VictorJuiz/thesis huggingface dataset:
Physical Modeling of Chromatin with Heterogeneous Nucleosome Spacings

The spatial organization of chromatin — genomic DNA and its associated proteins — underpins key biological processes from controlling gene expression to facilitating DNA damage repair. At the most basic level of organization, 147bp segments of DNA wrap histone proteins to form nucleosomes, which create heterogeneously spaced kinks in an otherwise semiflexible double-helix. This geometrical effect has not previously been included in analytical treatments of chromosomal DNA. As a result, the relative contributions of this structural heterogeneity and the thermal fluctuations in the DNA on chromatin organization is currently unknown. To address this gap, we present an analytical model of chromatin, treating nucleosomes as arbitrarily spaced, rigid kinks, in a wormlike chain backbone. We demonstrate that changing the positions of nucleosomes between two genomic loci can affect their probability of contact by up to six orders of magnitude. We also show that averaging over these heterogeneous binding configurations leads to chromatin tracing out an effective wormlike chain that is drastically more elastic than bare DNA. Since chromatin must bend back on itself in order for enhancers to bind their targets, this change in elasticity has a profound influence on transcriptional regulation. In particular, we examine the effects of nucleosome positioning around gene promoters on the spreading of epigenetic modifications through transient chromatin looping. Collectively, our work demonstrates that heterogeneity in nucleosome spacing dominates both local and global chromatin organization.

Keywords:  Program in Engineering Physics
biophysics
chromatin
DNA
polymer physics
epigenetics
Thesis
Advisor: Spakowitz Andrew J.
Das Rhiju
The physics of friction and fracture : applications to dike propagation, earthquake triggering, and slow slip mechanics

Friction and fracture processes are ubiquitous in the brittle crust. Thus understanding the physics of these processes is of paramount importance to successfully model and interpret a wide variety of geological phenomena such as seismic and volcanic activity. In this dissertation, I develop theory and models based on the current understanding of the physics of friction and fracture. These physics-based models are then applied to a broad class of problems related to dike propagation, induced and triggered seismicity, and slow slip mechanics. In order to couple together the underlying physics of friction and fracture to data and observable characteristic of transient behavior in the crust we need models and constitutive relationships. This dissertation is mainly on making this connection, the challenges involved, and comparison with observations. The first challenge addressed in this dissertation is to connect fault friction and microseismicity (Chapter 2). I use the experimentally derived theory of rate-and-state friction to compute the time to instability for a spring slider under arbitrary stressing history. This analytical result is used to describe a population of spring-sliders, which represents a population of seismic sources with varying initial conditions. This theory results in a constitutive relationship that relates to seismicity production and stressing history. The theory is extended well beyond what has been previously explored, in particular, where I account for interactions between seismic sources (Chapter 3). This new interaction theory is applied to several practical problems such as fault slip models and earthquake migration through cascading. Further applications of the theory from Chapter 2 are explored in Chapter 4. Where a physics-based model of a dike intrusion is developed and deformation and seismicity are modeled in a fully consistent manner. The results suggest that dike induced earthquakes are triggered on preexisting faults. Furthermore, the results give insight into the frictional structure of the crust, which needs to be heterogeneous to satisfy the temporal and spatial distribution of the seismicity. The last two Chapters (5 and 6) explore in more details the mechanics of faults and dike intrusions respectively and are mostly independent of other chapters. In chapter 5, I account for poroelastic coupling the nucleation of frictional instabilities. This work leads to a new novel theory of slow slip, which demonstrates that slow slip nucleates spontaneously on mildly rate-strengthening faults under certain circumstances when slip couples to normal stress perturbation. In the final chapter, I show how the growth of dikes and depressurization of magma chambers are coupled through fully coupled simulations. The simulations provide new insight into how a dike lengthens with time before finally arresting.

