Thesis advisor: Michael Grubb / Thesis advisor: Charles Murry / This dissertation consists of two self-contained papers that explore the Industrial Organization of the UK television broadcasting market and broadband procurement by US K-12 schools Chapter 1: Welfare Effects of Competition in the UK Television Broadcasting Market In this chapter, I study the consumer welfare effects of a regulation that ended the exclusivity of telecast rights of live English Premier League games and induced entry into the UK television broadcasting market. Historically rights were owned by a single broadcaster. The regulation divided the games into mutually exclusive bundles and stipulated that a single broadcaster cannot own rights to all of them. This resulted in a new channel entering the market and showing some games. I estimate a model of household viewing preferences, channel subscription demand, and pricing using proprietary viewing and subscription choice data. Simulations show a 6.4\% (\pounds 10m per season) decline in consumer surplus driven by the higher prices consumers had to pay to view all the live games. This offset increased surplus from new content on the entrant channel. I propose an alternate regulation that breaks the exclusivity of games telecast on a channel and show that the estimated surplus could have been 29\% higher. Chapter 2: Bundling Demand in K-12 Broadband Procurement In this chapter coauthored with Gaurab Aryal, Charles Murry and Pallavi Pal, we evaluate the effects of bundling demand for broadband internet by K-12 schools. In 2014, New Jersey switched from decentralized procurements to a new procurement system that bundled schools into four regional groups. Using an event study approach, we find that, on average, prices for participants decreased by one-third, and broadband speed purchased increased sixfold. We bound the change in school expenditures due to the program and find that participants saved at least as much as their total ``E-rate" subsidy from the federal government. Under weak assumptions on demand, we show that participating schools experienced large welfare gains. Using an informal model and simulations, we analyze the main mechanisms that could lead to lower prices in the regional auctions. / Thesis (PhD) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Economics.

Die vorliegende Arbeit befasst sich mit den Gleichgewichtseigenschaften und Phasenübergängen in verdünnten Teilchen- und Polymersystemen, mit einem Fokus auf Teilchenkondensation und Polymeraggregation. Dazu werden sowohl analytische Argumente als auch hochentwickelte Monte Carlo Simulationen verwendet. Um die in dieser Arbeit erreichten Systemgrößen zu simulieren, wurde eine parallele Version der multikanonischen Methode entwickelt. Die Leistungsfähigkeit dieser Erweiterung wird an mehreren relevanten Beispielen demonstriert. Um Teilchenkondensation und Polymeraggregation in finiten Systemen und in geometrisch beschränkten Strukturen besser zu verstehen, wird der Einfluss von verschiedenen Parametern auf die jeweiligen Übergange untersucht. Dies beinhaltet unter anderem die Systemgröße und Dichte, sowie im Speziellen für semiflexible Polymere deren Steifigkeit. Betrachtet werden sowohl kanonische Observablen (Energie, Tropfen- bzw. Aggregatgröße, etc.) mit der dazugehörigen Übergangstemperatur und -breite, als auch eine mikrokanonische Analyse sowie die Barrieren der Freien Energie. Für semiflexible Polymere wird insbesondere der Einfluss von Steifigkeit auf die resultierende Struktur der Aggregate untersucht, die von amorphen Kugeln für flexible Polymere bis hin zu verdrehten Bündeln für steifere Polymere reichen. Ein weiterer Fokus liegt auf der Untersuchung von Übereinstimmungen zwischen den generischen Mechanismen in Kondensation und Aggregation: dem Übergang zwischen einer homogenen Phase und einer inhomogenen (gemischten) Phase. Auf diesem Niveau kann man Polymeraggregation als Kondensation von ausgedehnten Objekten verstehen. Dies zeigt sich vor allem in dem Skalierungsverhalten von kanonischen und mikrokanonischen Observablen, insbesondere an einem unerwarteten aber konsistenten Bereich für mittelgroße (mesoskopische) Systemgrößen.

