VictorJuiz/thesis huggingface dataset:
Far-from-equilibrium phenomena in protein dynamics [electronic resource]

The diverse physical principles that govern living things conform to one common precept: all biological processes operate, to some extent, out-of equilibrium. As our understanding of biological pathways advances at the nanoscale, theoretical and simulation techniques that function under non-equilibrium conditions will play an important role in elucidating the working environment of the cell. In this research, large-scale molecular dynamics simulations, discrete dynamical network models, and sophisticated non-equilibrium theories are synthesized to study glassy and dissipative processes facilitated by protein molecules. Leveraging atomistic molecular dynamics data derived from the Folding@home distributed computing project, a number of detailed biophysical systems are examined. I first describe glassy solvent structures that emerge as functional components of a protein chaperone, and I connect such observations to the theory of disordered systems. By coupling Folding@home data, Markov state models of biomolecular dynamics, and the theory of large deviations, I go on to characterize [beta] sheet-rich, amyloid-like misfolded states that appear on protein folding landscapes; I explore the relationship between these misfolded states and so-called dynamical glass transitions. Applying theory related to the Crooks fluctuation theorem, I next explicate the dissipative dynamics in detailed models of signaling proteins, and I illustrate how the input of external energy harmonizes with equilibrium fluctuations to yield functional signaling components. Lastly, I discuss methods by which protein landscapes can be sampled in an adaptive fashion and means for recovering equilibrium kinetics from biased, non-equilibrium simulation data.

Keywords: Chemistry.
Advisor: Pande Vijay primary advisor. Thesis advisor
Markland Thomas E.
Martinez Todd J. (Todd Joseph)
Fault reactivation potential and stress path due to severe depletion and subsequent injection in Paleogene (Lower Tertiary) reservoirs of the Gulf of Mexico [electronic resource]

This thesis applies the principles of geomechanics to model and better understand the implications of production in a new and prolific oil province in ultra-deepwater Gulf of Mexico. The larger problem at hand is to characterize the geomechanics of the Paleogene in order to understand how the change in stress can affect wellbore stability, production-related fault slip, injection-related fault slip, and reservoir deformation leading to rock failure. We determine depletion and subsequent injection reservoir stress paths, the potential for fault reactivation, and depletion-related compaction in order to aid in future reservoir management and planning.

Keywords: Geophysics.
Advisor: Zoback Mark D. primary advisor. Thesis advisor
Beroza Gregory C. (Gregory Christian) advisor. Thesis advisor
Hornby Brian E. advisor. Thesis advisor
Sleep Norman H. advisor. Thesis advisor
Fluorine passivation of defects in germanium devices [electronic resource]

Today, new materials and structures are being deployed in MOSFET devices as the research/industry is facing challenges to ensure continued scaling for next generation technology. Germanium is one of the promising candidate materials to replace silicon-based devices, having higher mobility than silicon for better MOSFET performance. In addition, its optical operation above 1um wavelength regime makes it a suitable material for opto-electronic applications such as optical interconnects and infrared image sensors. However, due to its low band-gap (0.66eV) and fragile nature, germanium is affected severely by the presence of defects within the crystal and the surface. The effect of these defects mainly results in low n-type dopant activation, high leakage current and low carrier lifetime, which hinder the successful adaptation of germanium devices by the industry. To prevent these defect related degradation in germanium devices, we investigate the effect of fluorine passivation of defect sites. Fluorine, being the most reactive element in the periodic table has high potential to bond with the defect sites, thereby eliminating their degenerate effects. In this dissertation, we will first introduce the effect of defects in germanium. Then we will discuss the effects of fluorine as a passivation element for germanium defects. With this knowledge, we will explain the application of fluorine passivation for the following devices: 1. Forward current enhancement and leakage current reduction in n+/p diode. 2. Source and drain series resistance reduction by defect passivation in Ge nMOSFET. 3. Mobility enhancement by gate-stack fluorine passivation in Ge MOSFET. 4. Carrier lifetime enhancement in n+/p diode. Such applications of the fluorine passivation of germanium defects open new potential for high performance Ge-based devices for both MOSFET and optical devices.

