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Towards Multimodal Foundation Models in Molecular Cell Biology
No full textThe rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive data sets into a joint model with manifold downstream use cases. Here, we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes, and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell type recognition, biomarker discovery, gene regulation inference, to in silico perturbations. This new paradigm could launch an era of AI-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design, and, more broadly, to profoundly extend our understanding of life sciences.Stem Cell and Regenerative BiologyProo
FL* theory of the pseudogap, and the transition to d-wave superconductivity in the cuprates
No full textPhysicsAuthor's Origina
Calibrating Scale in Motion: Leveraging the Present State of a Social Venture to Clarify Mission, Refine Strategy, and Build Capacity for Lasting Impact
No full textThis capstone chronicles my journey toward understanding how mission-driven organizations can balance immediate needs with long-term aspirations—particularly when growth accelerates and complexity rises. I focus on a core question: How can a social venture scale effectively while preserving both financial viability and its social mission? Drawing on nearly two decades of leadership experience in PK-12 public education, I learned firsthand that no universally “perfect” model can be seamlessly replicated across contexts; rather, strong systems demand adaptability, continuous learning, and alignment between resources, processes, and priorities. These realizations, coupled with coursework focused on systems thinking, scaling impact, and organizational design, inspired me to explore how for-profit ventures in the broader education ecosystem could work toward greater internal coherence in service of driving meaningful, equitable change and lasting impact.
My residency at 2Revolutions (2Rev), a social venture focusing on building capacity for and sustainability in support of personalized learning, served as a testing ground for these ideas. Through a combination of interviews, empathy sessions, and strategic planning, I examined the tensions inherent in balancing a social mission with financial sustainability. I led efforts to define and refine organizational coherence by clarifying the mission, vision, and theory of action, aligning internal structures with these foundational elements through honest reflection, collective ownership, and readiness to confront both technical and cultural shifts. The strategies and frameworks that shaped my work—ranging from the PELP Coherence Framework to Mark Moore’s Strategic Triangle—affirm that sustainable growth requires more than technical fixes. In conversation with one another, these and other models illuminated a broader theory of action for scaling impact that went beyond my immediate context. I explore how coherent strategy, mission clarity, and organizational capacity can continually reinforce one another. Organizations must develop robust structures for decision-making, establish clear priorities, and maintain a culture that encourages experimentation and shared responsibility. Ultimately, this work resulted in a codified set of strategic priorities and common language at 2Rev, underscoring the importance of unifying vision and processes before scaling widely. By integrating systems-thinking principles, building trust, and systematically assessing—and reassessing—how core processes support both profitability and mission fidelity, leaders can chart a path toward scalable change that holds true to the ultimate goal: improving educational experiences and outcomes for each learner.Educatio
Utilizing Abandoned Oil and Natural Gas Wells in the LA Basin for Carbon Sequestration and Hydrogen Storage
No full textThis thesis evaluates the potential of abandoned oil and natural gas fields in the LA Basin for carbon sequestration and hydrogen storage by gaining a deeper understanding of the storage capacity of these depleted reservoirs. The research began with conducting a thorough literature review of all the data collected on the 69 well fields since the 1920s. This involved sorting through well logs and contour maps in search of tops and indicators of the top producing reservoir in each field. Identifying the top producers made it possible to define one regional horizon that represented all top producers and therefore could be used to accurately simulate the storage capacity of reservoirs across the basin. This basin-wide surface computation mesh was created by digitizing data from 20 fields, converting all the surfaces across the basin into point sets, pulling data from other surfaces, and adding regional faults from the California Statewide Earthquake Center’s (SCEC’s) Community Fault Model (CFM). After iterating different surface interpolation methods, a mesh was created that could be used to quantify storage capacity and analyze how faults could be impacted by fluid injection. Utilizing this horizon, a volumetric assessment was done to evaluate the potential of the top 5 fields across the basin. Simultaneously, the research process was started for a hydrogen flow simulation to determine how its injection could differ from carbon dioxide. Through these final results, a contribution was made to further the research into the plausibility of carbon sequestration and hydrogen storage in the LA Basin.Environmental Science and Engineering A
Building a Science of Teaching Reading and Vocabulary: Experimental Effects of Structured Supplements for a Read Aloud Lesson on Third Graders’ Domain-Specific Reading Comprehension
No full textPurpose: This study contributes to the science of teaching reading and vocabulary by illustrating how a ubiquitous classroom practice – read alouds – can be enhanced by structured supplements. This experimental study examines whether and to what extent providing structured supplements can improve student comprehension outcomes by helping teachers foster discussions about academic vocabulary that support schema transfer as students make connections between known and new topics.
