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Flow Induced by Collective Vertical Migration: Impact of Swimmer Distribution, Buoyancy, and Wake Interactions
No full textVarious animal species exhibit collective motion, characterized by coordinated movement within groups of organisms. A prominent oceanic example is diel vertical migration (DVM), wherein zooplankton migrate vertically from deeper waters during the day to shallower regions at night, often covering distances of approximately 1 kilometer. Despite numerous field measurements, laboratory observations, and theoretical studies of biogenic mixing resulting from collective swimming, the scale of fluid mixing induced by DVM remains unresolved. A key challenge is linking the behavior and flows created by large numbers of individual organisms to collective-scale fluid dynamics. Since most swimmers involved in DVM operate at intermediate Reynolds numbers, the dynamics of these systems are nonlinear and span a wide range of spatial and temporal scales.
This thesis investigates flow scaling generated by vertical migration of brine shrimp (Artemia salina) aggregates, using laboratory measurements complemented by semi-analytical modeling. A volumetric laser scanning system first measured swimmer behaviors and flow interactions during laboratory-induced vertical migrations. Swimmers consistently maintained vertical swimming velocities under varying environmental conditions, showed a Gaussian horizontal distribution within the tank cross-section, and exhibited a pronounced tendency toward the tank center, where illumination was brightest. A scaling relationship between swimmer buoyancy, ascent speeds, and resulting flow velocities was developed to contextualize these results.
A semi-analytical model was then developed to estimate the flow generated by wakes of multiple swimmers in proximity. Individual swimmer behaviors were informed by empirical observations and combined through an iterative approach that conserves mass and momentum, providing an aggregation-scale flow solution. Numerical results indicated that induced upstream flows within the aggregation were relatively insensitive to downstream swimmer presence, that average flow speeds approached a plateau beyond a critical aggregation length, and that closer swimmer spacing significantly enhanced induced flow velocities.</p
Dynamics of Charged Polyionic Liquids
Get PDFPolymerized ionic liquids (PILs) exhibit complex ion transport dynamics that are central to advancing technology in energy storage and efficient energy conversion. In this work, we probe the behavior of charged polymer systems in the solvent‐free limit using a coarse‐grained Gaussian core model that explicitly incorporates long‐range electrostatic interactions. Our simulations span a wide range of chain lengths, from monomeric units to highly entangled polymers, revealing how both intrachain and interchain interactions govern key properties such as the radius of gyration, relaxation time, and diffusivity. Notably, charged polymers adhere to classical reptation scaling, indicating that electrostatic forces do not inhibit standard polymer melt scaling behavior. We quantify these effects by evaluating both the Onsager transport coefficients and the direct drift response under applied electric fields, thereby linking molecular trajectories to macroscopic ion conductivity.
Our findings show that as the chain length increases, the motion of polymerized ions becomes increasingly correlated, a trend that stabilizes ion conductivity despite decreasing diffusivity. This study demonstrates that the complex interplay between correlated motion and cooperative chain dynamics results in a relatively stable conductivity that increases over short chain length, plateaus in the transition regime, before decreasing in the fully entangled regime — contrary to idealized predictions based solely on diffusivity. By explicitly modeling the microscopic interactions and accounting for both hydrodynamic and electrostatic effects, we provide a physically grounded framework that captures the emergent behavior of these charged systems. In doing so, our work offers a robust platform for the rational design of next-generation PIL electrolytes, distinguishing itself from phenomenological models through clear, simulation-based insights.</p
Tensions, Trade, and Transformation: Essays on Chinese Economic History During the Warlord Era
Get PDFThis thesis comprises three chapters on politics, trade, and industrialization during the Warlord Era (1912–1928) in China. The Warlord Era marked the beginning of China’s modern history—a pivotal transitional period that remains largely understudied. This thesis offers an in-depth examination of this era by addressing a central puzzle: why did large-scale industrialization take place during this period of persistent political instability? The unique historical context and the rich historical data of this period yield a deeper understanding of the economic transformation not just in China but in other late-developing countries as well.
The first chapter examines the effects of military factions on domestic trade costs. Using newly collected inland transit data from the Chinese Maritime Customs, it shows that bilateral trade costs between a province and a port increased significantly when they were controlled by different military factions. Leveraging the 1917 Russian Revolution as an exogenous supply shock, the chapter further demonstrates that demand for foreign goods was elastic across all regions in China, with poorer regions exhibiting even more elastic demand than wealthier ones. Taken together, these findings show that political instability significantly influenced regional access to foreign goods by shifting domestic trade costs. Given that foreign trade was crucial for China’s early industrialization, these results have important implications for understanding regional industrial development.