Keywords: Electrical Engineering.
Advisor: Saraswat Krishna primary advisor. Thesis advisor
Nishi Yoshio
Wong Hon-Sum Philip
FOMC Responses to Calls for Transparency: Evidence from the Minutes and Transcripts Using Latent Semantic Analysis

The Federal Reserve has become increasingly transparent in recent years in response to both internal inclinations and external calls from Congress and the private sector, yet it has stopped short of holding open FOMC meetings. Instead, the Fed releases minutes and statements to summarize its policy decisions. This paper applies Latent Semantic Analysis to FOMC transcripts and minutes from 1976—2008 in order to analyze the FOMC’s responses to calls for transparency. It reveals that two notable events explain much of the variation in transparency over this 32-year period. First, the 1978 Humphrey-Hawkins Act increased the degree to which the FOMC used meeting minutes to convey the content of its meetings. Historical evidence suggests that this was done because the Act required the Fed to tie its objectives to short-run Congressional and Presidential economic goals. Second, the 1993 decision to publish nearly verbatim transcripts also increased transparency. However, the cost was a decreasing degree of deliberation at each meeting, as evidenced by lower variance in content disagreement at the member level. By applying LSA to FOMC documents, this study presents a unique way of quantifying transparency and suggests LSA’s usefulness to other empirical studies in Economics.

Keywords:  Department of Economics
Federal Open Market Committee
Deliberation
NLP
Central Bank
Stanford University
Department of Economics
Thesis
Advisor: Taylor John B.
A freely-moving monkey treadmill model [electronic resource]

Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. In this dissertation, I present a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. The freely-moving rhesus monkey model employs technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. This dissertation demonstrates the flexibility and utility of this new monkey model, including the first recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Using this monkey model, it is shown that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average firing rate of the threshold crossings covaries with the speed of individual steps. On a population level, neural state-space trajectories of walking at different speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment, and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.

Keywords: Electrical Engineering.
Advisor: Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Meng Teresa H. advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Fully implicit and semi-implicit hybrid discontinuous space-time Galerkin methods for acoustic wave propagation [electronic resource]

This dissertation, based on the concept of the existing discontinuous Enrichment method (DEM) for frequency domain analysis, proposes a hybrid discontinuous Galerkin method (DGM) for the numerical solution of transient problems governed by the wave equation in two and three spatial dimensions. This hybrid DGM extends concepts of DEM into the time domain for problems that are better suited for analysis in time domain. The discontinuous formulation in both space and time enables the use of solutions to the homogeneous wave equation in the approximation. In this dissertation, within each finite element, the solutions in the form of polynomial waves are employed. The continuity of these polynomial waves is weakly enforced through suitably chosen Lagrange multipliers. Numerical results for two and three dimensional model problems, in both low and mid frequency regimes, show that the proposed DGM outperforms the conventional space-time finite element method and Newmark family semi-discrete schemes. Additionally an alternative semi-implicit formulation is proposed where global level linear systems stemming from the implicit formulation is traded in favour of smaller and independent local systems. Numerical results for two dimensional model problems, in both low and mid frequency regimes, show that for a fixed mesh resolution, the semi-implicit DGM requires far less memory than its fully implicit counterpart. The semi-implicit scheme also parallelizes and scales very well with the number of available CPUs.

Advisor: Farhat Charbel primary advisor. Thesis advisor
Lew Adrian advisor. Thesis advisor
Papanicolaou George advisor. Thesis advisor
The future of terror [electronic resource] : musical settings of the poetry of Matthea Harvey

This dissertation is comprised of two musical works that set the poetry of Matthea Harvey. These songs explore themes of terror, contingency, complacency, and the grotesque. The first musical work presented here is "as if to hold the hemispheres of their own heads together (black; dahlia 1)" for flute, oboe, tenor saxophone, soprano, violin, violoncello, and double bass. This piece sets Harvey's "How We Learned to Hold Hands, " from the poet's collection Modern Life. Ensemble Dal Niente premiered "as if to hold the hemispheres of their own heads together (black; dahlia 1)" in January, 2014. The second musical work presented here is "the future of terror, " for flute and soprano. This song cycle sets Harvey's series "The Future of Terror, " also from her collection Modern Life. Liz Pearse and Élise Roy — for whom this work was written — premiered "the future of terror" in May, 2014.