Keywords: Geophysics.
Advisor: Segall Paul
Dunham Eric 
Ellsworth William L.
Physics-based sound synthesis using time-domain methods

Physics-based sound synthesis is an increasingly popular technique in computer graphics to automatically generate realistic sounds associated to (otherwise silent) visual events, such as a spolling green plastic bowl or a dripping faucet. Previous work has shown very promising results; however, these algorithms still suffer from several shortcomings, such as long precomputation time or difficult integration for complex sound sources. In this thesis, we explore new simulation frameworks that leverage time-domain methods and insights to improve both the quality and speed of physics-based sound synthesis algorithms. First, we introduce KleinPAT, a new time-domain algorithm that rapidly estimates acoustic transfer fields of a vibrating rigid object (modeled by the linear modal model). Instead of estimating the transfer fields by (sequentially) solving the frequency-domain Helmholtz equations, our method partitions all vibration modes into chords using optimal mode conflation, performs a single time-domain wave simulation for each chord, and then separates the per-mode transfer fields using a deconflation solver. We show that our method achieves thousand-fold speedup compared to the more traditional fast boundary element methods, and maintains accuracy suitable for sound synthesis. Second, we present an integrated time-domain acoustic wavesolver to support sound rendering of a wide variety of physics-based simulation models and computer animated phenomena. We target high-quality offline rendering, and introduce methods including a sharp-interface boundary handling method, the acoustic shaders abstraction to integrate various sound sources, and a parallel-in-time synthesis algorithm for this task. We demonstrate the generality and quality of the solver by rendering sound sources of dynamic, multi-physics nature, such as vibrating solids, thin shells, water, and character. Finally, we will switch gears and introduce a new method to enrich standard rigid-body impact models with spatially varying coefficient of restitution maps, or Bounce Maps. We demonstrate that the commonly accepted hypothesis of constant restitution value per object is wildly incorrect, and propose a fast precomputation algorithm to sample and compute it. The resulting Bounce Maps can be queried in negligible time and can be used easily to enhance existing solvers. Although it is not directly related to sound synthesis, we will show that a dominant factor for varying restitution responses is the post-impact vibrations, which can cause sound.

Advisor: James Doug L. 
Hanrahan P. M. (Patrick Matthew) 
Smith Julius O. (Julius Orion)
Physiological constraints of aquatic invasions in tetrapods

Tetrapods invaded land more than 350 million years ago and have diversified enormously over time. Re-invasion of the aquatic realm has occurred across the tetrapod tree over the past 300 million years, but secondarily aquatic tetrapod lineages have not diversified to the same extent upon reinvasion of the water nor have they lasted for nearly as long. Such invasions are relatively uncommon most likely due to the differences in the physical and chemical conditions on land versus in water. Such differences require or favor different solutions to physiological challenges such as dehydration, thermoregulation, and salt balance as well as to other functions such as reproduction and locomotion. Many morphological changes associated with the transition to an aquatic lifestyle have been identified in extinct and extant tetrapods, such as vertical flattening of the tail and paddle-like limbs for more efficient swimming and dorsoventral flattening of the head for capturing prey in water. However, one remaining question in the evolution of these invaders is how these differing boundary conditions impacted the evolution of body size within these invading lineages. Chapters 1 and 2 address this question in two disparate tetrapod groups, Mammalia and Crocodyliformes. Comparative phylogenetic methods reveal that modern and fossil marine representatives of both groups have evolved to significantly larger sizes than their terrestrial counterparts, while they also maintain smaller degrees of variation and significantly faster rates of evolution. Physiological models that combine constraints from thermoregulation, metabolism, lung capacity, and feeding indicate that the regulation of body heat plays a major role in determining minimum viable sizes for mammals and crocodyliforms, while metabolism and feeding capacity may limit maximum sizes. Chapter 3 investigates similar aquatic invasions in snakes. While there is a significant increase in size as these marine snakes invade the ocean, it doesn't compare to the multiple orders of magnitude increases seen in mammals and crocodyliforms. Instead, it appears that the prior evolution of viviparity, coupled with the circumstantial occupancy of warm and low-elevation environments, facilitated these marine invasions by many ecologically diverse lineages. Combined, these studies reveal the strict demands of the aquatic medium that have caused a variety of adaptions by tetrapods before and during their aquatic invasions. In most cases, one or many key innovations are required in order to make such invasions possible. Further, these findings suggest that broad-scale patterns of morphological evolution within higher taxa are often determined more by physiological constraints than by ecological interactions or environmental fluctuations.