Building on the first chapter, the second chapter examines the impact of foreign trade access on regional industrial development. It develops a simple model, wherein access to foreign trade influenced private firms' entry decisions through its effect on market prices. In particular, access to foreign capital goods relative to foreign consumer goods determined the number of new industrial firms in a region. Better access to foreign consumer goods discouraged industrial firm entry, whereas better access to capital goods encouraged domestic producers to enter the market. This model is then tested by combining the trade costs measured in Chapter 1 with a large dataset of firm entry on the provincial level. These findings highlight the importance of private initiatives in driving industrialization. Private participants, even in a late-developing country like China, actively responded to market incentives. It was their entry that made industrialization possible even during a period of persistent political instability. A liberalized market alone was able to induce some industrialization. At the same time, high domestic trade barriers were not inherently disadvantageous, as they could offer protection to domestic producers from foreign competition in certain regions.
The third chapter further examines coal markets using a dataset of county-level coal prices and output from 1912 to 1919, newly compiled from archival records of the Nongshang Tongji Biao (Survey of Agriculture and Commerce). Adding to the first two chapters, which focus on the movement of foreign goods within China, this chapter turns to a domestically produced good. Consistent with the previous chapters, it finds that political instability introduced trade barriers, that the entry of small private coal mines played a key role in driving market integration, and that limited market integration may have encouraged local mining activities. More important, this chapter revisits Pomeranz’s influential argument that China’s late industrialization was largely “a geographic accident.” While the distribution of coal deposits may reflect geological randomness, the high energy costs faced by China’s commercial centers during the Qing were not purely a misfortune of geography but also a consequence of unfavorable institutions.</p
Essays in Empirical Industrial Organization and Corporate Finance
Get PDFThis thesis consists of three chapters.
Chapter 1 introduces a novel empirical framework to assess the impact of ownership consolidation on labor markets, addressing growing concerns about labor market power. I develop a two-sided matching model tailored to the creative labor force, a segment characterized by strong worker-firm complementarities. Applying this model to a major merger in the U.S. publishing industry, I leverage rich text data to analyze its effects on the author labor market. Counterfactual merger simulations reveal a trade-off between efficiency gains, creative misalignment, and redistributive effects. While the merger alleviated capacity constraints, post-merger integration led to significant creative misalignment between authors and publishers. The merger also induced substantial value transfers from competing publishers and authors to the merged entity, with established authors bearing the heaviest losses. Notably, the merger's anticompetitive effects manifested primarily in labor markets rather than in consumer markets. This research extends merger evaluation beyond consumer impact, offering a framework to analyze the broader consequences of mergers in labor markets characterized by worker-firm complementarities.
Chapter 2, coauthored with Miguel Alcobendas, Shunto J. Kobayashi, and Matthew Shum, studies the impact of online privacy protection, which has gained momentum in recent years and spurred both government regulations and private-sector initiatives. A centerpiece of this movement is the removal of third-party cookies, which are widely employed to track online user behavior and implement targeted ads, from web browsers. Using banner ad auction data from Yahoo, we study the effect of a third-party cookie ban on the online advertising market. We first document stylized facts about the value of third-party cookies to advertisers. Adopting a structural approach to recover advertisers' valuations from their bids in these auctions, we simulate a few counterfactual scenarios to quantify the impact of Google's plan to phase out third-party cookies from Chrome, its market-leading browser. Our counterfactual analysis suggests that an outright ban would reduce publisher revenue by 54% and advertiser surplus by 40%. The introduction of alternative tracking technologies under Google's Privacy Sandbox initiative would partially offset these losses. In either case, we find that big tech firms can leverage their informational advantage over their competitors and gain a larger surplus from the ban.
