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Data-Driven And Mechanistic Modeling For The Optogenetic Control Of Microbial Consortia
No full textMetabolic engineering offers a sustainable way to manufacture bulk and specialty chemicals through microbialfermentation of renewable feedstocks. However, maintaining high productivity is a challenge, primarily due
to the lack of tools to control cellular metabolism. Microbial optogenetics offers a solution by enabling the
dynamic and reversible modulation of metabolism using light as an input. With the possibility for any gene
to be put under light-control, and for a time-varying light input to dynamically control gene expression, this
represents a huge parameter space. Hence, there is a need for high-throughput experiments and for data-driven
and mechanistic models to drive understanding, optimization, and control of the biological systems.
This thesis outlines the development of novel optogenetic hardware and software that facilitates bothhigh-throughput experiments and automated closed-loop regulation using fluorescent biosensor outputs. For
data-driven learning from these experimental data, machine learning algorithms are developed that enable
learning from data with various 'pathologies' often encountered in experimental systems without the need
for data modification. These include data collected at variable time intervals, and data with only partial
state-space observations at each point. To demonstrate how the model can leverage not just experimental
data but also a priori knowledge, the data-driven models are merged with existing partial physical insights in
"physics-informed gray-boxes" to enable learning of understandable functions like unknown kinetic rates and
microbial growth functions. Optogenetics can permit the multi-modal regulation of microbial growth rates
using a single light wavelength. By employing forcing periods and pulsing fractions as dual and independent
parameters of optical input, it is possible to manage both the relative growth rates of two species grown
in consortia and their absolute growth rates. Finally, closed-loop control over microbial growth rates is
demonstrated in continuous cultures and the extension to the control of population ratios in microbial
consortia is discussed
HYBRID NANOPHOTONICS FOR QUANTUM NODES BASED ON DEFECTS IN DIAMOND
No full textIntegrating atomic quantum memories based on color centers in diamond with on-chip photonic devices could enable entanglement distribution over long distances. However, efforts towards integration have been challenging as color centers can be highly sensitive to their environment, and their properties degrade in nanofabricated structures. Here, we describe a heterogeneously integrated, on-chip, III-V on diamond platform for integrating color centers in diamond with nanophotonic devices including photonic crystal cavities and ring-resonators. A key challenge to realizing high quality factor (Q) hybrid photonic crystals is the reduced index contrast on the substrate compared to suspended devices in air. This challenge is particularly acute for color centers in diamond because of diamond's high refractive index, which leads to increased scattering loss into the substrate. Here we develop a design methodology for hybrid photonic crystals utilizing a detailed understanding of substrate-mediated loss, which incorporates sensitivity to fabrication errors as a critical parameter. Using this methodology we design robust, high-Q, GaAs-on-diamond photonic crystal cavities, and by optimizing our fabrication procedure we experimentally realize cavities with Q approaching 30,000 at a resonance wavelength of 955nm. We then propose a nonlinear photonics based quantum frequency conversion scheme to effectively scatter the qubit emission into the telecom band using an integrated photonic device, thus minimizing transmission loss. By integrating color centres in diamond with hybrid photonic cavities and quantum frequency conversion units, the platform could be scaled to longer entanglement distances and faster entanglement generation rates. Owing to the generality of the design process, the model could be readily applied to arbitrary wavelengths and material stacks. By separating device fabrication from the substrate, the hybrid photonics platform could be utilized to significantly expand the space of candidate qubits for quantum network experiments
Teledrumming (1922-1971)
No full textTeledrumming (1922-1971) examines the cultural history of Francophone anticolonialism through the lens of media studies and critical theory. I argue that African drumming and women’s labor function as the “media” of anticolonialism in the French empire. My analysis centers on an object called the “tam-tam,” which refers to African drums as both musical instrument and communication technology. Since antiquity, people in West and Central Africa have used drums to “talk” across long distances, much like telephones. I use the term “teledrumming” to name this mediatic process instantiated by African drums. From the Haitian Revolution onwards, anticolonial groups have consistently used teledrumming to send out a “call” for revolution, beckoning colonial subjects to rise against their domination. Focusing on the twentieth century, this dissertation examines how both original and remediated forms of teledrumming structure anticolonialism.