Keywords: Geological Sciences.
Advisor: Payne Jonathan L. 
Boyce C. Kevin 
Sperling Erik
Physiological properties of low-density ganglion cells in the primate retina

The retina provides the sole source of visual information to the brain, yet the signal from the retina is only partially understood. In primates, there are ~20 types of output cells of the retina, called retinal ganglion cells, with each type extracting specific information about the visual scene and projecting to distinct targets in the brain. The five numerically dominant retinal ganglion cell types have been extensively studied, but much less is known about the computations of the remaining ganglion cell types. To understand the visual function of the retina in health and in disease, it is necessary to understand how distinctive signals in the diverse retinal ganglion cell types emerge within retinal circuits, and how they collectively encode visual inputs. This thesis explores the physiological properties of the low-density ganglion cell types. In total, large-scale multi-electrode recordings revealed the responses of 12 retinal ganglion cell types, each with distinctive spatial, temporal, and chromatic properties. Focusing on the ON and OFF smooth monostratified cell types, strikingly irregular receptive field structure composed of spatially segregated hotspots were observed, quite different from the classical view of retinal receptive fields. Direct visual stimulation and computational inference demonstrate strong nonlinearities in the retinal circuit which contribute to receptive field hotspots. Surprisingly, visual stimulation of different hotspots produced subtly different extracellular spike waveforms in the same cell, consistent with a dendritic contribution to hotspot structure. These findings suggest a unique visual computation and spike generation mechanism in the signals carried by smooth monostratified cells to the brain.

Keywords: Bioengineering.
Advisor: Chichilnisky E. J.
Baccus Stephen A. 
Nuyujukian Paul Herag
Pinning Down Narrative; or, Wrestling in the Novels of John Irving

This thesis tackles the contexts and effects of sports within various forms of literature, using the work of American novelist John Irving as a case study. The thesis focuses on the enterprise of wrestling, and how the sport functions as a narrative device in Irving's novels, both to facilitate characterization and narrative structure. Drawing on Roland Barthes' "Mythologies," the work creates a framework for reading wrestling within the novel, and participates in a close reading of "The World According to Garp" and "The 158-Pound Marriage."

Keywords:  Department of English
John Irving
Stanford English
Bobby Pragada
The World According to Garp
The 158-Pound Marriage
Sports
Sports in Literature
Roland Barthes
Mythologies
The World of Wrestling
Collegiate Wrestling
Professional Wrestling
Wrestling
Sports Writing
Thesis
Advisor: Vermeule Blakey
Poetry as Decreation: Impersonality and Grace in T.S. Eliot and Simone Weil

This thesis posits that however separated T.S. Eliot and Simone Weil are by circumstance, political affinity, and church affiliation, their thoughts intersect at a crucial point. While Weil’s theory of decreation and Eliot’s notion of impersonality are often cast as theological and poetic innovations, they both hearken back to the Christian mystical tradition – specifically, the aspect of via negativa. Placed alongside one another, Weil’s poetic mysticism and Eliot’s concern for the spiritual reveal the capacity of poems to decreate and bring the reader to a moment of void that awaits the fulfillment of grace. This thesis will study these topics with express consideration of Eliot’s Four Quartets and Weil’s notebooks, especially Gravity and Grace.