Chapter 3 examines how informal and formal networks shape performance in the venture capital (VC) industry. Using data on all U.S.-based VC investments from 1990 to 2009, supplemented with partner-level educational and employment histories from LinkedIn, I develop a structural framework that connects three types of networks: coinvestment ties, historical affiliations, and latent social connections. In the baseline model, VC performance is a function of peer performance, capturing network spillovers through a micro-founded production function. To address endogeneity in network formation, I extend the model using a two-step instrumental variables strategy that leverages variation in past professional and alumni ties. Finally, I introduce endogenous network formation where VCs strategically choose connections based on expected peer quality, allowing for the recovery of latent social networks from equilibrium outcomes. Across specifications, better-connected VCs exhibit significantly higher exit rates. Estimates from the endogenous model suggest that a 1% increase in social connectedness raises a VC's exit rate by 0.2 percentage points, while a 1% improvement in peer performance leads to a 0.74 percentage point increase in connection intensity. Informal relationships thus carry measurable economic weight, and the empirical approach developed here provides a new lens for identifying network effects in private capital markets.</p
Diversity, Activity, and Adaptations of Phage Communities in Anoxic Hydrocarbon-Rich Marine Sediments
Get PDFThe viruses of the global ocean, especially those infecting prokaryotic taxa, are known to play an important role in maintaining the genetic and taxonomic diversity of their host communities and in the cycling of atmospheric carbon and key nutrients like nitrogen and iron. However, the vast majority of these conclusions are drawn from the surface ocean and upper water column, while the sediments, which constitute one of the largest biomes on earth, are understudied in comparison. Of special interest are areas on the ocean floor where methane and other hydrocarbons are produced and released by geological activity and oxidized by a consortium of archaea and bacteria. Using direct genomic sequencing of the viruses from a variety of simplified sediment-free enrichments of hydrocarbon oxidizers, I compare viral communities sampled from different locations and incubated under a range of temperatures to understand the role these parameters might play in shaping distribution and community structure. I then present the most comprehensive picture thus far of viral diversity and distribution from a methane cold seep and discuss whether the viral assemblages are influenced by the steep geochemical gradients that characterize seep sediments. From these datasets, I propose that viral communities in methane-oxidizing sediments are tailored specifically to the physical constraints of the sediment matrix rather than to the dominant members of the cellular community or to other physicochemical parameters such as temperature, sampling location, or depth below the seafloor. I then outline the development of two methods, stable-isotope probing coupled to nanoSIMS and biorthogonal non-canonical amino acid tagging, to work in heterogenous sediment virus samples rather than the liquid pure cultures on which they had previously relied. Implementation of these methods, which allow us to temporally constrain viral production and virus-influenced nutrient flow, resulted in the hypothesis that viral production likely responds to shifts in the major metabolic processes within an ecosystem and may influence cellular community composition
Biomolecular Engineering of Gas Vesicles with Thiol Functionality
Get PDFTherapies involving the administration of engineered cells, such as CAR-T cell therapy and the delivery of genetically modified gut microbes, have enjoyed clinical success and increasing interest in recent years. While these therapies continue to show great promise, the opacity of tissue precludes the use of light in the observation and potential manipulation of these engineered cells as they carry out their functions within the body. To access these cells non-invasively in deep tissue requires the use of imaging modalities that do not involve light, of which ultrasound (US) is especially appealing due to its relatively low cost, safety, and widespread availability. Engineered cells can exhibit US contrast by expressing gas vesicles (GVs), air-filled polymeric proteinaceous nanostructures; GVs have already been used as acoustic reporters for gut colonization, tumor cell activity, and more.
Whereas GVs are most notable for their acoustic properties, we set out to further expand the function of GVs by chemically modifying them at the genetic level. Our goals were twofold: we wished to equip the external, solution-facing side of GVs with a unique chemical handle; and we wished to hide a reactive group within the internal, air-facing side of GVs that could only be revealed when the GV structures are irreversibly collapsed. To accomplish both these goals, we chose to incorporate cysteine into the shell of GVs because cysteine’s thiol side chain is chemically unique among all natural amino acids and because wild-type GVs do not contain cysteine in their shells. We set up a cysteine scanning mutant library of the GV shell protein, GvpA/GvpA1, and screened for cysteine-tolerant mutations in the gene. Through this process, we discovered cysteine substitutions that furnished thiol groups facing both the GV exterior and interior.
The GV-exterior-facing cysteines were leveraged to develop a modified GvpA that contains the bioorthogonal six amino acid tetracysteine tag, or TC tag. The TC tag reacts with the membrane-permeable molecule FlAsH, which becomes fluorescent upon reaction. We used TC-tagged GvpA, or tcGvpA, to express GVs in HEK 293T cells, and used confocal microscopy of FlAsH to study those GVs. Notably, we only substituted a small percentage of GvpA to tcGvpA, leaving the rest of the GvpA as wild type; to our knowledge, this is the only report of a polymeric proteinaceous structure that employs this chimeric assembly approach being successfully expressed and labeled with FlAsH. The microscopy results from this study were used to generate three-dimensional renderings that provided insights into the size and positioning of GV clusters expressed within HEK 293T cells.
