results revealed a surprising number of unexpected behaviors ranging from unexpected morphologies, control of thermal properties even to complete suppression of phase transitions, and control of the orientation of crystal stem with respect to the morphological interface, which highlights the potential of the bottlebrush architecture.</p
Improving Site Response Analysis for Earthquake Ground Motion Modeling
Get PDFThe modeling of earthquake-induced ground motions plays an important role in the quantification of seismic hazards, which contributes to the ultimate goal of saving lives and reducing economic loss. Site response is a natural phenomenon in which soils in the earth’s shallow crust alter the amplitude, frequency content, and duration of earthquake-induced ground motions. Therefore, improvements in the research of site response directly contribute to ground motion modeling, and eventually to seismic hazard quantification.
This thesis presents two models that advance the current research in site response.
The first model provides a tool to predict near-surface shear-wave velocity profiles from Vs30 (a proxy that represents the general stiffness of a site). This model bridges the gap between the lack of information about near-surface soil properties and the need to model site response on a regional scale (city, county, or above).
The second model is a stress-strain model for describing 1D shearing behaviors of soils. It is capable of capturing both the small-strain and the large-strain behaviors, which makes it suitable for modeling very strong ground motions. More importantly, this model enables seismologists to construct stress-strain curves from only shear-wave velocity information, again improving our ability to model site response on a regional scale. Our validation study shows that this model outperforms the prevalent stress-strain model (namely, the MKZ model) by a considerable margin.
Lastly, we demonstrate how the two models above can improve earthquake ground motion modeling: we develop an improved version of site factors for the Western United States. These site factors are provided as Fourier spectral ratios, and phase factors are provided for the first time, which enables the time delay of earthquake waves to be modeled. They can be used for incorporating site response in earthquake ground motion simulations, as well as for improving seismic hazard maps for the Western United States.</p
Development and Dynamics of Microfabricated Enzymatic Biosensors
Get PDFWe have extended the application of microfabrication techniques to all parts of electrochemical enzymatic sensor processing and characterized the behavior of the resulting new sensor geometries. Improved and parallelized enzyme immobilization techniques utilizing spin coating along with porous sputtered platinum barrier layers are implemented on microfabricated platinum electrodes on silicon wafer substrates as well as on millimeter-scale wireless CMOS potentiostats. Functional biosensor sensitivities and linear ranges were observed with multi-month lifetimes, demonstrating that the enzyme layer fabrication process is compatible with precise and massively parallelized CMOS fabrication, making further progress toward the production of low cost and low-tissue impact fully implantable miniaturized biosensors
New Perspectives in Political Communication
Get PDFThis dissertation contains three chapters exploring the nature of political communication and public opinion formation by analyzing social media data. Each chapter uses original sets of Twitter data to examine the public’s response to major shifts in public policy (Chapter Two), the differences between partisan networks (Chapter Three), and how citizens engage with gun policy after mass shootings (Chapter Four).
Chapter Two examines how public opinion towards gay marriage changed before and after the legalization of same-sex marriage as a result of the 2016 Obergefell v. Hodges Supreme Court decision. Exploiting the variation in state law prior to the Court’s decision, I use a difference-in-difference approach to find causal evidence that citizens residing in states where the Supreme Court overturns state laws are more likely to have a negative opinion of the federal decision.
In Chapter Three, I collect an original dataset of Twitter conversations about the American political parties to develop a supervised learning algorithm that classifies users as liberal or conservative, using these labels to then map out separate ideological network structures. Analyzing these networks, I find significant differences in how conservative and liberal citizens form online networks, leading to important consequences for information diffusion and action coordination.
In Chapter Four, I examine how messages from the political and media elite concerning gun control impact citizen engagement with gun policy issues in the wake of high-profile mass shootings. I analyze the impact of elite messaging with a panel data set of sixty thousand partisan Twitter users, data that includes each user’s full Twitter history as well as information on which accounts they follow. By building this Twitter panel, I am able to better determine which elite messages each user receives and whether the recipient chooses to engage with gun policy. I find that elite messages increase the likelihood a user will engage with gun policy issues, but further determine that we must broaden the notion of elite to include users only considered influential on the Twitter platform.</p