Method: A total of 80 third-grade teachers and their students (N = 965; 32% Black, 31% Hispanic, 25% white, 9 Asian, 48% Male) were randomly assigned to treatment or control conditions. Treatment students received a single social studies read aloud on the story of Apollo 11 with structured supplements while control students received the same read aloud story but without structured supplements. Students were from linguistically, economically, and ethnically diverse backgrounds.
Results: Effect sizes from hierarchical linear models indicated that students in the treatment condition outperformed students in the control condition on four measures of domain-specific reading comprehension: recall (ES=.17), near-transfer (ES=.17), mid-transfer (ES=.18), and content comprehension (ES=.18). Further exploratory analyses using structural equation modeling revealed that teacher language scaffolds—that is, temporary dialogic supports in which teachers went above and beyond the intervention script—explained 66% of the treatment effect on domain-specific reading comprehension.
Conclusion: Results from this study suggest that read alouds, when enhanced with structured supplements designed to facilitate schema transfer, can increase the amount of academic vocabulary teachers use during classroom instruction and improve their students’ ability to comprehend disciplinary texts.Accepted Manuscrip
The United States and Industrial Policy: A Look Inside the CHIPS Program Office
No full textThe “Creating Helpful Incentives to Produce Semiconductors” (CHIPS) and Science Act of 2022 represents the United States’ most significant industrial policy initiative in recent decades, allocating $52.7 billion to revitalize domestic semiconductor manufacturing. This thesis examines the implementation of the CHIPS Program Office (CPO), analyzing how the American approach to industrial policy creates opportunities and challenges. Via an evaluation of the CPO’s organizational structure, funding mechanisms, and application processes, this research identifies key tensions in the program’s execution.
The study finds that, despite the CPO’s efforts to align with commercial and industry growth objectives, substantial challenges remain. The root causes of these execution challenges can be traced to the dual objectives of the program: improving supply chain resilience and advancing social policy goals within the constraints of a very low tolerance for risk in the context of protecting taxpayer dollars. These elements, not clearly aligned with economic interests, complicate the program’s execution. The significant attrition rate—marked by over 640 initial Statements of Interest but fewer than 200 sustained applications—highlights tensions between the program’s broad scope and its regulatory demands. Key obstacles include compliance with the retroactive Davis-Bacon Act, National Environmental Policy Act requirements, and rigid milestone-based funding structures, which may hinder flexibility in adapting to rapidly changing market conditions.
This research also contrasts the CPO’s expansive approach with more targeted strategies employed in East Asia. While East Asian countries tend to focus their efforts more narrowly, the American approach simultaneously seeks to expand manufacturing capacity, develop the workforce, protect the environment, and pursue social policy goals. The thesis concludes that this broad scope, while commendable, may dilute the program’s effectiveness in achieving its primary goal of strengthening supply chain resilience and enhancing national and economic security. Ultimately, policymakers must strike a balance between the social policy goals included to gain support for the bill and the practical economic realities involved in its implementation. Some key considerations include the adaptability of regulatory frameworks, the need for focused objectives, and the overall design of government intervention in industrial development. Indeed, the findings have significant implications for American industrial policy and global semiconductor manufacturing competitiveness.Extension Studie
Guardians of the Steppe: Grassroots Activism, Deliberative Democracy, and the Fight for Cautious Resource Politics in Mongolia
No full textUsing Mongolia as a case study, this thesis explores how democracy can emerge
and endure in a non-Western context through deliberative democratic theory. Mongolia’s
traditions of communal governance, culture of deliberation, and dense social networks
create social capital that supports democratic processes, while challenging the notion that
strong top-down formal institutions are necessary for democracy. The thesis utilizes
qualitative process tracing to analyze the environmental grassroots Ongi River Movement
using the deliberative criteria of authenticity, inclusivity, and consequentiality.