Second, we identified several interior-facing cysteine mutants to the GV shell protein GvpA1, which we used to develop “SonoCages”: chemical entities whose reactivity is gated by US. We purified GVs with one mutation from our screen, V47C, and reacted them with monobromobimane (mBBr), a fluorogenic, thiol-reactive molecule. The mutant GVs only reacted with mBBr after treatment with US, which collapsed the GVs and exposed their hydrophobic interiors to the bulk solution. Thus, we had developed thiol-bearing SonoCages whose cysteines could only engage in reactions after US-mediated collapse of the GVs—a process we call “sono-uncaging” in analogy to photo-uncaging. We further demonstrated the utility of SonoCages by preparing a hydrogel containing SonoCages and mBBr and using US to create fluorescent patterns corresponding to regions of GV collapse.
The work presented in this thesis not only demonstrates the functionalization of the GV interior and exterior, but also establishes a framework through which further modifications can be performed. Whereas we used cysteine as our reactive chemical of choice, other amino acids (including non-canonical amino acids) could be used to explore a much wider library of reactivities. The vast potential of GV chemical modification, along with the amazing results from the rest of the Shapiro Lab and in labs across the world, serves as a reminder that GVs and GV-based technologies are not just a bubble (pun intended)—they are going to be around for a long time.</p
Phonon-Phonon Interactions in Highly Anharmonic Systems
No full textThe phonon, a quantum of atomic vibrations, is a core ingredient in the description of materials’ behavior at both high and low temperatures. A harmonic theory of lattice dynamics treats phonons as independent, noninteracting normal modes with long lifetimes. The proper description of phenomena in solids requires the phonons to interact depending on temperature, or in other words, to act anharmonically. The phonon interaction in highly anharmonic crystals can result in intermodulation and an additional coherent scattering intensity at frequencies of the sums and differences of classical normal modes. At low temperatures, anharmonic interaction is triggered by nuclear quantum effects of zero-point motion, which can be observed
as intermodulation and negative thermal expansion (NTE). In the thesis, I expand the general understanding of intermodulation phenomena using computational and experimental methods by adding missing parts expected in the theoretical intermodulation picture, such as phonon second harmonic generation and nuclear quantum intermodulation.
The phenomenon of second harmonic generation (SHG) was found for phonons in anharmonic NaBr by inelastic neutron scattering. The temperature dependence of this phonon SHG was measured from 300 K to 650 K. At 300 K the second harmonic (SH) is seen as a high-energy branch around 33 meV, nearly independent of Q. The temperature effective potential (TDEP) method and classical molecular dynamics (MD) simulation with machine learning interatomic potential were able to reproduce the SH, and showed that SHG occurs with the flat transverse optical (TO) phonon branch. A classical model of a nonlinear medium explains the intensity and lifetime of the SH, compared to those of the TO modes. Also successful was a quantum model based on the Heisenberg-Langevin equation for interacting phonons coupled to a thermal bath, which also predicts a spectral distribution of the SH. The measured temperature dependence of the intensity of the second harmonic showed that it follows the Planck distribution of a one-phonon quasiparticle, and not two TO phonons.