Keywords: T.S. Eliot
Simone Weil
decreation
impersonality
grace
theology
poetry
St. John of the Cross
Christian mysticism
mysticism
Gravity and Grace
Four Quartets
The Waste Land
Via Negativa
Negative Theology
George Herbert
Department of English at Stanford University
Stanford University
catholicism
void
imagination
apophatic
kenosis
post-secular.
Thesis
Advisor: McGurl Mark
Nemerov Alexander
Polarization field enhanced transport in Gallium nitride heterostructures for energy harvesting and sensing

Over the past decade, we have witnessed a renaissance in power and RF electronics -- enabled by breakthroughs in wide-band gap semiconductors made using III-nitride materials. Yet, an exciting but emerging application of these materials is their use in extreme temperature environments such as oil/gas, combustion and space, where traditional silicon electronics do not operate. In this thesis, I discuss how polarization fields in gallium nitride on silicon (GaN-on-Si) can be used to make thermoelectric energy harvesting and sensing devices to achieve this ambitious goal of "extreme environment" operation. In the first part of this thesis, I discuss measurements of the thermoelectric properties of the aluminum gallium nitride/gallium nitride (AlGaN/GaN) two-dimensional electron gas (2DEG) from room temperature to 300 degrees Celsius. Our experiments demonstrate state-of-the-art thermoelectric power factors and thermoelectric figures of merit ~4x better than doped III-nitride materials. These properties can enable a monolithic GaN-on-Si micro-thermoelectric generator with a power density of ∼1 mW for 1 cm by 1 cm footprint, which can be used to power an extreme environment IoT node. I follow this with a brief digression on the thermoelectric properties of AlGaN/GaN films on a pyramidal Si substrate, a strategy that can increase power density in micro-thermoelectric generators. Switching gears, I next discuss how the transfer of momentum from lattice phonons to electrons, a phenomenon called phonon drag, can be used to boost the low temperature thermoelectric performance in the AlGaN/GaN 2DEG. The measurements of the phonon drag Seebeck coefficient are conducted by varying the thickness of the underlying GaN layer. For large GaN thickness (∼1.2 micrometers), we find that ∼32% of Seebeck coefficient at room temperature can be attributed to phonon drag. At 50 K, the drag component increases significantly to ∼88%. In the last part of my thesis, I discuss how manipulation of the polarization fields in the AlGaN/GaN 2DEG can be used for high-performance sensing applications. I first discuss a model for studying electronic transport in AlGaN/GaN transistors under small applied strains, which may find use in pressure sensing and device packaging. Then, I present measurements of a novel ultraviolet (UV) photodetector employing the 2DEG formed at the AlGaN/GaN interface as an interdigitated transducer. This photodetector exhibits a record high normalized photocurrent-to-dark current ratio, which enables highly sensitive detection of UV optical stimuli. Overall, the techniques explored in this thesis are an important step towards the maturation of the AlGaN/GaN-on-Si platform as an extreme environment IoT node.

Keywords: Mechanical Engineering.
Advisor: Goodson Kenneth E.
Senesky Debbie 
Pop Eric
A polarization-maintaining hollow-core fiber-optic gyroscope

Despite the success of the fiber-optic gyroscope as the world's most commercially successful fiber sensor, improving fiber-optic gyroscope (FOG) technology, particularly with regards to temperature stability, is increasingly important. Commercial FOGs have been able to meet these requirements through extensive engineering, including temperature modeling and control to reduce the drift caused by temperature-gradient variations in the sensing coil (the Shupe effect) and mu-metal shielding to reduce the drift caused by exposure to varying magnetic fields coupled to the Faraday effect. The use of a hollow-core fiber (HCF) in a fiber-optic gyroscope offers an attractive way to ease these and possibly other engineering requirements because in an HCF light travels mostly in air, where these two effects are greatly reduced. We propose and test the first implementation of a polarization-maintaining HC FOG. The HCF coil ends are directly attached to the multi-function integrated optics LiNbO3 chip, overcoming what has long been one of the biggest challenges in implementing a hollow-core fiber in this sensor. To fully characterize this FOG it was interrogated, in turn, by a broadband supersluorescent fiber source (SFS), a laser, and a laser broadened with Gaussian white noise. The SFS-driven HC FOG has a measured rotation-rate resolution comparable to that of a commercial FOG utilizing a solid-core fiber, and 3.4 times lower measured drift than previously reported for a hollow-core FOG. With a longer coil or a larger coil diameter, these values could approach the requirements for aircraft navigation. A theoretical model of optimal phase biasing was developed to further improve these results. This thesis will show that the noise of the broadened-laser-driven HC FOG is then dominated by a new effect, which is scattering mediated by coupling to the highly scattering surface modes of the HCF. Previous models of the backscattering drift in FOGs had uncertain convergence for broad source linewidths due to computation requirements. We present a new model of backscattering drift that solves the previous convergence issues by introducing a coherence function. This model was important for identifying the source of drift in the HCF FOG driven by light sources of various linewidths, and it was used to verify the backscattering coefficient for the HCF and confirm the existence of highly scattering surface modes.