Keywords: Music.
Advisor: Ferneyhough Brian
Kronengold Charles (Charles Stewart) advisor. Thesis advisor
Ulman Erik
Generating synthetic noncoding RNAs for programmable and tunable gene control [electronic resource]

The engineering of biological systems offers significant promise for advances in areas including health and medicine, scalable manufacturing, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for genetically encoding molecular sensing, catalysis, data storage, information processing, and gene regulatory capabilities. We describe the development and application of methods for generating and characterizing functional noncoding RNA sequences, including novel biological sensing capabilities and regulatory switches in microbial and mammalian hosts. We developed a surface plasmon resonance-based platform for the rapid characterization of kinetic and equilibrium binding properties of aptamers to small molecules and a high-throughput, quantitative, cell-based screening strategy to support rapid generation of ribozyme-based RNA switches with user-specified regulatory activities. We applied these screening and characterization strategies to construct synthetic RNA regulatory switches to the pharmaceutical drug folinic acid in both microbial and mammalian cells in response to drug administration.

Keywords: Chemistry.
Advisor: Smolke Christina D. primary advisor. Thesis advisor
Cochran Jennifer R. advisor. Thesis advisor
Khosla Chaitan
Generation of Induced Pluripotent Stem Cells for Study of MHC I - Mediated Neural Plasticity

Although it has long been known that major histocompatibility complex (MHC) markers play an important role in the adaptive immune system, recent work has implicated MHC Class I in neuronal plasticity in the central nervous system (CNS). However, little is known about the consequences of the innate immune response on neuronal MHC I expression and its subsequent effect on plasticity, an aspect critical to stem cell-derived neurons and their use in transplantation therapy. In this study, we generate neurons from induced pluripotent stem cells (iPSCs) derived from wild type and MHC I – deficient mice to use as a knockout model. We then utilize the inflammatory cytokine interferon-gamma (IFNγ) as a model of the innate immune response to induce MHC I expression in these neurons. We observe that wild type neurons exhibit an increase in MHC I, whereas the knockout-derived neurons display no changes in MHC I levels as predicted. The iPSCs and resulting neurons produced were further characterized for use in future connectivity and transplantation studies to probe the effects of MHC I on stem cell transplant survival and incorporation, with the final goal of employing non-steroidal anti-inflammatory drugs (NSAIDs) to attenuate the inflammatory cytokine effect and increase transplant efficacy. These results provide important insight into the relationship between the innate immune response and stem cell-derived neuronal integration, taking a crucial step toward the future goal of using patient-specific iPSCs in clinical transplant therapies.

Keywords:  Department of Biology
Biology
Neurobiology
MHC I
Neuronal Plasticity
Interferon-gamma
iPSC
Innate immune response
Thesis
Advisor: Palmer Theo
McConnell Susan
A genomic analysis of NKX2-1-driven oncogenesis in non-small cell lung cancer [electronic resource]

Human cancer is a complex set of diseases, but as the tools and techniques of genomic analysis expand, each newly explored cancer genome furthers our understanding of the genetic factors that drive and sustain malignant cells. In the case of lung cancer, many efforts are being made to define the mechanisms by which specific genetic alterations drive the oncogenic activity of these malignancies. Genomic analysis studies have uncovered a focal amplification located at the cytoband 14q13.3 in the adenocarcinoma subtype of non-small cell lung cancer (NSCLC). The minimal 14q13.3 amplicon includes NKX2-1, a homeobox transcription factor that plays a crucial role in lung organogenesis. Preliminary studies with NKX2-1 have revealed that the overexpression of the protein secondary to gene amplification in lung adenocarcinoma creates a context-specific, or, alternatively, a "lineage-dependent", environment in which NKX2-1 becomes essential for tumor cell line survival when expressed outside of its normal developmental context. While there is unequivocal evidence that NKX2-1 is crucial for the survival of lung adenocarcinoma cell lines with the 14q13.3 amplification, its mechanism of action has yet to be fully deduced. The work presented in this dissertation focuses on uncovering the mechanisms by which NKX2-1 drives proliferation and survival of a subset of NSCLC tumors.