Nonionic surfactants are commonly used to stabilize proteins during upstream and downstream processing and drug formulation. Surfactants stabilize the proteins through two major mechanisms: (i) their preferential location at nearby interfaces, in this way precluding protein adsorption; and/or (ii) their association with protein into "complexes" that prevent proteins from interacting with surfaces as well as each other. In general, both mechanisms must be at play for effective protein stabilization against aggregation and activity loss, but selection of surfactants for protein stabilization currently is not made with benefit of any quantitative, predictive information to ensure that this requirement is met. In certain circumstances the kinetics of surface tension depression (by surfactant) in protein-surfactant mixtures has been observed to be greater than that recorded for surfactant alone at the same concentration. We compared surface tension depression by poloxamer 188 (Pluronic�� F68), polysorbate 80 (PS 80), and polysorbate 20 (PS 20) in the presence and absence of lysozyme and recombinant protein, at different surfactant concentrations and temperatures. The kinetic results were interpreted with reference to a mechanism for surfactant adsorption governed by the formation of a rate-limiting structural intermediate (i.e., an "activated complex") comprised of surfactant aggregates and protein. The presence of lysozyme was seen to increase the rate of surfactant adsorption in relation to surfactant acting alone at the same concentrations for the polysorbates while less of an effect was seen for Pluronic�� F68. However, the addition of salt was observed to accelerate the surface tension depression of Pluronic�� F68 in the presence of lysozyme. The addition of a more hydrophobic, surface active protein (Amgen recombinant protein) in place of lysozyme resulted in greater enhancement of surfactant adsorption than that recorded in the presence of lysozyme. A simple thermodynamic analysis indicated the presence of protein caused a reduction in ���G for the surfactant adsorption process, with this reduction deriving entirely from a reduction in ���H. We suggest that protein accelerates the adsorption of these surfactants by disrupting their self associations, increasing the concentration of surfactant monomers near the interface. Based on these air-water tensiometry results, it is fair to expect that accelerated surfactant adsorption in the presence of protein (observed with PS 20 and PS 80) will occur with surfactants that stabilize protein mainly by their own adsorption at interfaces, and that the absence of accelerated surfactant adsorption (observed with F68) will be observed with surfactants that form stable surfactant-protein associations. Optical waveguide lightmode spectroscopy was used to test this expectation. Adsorption kinetics were recorded for surfactants (PS 20, PS 80, or F68) and protein (lysozyme or Amgen recombinant protein) at a hydrophilic solid (SiO���-TiO���) surface. Experiments were performed in sequential and competitive adsorption modes, enabling the adsorption kinetic patterns to be interpreted in a fashion revealing the dominant mode of surfactant-mediated stabilization of protein in each case. Kinetic results confirmed predictions based on our earlier quantitative analysis of protein effects on surface tension depression by surfactants. In particular, PS 20 and PS 80 are able to inhibit protein adsorption only by their preferential location at the interface, and not by formation of less surface active, protein-surfactant complexes. On the other hand, F68 is able to inhibit protein adsorption by formation of protein-surfactant complexes, and not by its preferential location at the interface. / Graduation date: 2013 / Access restricted to the OSU Community at author's request from Sept. 24, 2012 - Feb. 24, 2013.

Self-organized aggregation is the global level gathering of randomly placed robots using local sensing. Developing high performance and scalable aggregation behaviors for a swarm of mobile robots is non-trivial and still in need, when robots control themselves, perceive only a small part of the arena, and do not have access to information such as their position, the size of the arena or the number of robots. In this thesis, we developed a non-spatial probabilistic geometric model for self-organized aggregation as a tool to analyze aggregation. The model consists of four formulas for predicting the probabilities of aggregation events: creation, growing, shrinking and dissipation of an aggregate. The creation probability is derived mathematically using kinetic theory of gases. In order to derive formulas for growing, shrinking and dissipation probabilities, first, it is assumed that aggregates formed by robots are circular. Then, these formulas are derived geometrically using circle packing theory. We proposed an aggregation behavior and implemented this behavior in the Stage multi-robot simulator. The behavior consists of four sub-behaviors: search, wait, leave and change direction. The wait sub-behavior is specially designed to force aggregates to be circular so that our assumption for the model holds in simulation experiments. We verified each formula using simulation experiments conducted in the Stage multi-robot simulator. Through systematic experiments, we showed that model predictions and simulation results match well and the formulas proposed for growing and shrinking probabilities predict these probabilities better for larger aggregates compared to predictions of previous self-organized aggregation models. We also conducted experiments, in which certain aggregation events are disabled systematically, in order to verify the model further and show that our model can be used to predict the steady-state performance of generic simulation experiments. We use two different methods to predict the steady state performance with our model: microscopic model execution and steady state analysis. It is shown that the largest aggregate size, the number of aggregates, the number of searching robots and the aggregate distributions at the steady state-obtained from microscopic model execution, steady state analysis and simulation experiments are close to each other and our model can be used to predict steady-state performance of aggregation experiments.