The anharmonic behavior of phonons and thermal expansion of hexagonal zinc were studied from 15 to 690 K by inelastic neutron scattering (INS) and ab initio simulations. Phonon spectra were measured for Q-points over the full Brillouin zone, giving the phonon density of states (DOS), and dispersions along high-symmetry directions. The dispersions were crisp at 15 K, but diffuse intensity was observed at energies above them. The dispersions broadened with temperature, T, and the diffuse intensity grew relatively stronger. This diffuse intensity appeared in all INS measurements and simulations, except for classical molecular dynamics at 15 K. The TDEP method was used to calculate the free energy and thermal expansion with the nuclear quantum effect from zero-point vibrational dynamics. For T < 100 K the nuclear quantum effect was essential for obtaining the negative thermal expansion, and path integral molecular dynamics (PIMD) was particularly effective for obtaining the negative thermal expansion in the basal plane. A Heisenberg-Langevin model for interacting phonons coupled to a thermal bath was able to reproduce the shape and intensity of the diffuse spectral features.</p
Mechanisms of Pharmacological and Cellular Regulators of Mitophagy
No full textAutophagy is a highly conserved cellular process that isolates and degrades damaged or unnecessary intracellular structures. Mitochondria, well known as metabolic centers, provide ATP and critical metabolites essential for life. Unchecked mitochondrial damage impairs metabolism, releases immunogenic mitochondrial DNA, and triggers apoptosis. Mitophagy, the selective removal of mitochondria via autophagy, is vital to preventing these harmful outcomes. The PINK1/Parkin pathway detects damaged mitochondria and targets them for mitophagy. Dysfunction in this pathway underlies certain subset Parkinson’s Disease (PD) cases. Efforts to understand the mechanistic basis of this pathway and its regulators provides a pathway to development of potentially disease modifying therapeutics for PD. In this thesis, I characterize the mechanism of action of a series of clinical stage mitophagy activating drugs. We find that these compounds reduce the threshold for which mitochondrial stress initiates mitophagy. However, contrary to reported literature, I demonstrate that these compounds do not directly activate PINK1 or Parkin. Rather, they act as weak mitochondrial toxins sensitizing cells to mitochondrial insult. I reveal that this phenomenon is characteristic of any weak mitochondrial toxin, revealing a potent pitfall for current drug discovery campaigns. Next, I detail a novel endogenous regulator of PINK1/Parkin mitophagy, the immune-related protein TNIP1. We show through a series of cell, biochemistry, and biophysical assays, that TNIP1 competes for autophagy machinery to slow down mitophagy. These data center TNIP1 as a important regulator of autophagic processes, and a unique negative regulator of mitophagy. Finally, I describe a biophysical analysis of the mitochondrial ion channel, VDAC2, critical in apoptosis and PINK1/Parkin pathways. Using a series of single-molecule approaches, I reveal how its structural plasticity regulates its interactions with protein partners. These finding provide a mechanistic basis for understanding its role in disparate cellular processes. I also explore the biological impact of KO of each VDAC isoform on mitochondrial and cell function. Unexpectedly, we find that the lowest expressed isoform, VDAC3, has an outsized impact on mitochondrial function
Neutron Stars: Robust Constraints on Dense Matter from Astrophysics
No full textNeutron stars are exceptional astrophysical objects, harboring likely the densest matter in the universe outside of black holes.
However, uncertainty in the properties of matter at the densities achieved inside of neutron stars means that the structure of neutron stars cannot be fully understood from first principles.
Modern statistical and computational tools however, along with cutting-edge observational strategies have enabled the properties of neutron stars to be constrained using astrophysical data.
In this thesis, I will discuss work I have carried out examining what can be learned about neutron stars, and the dense matter inside of them, using electromagnetic and gravitational-wave observations of neutron stars.
In particular, I will discuss constraints on nonparametric models of the dense-matter equation of state, and why nonparametric models are an effective strategy for faithfully representing uncertainty.
I will also discuss the interplay between understanding the astrophysical channels for forming neutron stars, and the neutron-star matter equation of state, including how we can use our understanding of dense matter to classify objects.
Finally, I will discuss some considerations for simulating astrophysical neutron stars, which is necessary in order to interpret the full range of astrophysical observations of merging neutron stars, such as the neutron star merger GW170817.</p
Elucidating the Products and Kinetics of Bimolecular Alkene-Derived Peroxy Radical Reactions in the Lab and in the Field
No full textAlthough peroxy radicals, reactive compounds formed in the atmospheric oxidation of hydrocarbons, are primary drivers of atmospheric composition, several uncertainties remain with respect to their fates in both low and high NO environments.
This thesis uses gas chromatography chemical ionization mass spectrometry (GC-CIMS) to identify and quantify the products of bimolecular peroxy radical reactions formed in both of these regimes in the lab and in the ambient environment. The
first two chapters use laboratory experiments to probe the formation of a peroxide accretion product (ROOR) via peroxy radical self- and cross-reactions. In the first chapter, a method for studying the formation of the peroxide accretion product is developed and used to observe the formation of the accretion product of the ethene-derived hydroxy peroxy radical self-reaction. The self-reaction rate constant and the
branching to the formation of the accretion product are measured, and the identity of the accretion product is confirmed by comparison to a synthesized standard. In
the second chapter, the formation rate of the accretion product for a variety of small alkene-derived peroxy radical self-reactions is measured, and the observed relation-
ship between peroxy radical structure and accretion product formation is discussed. Finally, the third chapter presents observations of organic nitrogen compounds formed via the
reactions of biogenic and anthropogenic hydrocarbons in the Los Angeles urban atmosphere. The identities of several of these organic nitrates are confirmed by comparison to laboratory oxidation experiments, and the role these compounds play in the local nitrogen budget is discussed