Teledrumming, I argue, is entangled with women’s labor: the tam-tam’s call is inseparable from women’s song, performance, and invisible work. Chapter 1, “Racial Melancholia,” studies the works of André Gide, Marc Allégret, and Joséphine Baker. I argue that drumming and women’s performances melancholically resist the white French psyche, as in Baker’s 1935 film Princesse Tam-Tam. Chapter 2, “Fellow Drummers,” examines how Négritude men such as Aimé Césaire imitate tam-tam rhythms in their poetry (for example, in “Tam-Tam I”) to create an anticolonial consciousness. At the same time, Négritude women such as Suzanne Césaire invisibly labor to transcribe and publish the men’s poetry. “Tele” and “drumming” thus take starkly gendered, remediated forms for Négritude. Chapter 3, “Interpellation,” studies historical representations of anticolonialism in the works of Ousmane Sembène, Bernard Binlin Dadié, and Ferdinand Oyono. I argue that tam-tams and women’s song interpellate, or produce, anticolonial subjects in 1940s French West Africa. Chapter 4, “Percussive Echoes,” primarily considers the relationship between drumming and women’s ululating song in the Algerian Revolution (1954-1962), with a focus on the works of Frantz Fanon and Gillo Pontecorvo.
The central tasks of this dissertation, as such, are to valorize the tam-tam as a sophisticated African technology and to recover the subjectivity of women who have been relegated to techne
Harmonic Expression in a Stylistic Frame
No full textThis dissertation investigates whether U.S. listeners are sensitive to musical harmonic style, in terms of being able to make consistent genre and emotion associations to the typical harmonic vocabularies of different styles of music. Research in music cognition rarely takes into account different styles of harmony, either privileging Western classical style or presenting harmonic stimuli to participants without any discussion of the stylistic characteristics that shape them. In three behavioral experiments, this project investigates four research questions: (1) Can listeners identify different styles of harmony based on harmonic cues alone? (2) Can different styles of harmony be perceived as expressive of specific emotions? (3) What is the effect of musical training, familiarity and preference for different genres on these processes? (4) To what extent is timbre a more reliable cue than harmony when it comes to genre and emotion identification? These questions were pursued by creating stimuli that isolated the harmonic and timbral characteristics of 5 styles: classical, country, hip-hop, jazz and pop-rock, and presenting them to participants who were asked to associate them to genre labels and a set of emotion terms.
The results suggest that, while timbre is a more salient cue of musical genre, style of harmony can still be consistently associated to the predicted genre labels at above-chance levels. It was found that specific styles of harmony and of timbre can be consistently associated with certain emotions, and that style of harmony affected perceptions of emotional valence much more so than timbre, while timbre affected perceptions of energy more intensely. The effects of musical training and listening habits on these results were small to null. Overall, these results present novel evidence for the expressive potential of harmonic style, and encourage music cognition and theory to widen the stylistic scope of what the study of musical harmony means
Union Influence, Corporate Interests, and Labor Policy: Essays on Labor and Employment Politics
No full textThe papers in this dissertation explore the competing influence of unions and business at various levels of the political process, from individual attitudes and voting behavior to federal policymaking. We know from a large body of work that businesses aggressively lobby the government to advocate for policy on a wide range of issues. We also know that unions, although considerably weaker than they once were, have vigorously fought to oppose the business lobby’s agenda in order to improve labor standards, particularly for their own members. In the first paper, “Politicization and Polarization at the NLRB,” I contribute original data-sets on the employment histories and decisions of presidentially appointed oofficials at the NLRB since the founding of the agency in 1935. I find that appointees with management backgrounds are more likely to make pro-business decisions while those with union backgrounds are more likely to make pro-labor decisions; although those with union backgrounds only appear in the last two decades. The second paper, "Labor vs. Big Business: interest groups, cue-taking, and voting behavior," shifts the focus to the mass public to explore the implications of a California proposition in which the majority of Democrats voted for a pro-employer independent contractor policy. I theorize that voters were persuadable due to the low attitude crystallization and a new information environment with respect to independent contractor status as a policy issue. I find support for the theory in an experiment in which I expose Democrats to a series of cue-taking treatments from businesses and labor unions regarding legislation on an independent contractor status policy or a paid family/medical leave program. Finally, in "Republicans for Labor? State-level Labor Power and Senate Policy-making," I examine the influence of unions on potentially pivotal actors in the U.S. Congress. I construct a dataset of employment legislation from 1970 to 2021 to examine the influence of state-level unionization rates on Republican Senators’ votes. I use an instrumental variable design to provide causal estimates of this influence, the results of which suggest that unionization is strongly predictive of whether Republicans will side with Democrats in favor of more progressive employment policies