The study of crystal nucleation represents a considerable challenge to both experiment and theory. Crystallisation from solutions is initiated by the association of only a few ions. The resulting aggregates are the embryonic precursors to crystals and exhibit diameters of less than a nanometre. While experimental studies offer a wide variety of insights at the macroscopic scale, the atomistic level of detail often remains elusive. On the other hand, computer simulation approaches may easily achieve microscopic resolution and hence appear particularly suited for analysis of the mechanisms of ion aggregation. On the basis of atomistic models, new insights are obtained into the early steps of ion association and the self-organisation of disordered aggregates into crystalline structures. / Das Studium der Nukleation von Kristallen stellt eine immense Herausforderung sowohl an die Experimentatoren als auch an die Theoretiker dar. Die Bildung eines Kristalls aus einer Lösung beginnt mit dem Zusammenschluss einzelner Ionen zu kleinen Aggregaten. Diese embryonalen Vorstufen von Kristallen umfassen nur einige Teilchen und weisen Durchmesser von weniger als einem Nanometer auf. Experimentelle Untersuchungen sind oftmals auf die makro- und mesoskopische Größenskala beschränkt und können vergleichsweise wenige Informationen über die atomaren Aggregationsprozesse liefern. Molekulare Simulationen verlaufen im Gegensatz dazu unmittelbar auf der atomaren Detailstufe und stellen so eine hervorragende Ergänzung zum Experiment dar. Im Computer werden dabei Modellszenarien entwickelt, die Aufschlüsse über die elementaren Schritte der Aggregation von Ionen geben können und aufzeigen, wie sich zunächst ungeordnete Agglomerate allmählich zu periodisch geordneten Strukturen organisieren.

TAR DNA binding protein of 43 kDa (TDP-43) has been implicated in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Pathologically misfolded and aggregated forms of TDP-43 are found in cytoplasmic inclusion bodies of affected neurons in these diseases. The mechanism by which TDP-43 misfolding causes disease is not well understood. We postulate that the aggregation process plays a major role in pathogenesis, and we hypothesize that oligonucleotide ligands of TDP-43 can stabilize the native functional state of the protein and ameliorate aggregation of this aggregation-prone protein. Using recombinant TDP-43 we were able to examine the extent to which various oligonucleotide molecules affects its aggregation in vitro. We have found that certain natural sequence and de novo designed oligonucleotides bind TDP-43 and prevent its natural tendency to aggregate. The clinical and therapeutic implications of these findings are discussed.

TAR DNA binding protein of 43 kDa (TDP-43) has been implicated in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Pathologically misfolded and aggregated forms of TDP-43 are found in cytoplasmic inclusion bodies of affected neurons in these diseases. The mechanism by which TDP-43 misfolding causes disease is not well understood. We postulate that the aggregation process plays a major role in pathogenesis, and we hypothesize that oligonucleotide ligands of TDP-43 can stabilize the native functional state of the protein and ameliorate aggregation of this aggregation-prone protein. Using recombinant TDP-43 we were able to examine the extent to which various oligonucleotide molecules affects its aggregation in vitro. We have found that certain natural sequence and de novo designed oligonucleotides bind TDP-43 and prevent its natural tendency to aggregate. The clinical and therapeutic implications of these findings are discussed.

In der vorliegenden Arbeit werden Beiträge zur Entwicklung neuer qualitativer und quantitativer analytischer Methoden für die Untersuchung von Cetrorelix und anderen GnRH-Antagonisten während des Aggregationsprozesses vorgestellt. Für die qualitative Untersuchung von GnRH-Antagonisten wurden am Modellpeptid Cetrorelix massenspektrometrische Methoden entwickelt und auf weitere GnRH-Antagonisten übertragen. Eingesetzt wurde sowohl die ESI-TOF-MS als auch die MALDI-TOF-MS. Beide massenspektrometrische Verfahren zeigten für die untersuchten GnRH-Antagonisten polydisperse Verteilungen oberhalb der fluoreszenzspektroskopisch bestimmten kritischen Aggregatbildungskonzentration (cac). Bei den ESI-TOF-MS-Messungen konnte ein stark von Cetrorelix abweichendes Aggregationsverhalten für Ozarelix beobachtet werden. Für die Quantifizierung des Aggregatanteils in Cetrorelix- bzw. Ozarelixproben wurde eine Methode mit der MALDI-TOF-MS etabliert, die Untersuchungen an pharmazeutisch relevanten Peptidhormon-Formulierungen ermöglicht. Systematische Untersuchungen zum Einfluss verschiedener An- und Kationen sowie deren Konzentrationen auf die Cetrorelixaggregation erfolgten mit der Fluoreszenzspektroskopie. Die erhaltenen Ergebnisse ermöglichen eine bessere Charakterisierung der Aggregation und lassen Abschätzungen über das Aggregationsverhalten von Cetrorelix in verschiedenen Medien mit unterschiedlichen Elektrolyten zu. Mit dem Einsatz der Transmissionselektronenmikroskopie war es erstmals möglich, Aggregate von GnRH-Antagonisten visuell darzustellen.