The thesis examines the period from 2001 to the present, tracing the Movement’s
emergence and early deliberations at the start of the century, then analyzing its
consequences that continue to unfold today. This study highlights the potential and
constraints of participatory governance in Mongolia, contributing to a broader
understanding of how political culture and institutional development interact in non-
Western contexts. By rethinking Mongolia’s place in democratic theory, this thesis offers
new insights into democratic development beyond Western models.Extension Studie
Quantum States and Spectra of Small Cylindrical and Toroidal Lattices
No full textCaelan Brooks is affiliated with Harvard University as a Physics PhD candidate, Kunal K. Das is unaffiliated with Harvard.We examine the spectrum and quantum states of small lattices with cylindrical and toroidal topology subject to a scalar gauge potential that introduces a position dependent phase in the inter-site coupling. Equivalency of gauges assumed in infinite lattices is generally lost due to the periodic boundary conditions, and conditions that restore it are identified. We trace the impact of various system parameters including gauge choice, boundary conditions and inter-site coupling strengths, and an additional axial field. We find gauge dependent appearance of avoided crossings and persistent degeneracies, and we show their impact on the associated eigenstates. Smaller lattices develop prominent gaps in spectral lines associated with edge states, which are suppressed in the thermodynamic limit. Toroidal lattices have counterparts of most of the features observed in cylindrical lattices, but notably they display a transition from localization to delocalization determined by the relation between the field parameter and the number of lattice sites.PhysicsProo
Portrait of the arzet: The Doctor in German Literature of the High and Late Middle Ages
No full textThe healing arts in Western Europe of the traditionally termed High and Late Middle Ages, the period roughly from 1050 to 1500 CE, embraced a wide and dizzying range of practitioners, practices, and conceptual underpinnings. Regardless of who was trying to heal whom, medieval medicine, at least as practiced in Christian Europe, was largely ineffective. It may have had a placebo effect; the academic rhetoric that came to embellish it might have convinced some of its efficacy; but it did little to affect pathology or to stop the spread of diseases in a society, the majority of whose members subsisted in grossly unhealthful conditions. Nonetheless, the belief in and demand for therapeutic services of all types from a vast array of healers—secular and clerical, university trained and lay—remained strong through and beyond the Black Death in 1348. In light of this persistent faith in the possibility of healing, it is no surprise that the figure of the doctor—the arzet or arzatinne—appears so frequently in Middle High German texts of the period.
This dissertation examines the perceptions of medieval medicine as reflected in a variety of such texts across multiple genres. It explores the variety of “attitudes” evinced towards the medical practitioner, ranging from the adulation of the wundarzet in epic poetry and of the saintly healer in hagiography; to the skepticism voiced by the preacher of the people, Berthold von Regensburg; to the ambiguous portrayal of secular healing in works such as Hartmann von Aue’s Erec or Der arme Heinrich. Alternatively, the doctor is fiendish in Reinhart Fuchs, a fraudster in Der Pfaffe Amis, and a fool in the merchant scenes of the Easter Plays. Medieval mystics who chose to rely on Christ’s healing power alone welcomed illness and disdained secular healing. And all the while, university-trained professionals attempted to ground explanations for the course and outcome of the illnesses they encountered, for their own treatment successes and failures, in Galenic science—a system often indistinguishable from magic. Notably absent from medieval German literature is any instance of arrant contempt for the doctor. Such expressions of contempt would have to wait for the modern era—a time in which paradoxically, although medicine has become more reliable, respect for and fear of medical authority has waned.Germanic Languages and Literature