Keywords: Electrical Engineering.
Advisor: Digonnet Michel J. F. 
Fan Shanhui
Solgaard Olav
Polite language reflects competing informational and social goals

We use polite speech every day. We produce simple words of apology ("sorry") or gratitude ("thanks"), and more complex polite utterances ("these cookies could use a bit of salt" or "your dress is gorgeous!"). Why do people speak politely? This thesis proposes a goal-based framework to polite speech: that polite speech arises from competing informational and social concerns such as the speaker's desire to convey information most informatively ("informational goal"), and to be kind and respectful to the interactants ("prosocial goal") and/or present the speaker herself as a particular kind of individual ("presentational goal"). In Chapter 1, I provide an overview of this framework that aims to unify previous theoretical accounts of polite speech, and then I describe existing empirical data on comprehension and production of polite speech in adults and children. Then I present our own empirical studies investigating adults' and children's understanding of polite language. First, I present two sets of empirical studies looking at the development of polite language understanding in children: a study examining 2- to 4-year-old children's judgments for polite requests (Chapter 2), followed by a study probing 5- to 8-year-old children's judgments for polite lies versus blunt truths (Chapter 3). Results from these studies show that children are sensitive to speakers' social concerns behind language use, and that they consider tradeoffs between those goals based on the context at hand. In Chapter 4, we examine adults' understanding of polite speech: We present a computational model that formalizes the notion of goals as utilities that speakers try to maximize through language use, and show that this model successfully captures adults' predictions and judgments for polite lies and indirect speech. Overall, the work presented in this thesis reveals how children's and adults' understanding of polite speech reflects their understanding of speakers' informational and social goals and tradeoffs between them, and helps advance our knowledge of pragmatics and social cognition in general.

Keywords: Psychology.
Advisor: Frank Michael C. (Professor of human biology) 
Goodman Noah (Noah D.) 
Gweon Hyowon
Markman Ellen M.
Political Patronage from Programmatic Policy - the case of a primary health care initiative in Delhi, India

Mohalla Clinics are community-based clinics in India's capital city Delhi set up in 2015 by the Aam Aadmi Party, a newly founded political party (2012) currently at the helm of Delhi's government. Mohalla Clinics routinely provide essential health services including medicines, diagnostics, and consultation free of cost to traditionally underserved urban residents. From the outset, the initiative was touted as one that would bring free health care to the poor as well as more public and national recognition to the Aam Aadmi Party as a champion of the ordinary citizen's cause. In this paper, I study whether the establishment of Mohalla Clinics affected the share of votes received by its main opposition the BJP in municipal elections. Through this, I test whether programmatic policy which is expected to generate added public goods is effective for political patronage. I find suggestive evidence from OLS and IV results that the clinics did reduce BJP vote margins, but less so in places that were strongholds. In addition, the clinics generated substantial public goods in the form of unprecedented health care access even though they may have fallen short in vote-garnering.

Keywords:  Department of Economics
Stanford Department of Economics
Thesis
Advisor: Alsan Marcella