Amyloid $\beta$ (1-42) (A$\beta$42) is a seminal neuropathic agent in Alzheimer’s disease (AD), a multifaceted neurodegenerative disorder for which no preventative measures or disease modifying therapies currently exist. Aggregation of this peptide plays a key role in the synaptic dysfunction and neuronal death associated with the disease. Perturbing the aggregation process, therefore, represents a key strategy for the development of new AD therapeutics. A variety of issues with current screening methods, including lack of reproducibility, high reagent consumption and spectral interference from the test molecules, can limit efforts to identify new small molecule inhibitors. Furthermore, the lack of robust, time- and cost-efficient methods for screening compounds in cellular or in vivo models limits the throughput with which seemingly active small molecules can be validated and prioritised. Herein, this thesis describes efforts to overcome such limitations through the development of a unified in vitro to in vivo assay system, in which hits identified in the ‘nanoFLIM’ microfluidic-based assay can quickly be tested in cellular and whole organism disease models. The assay platform designed relies on the use of an amyloid aggregation fluorescence lifetime sensor. A$\beta$42 aggregation is monitored by changes in the fluorescence lifetime of an attached fluorophore, which is significantly quenched upon amyloid formation. To take advantage of the benefits associated with miniaturisation, an in vitro microfluidic platform was employed. A microfluidic chip capable of trapping 110 precisely ordered droplets was designed, allowing for increased sample size and greatly lowering reagent consumption relative to conventional assay formats. Optimisation of the lifetime sensor technique permitted real-time compound screening in SH-SY5Y neuroblastoma cells, as well as in disease model Caenorhabditis elegans (C. elegans). To demonstrate the potential of this assay, a selection of novel chemical libraries developed in the Spring research group was screened, resulting in the identification of a key library of interest. The inhibitory activity of the lead compound from this collection was validated using a variety of biophysical tests, and was also shown to suppress amyloid aggregation in the live cell fluorescence lifetime sensor assay, as well as in whole organism disease model C. elegans. Whilst assay development was underway, additional screening of structurally diverse chemical libraries was performed using a conventional Thioflavin T spectroscopic assay. Such work identified another molecular scaffold capable of exerting a strong inhibitory effect against A$\beta$42 aggregation. A selection of analogues was synthesised to improve the in vivo profile of this library, giving rise to a second lead inhibitory compound. The activity of this compound was subsequently validated in biophysical and cellular tests, and was also tested in disease model Drosophila melanogaster. The aggregation of A$\beta$42 lies at the root of Alzheimer’s disease. In light of the relatively few drug candidates in clinical trials for this disorder, the development of improved translational screening approaches and continued screening of novel chemical libraries is necessary to identify new potential therapeutics. In this study, an in vitro to in vivo fluorescence lifetime imaging assay has been established. Using this assay system and conventional screening approaches, two A$\beta$42 aggregation inhibitors have been identified and validated. These represent promising candidates for the development of new AD therapeutic agents, or for use as molecular probes to further dissect the mechanisms underlying this devastating disease.

Cysteinyl leukotriene receptor 2, a G-protein coupled receptor known to be expressed and functional on human platelets. However, it seems that upon ligand activation the cysteinyl leukotriene receptor 2 activates a variety of signaling pathways in multiple cell types among different species. Previously, a former laboratory member Vrinda Kulkarni found cysteinyl leukotriene receptor 2 to be expressed on the surface of adult zebrafish thrombocytes. In this work I studied the characteristics of aggregation in adult zebrafish thrombocytes with the knockdown of cysteinyl leukotriene receptor 2. I used a newly developed knockdown method to study the function of cysteinyl leukotriene receptor 2. Knockdown of the cysteinyl leukotriene was confirmed using RT-PCR results showed p=.001, reduced sell surface level of expression of the cysteinyl leukotriene receptor 2 results showed that p=.002. I found that the knockdown of cysteinyl leukotriene receptor 2 results in prothrombotic thrombocytes by using flow cytometry p=.0001.