Advisor: Pollack Jonathan R.
Morrison Ashby J.
Sweet-Cordero Eric advisor. Thesis advisor
West Robert advisor. Thesis advisor
Geologic history of the Chukchi Borderland, Arctic Ocean [electronic resource]

The Amerasia Basin in the Arctic Ocean is one of the least understood tectonic systems on Earth and radically different ideas have been proposed to explain the tectonic development and geologic nature of its intrabasinal ridges. Recently, a push for data collection by Arctic nations for Extended Continental Shelf (ECS) claims under the United Nations Convention for the Law of the Sea treaty has added greatly to the amount of information available about this poorly understood region. Over 380,000 km2 of multibeam bathymetric data were collected between 2003-2012 as part of the Unite States' ECS project as well as 17 dredges, most of which sampled rocks from submarine outcrops within the central Amerasia Basin. Joint operations with the U.S. and Canada resulted in over 15,000 linear km of multichannel seismic reflection data. In order to answer first order questions as to the nature of the bathymetric features within the Amerasia Basin, and their relationship to the surrounding margins, we report on dredged rock samples from the Chukchi Borderland and suggest that this important bathymetric feature is related to Paleozoic mountain belts of the northern Laurentian margin. The multibeam bathymetric dataset and regional muilti-channel seismic transect also documented in this study, are the basis for development of a chronology of sedimentation, deformation, and volcanism that link the geologic history of the poorly known bathymetric features within the Amerasia Basin. Together these data and geologic samples challenge long held ideas about the tectonic history of the Chukchi Borderland and provide constraint for tectonic reconstruction models.

Keywords: Geological and Environmental Sciences.
Advisor: Graham S. A. (Stephan Alan)
Grove Marty
Dunbar Robert B.
Meisling Kristian advisor. Thesis advisor
Caldwell Margaret R.
Germanium-tin [electronic resource] : a material and technology for group-IV photonics integration on silicon

The germanium-tin (GeSn) alloy system is a highly engineerable, Group-IV material system that has the potential to yield a useful direct bandgap, making it a desirable material for developing light emitters and other photonic devices. Furthermore, its Group-IV nature makes it electronically compatible with silicon and is important for ubiquitous integration into current silicon-based chips. In this dissertation, we explore several properties, features, design, and integration of GeSn alloys on silicon for photonics. Heterostructure devices with GeSn/Ge are developed in quantum-well microdisk resonators and quantum-well light-emitting diodes emitting beyond 2-[mu] m wavelength. Designs, considerations, and strategies towards developing GeSn-based lasers are presented and discussed.

Keywords: Electrical Engineering.
Advisor: Harris J. S. (James Stewart)
Saraswat Krishna advisor. Thesis advisor
Vuckovic Jelena advisor. Thesis advisor
Ge/SiGe quantum well devices for optical interconnects [electronic resource]

Increasing processing power has been at the heart of technological boom witnessed in the past few decades. However, the communication delay of electrical interconnects poses a fundamental limit to future improvements. On-chip optical interconnects are an alternative solution to allow for continued advancements in processing power. This thesis explores the potential of Ge/SiGe quantum well devices as a candidate for an on-chip optical interconnect system. The Ge and SiGe material system is particularly promising for optical interconnects because these materials are compatible with Si CMOS technology. Our work demonstrates that these devices can perform as light emitters, modulators and detectors—the most important components in an optical interconnect system. Furthermore, we developed vertically coupled waveguide Ge quantum well devices and discuss their performance as well as our efforts to integrate these devices into a functioning optical interconnect system.

Keywords: Electrical Engineering.
Advisor: Harris J. S. (James Stewart)
Kamins Theodore I.
Miller D. A. B. advisor. Thesis advisor
Getting a Head Start on Culture

Head Start is a government pre-school program run through the United Stated Department of Health and Human Services. Head Start’s goal as an organization is “Helping people. Changing lives. Building communities” and it primarily serves low socio-economic communities and the children that live within them. Head Start has a long history of improving academic success by correcting or buffering against the negative effects of poverty so children coming through its program are developmentally on par with their peers. However Head Start has vested interest in many other non-academic areas of development, such as cultural development. Head Start has long worked with ethnically dense and diverse communities to encourage the cultural growth of its students and local community. However, fostering cultural development is a difficult task as there are many sensitive issues, rules, and obligations that any organization should adhere to when trying to improve cultural development. One particular area of Head Start where the teaching of culture is especially difficult is within Native American reservation centers. The Office of Head Start (OHS) regularly encounters requests for assistance from reservations in improving their ability to support children’s cultural development, which is understandable considering the fact that Native American culture has a long history of mistreatment in this nation and is severely damaged. The goal of this particular thesis is to explore how parents and teachers within one reservation community want their children to develop culturally. I asked three particular questions regarding the relevance of traditional culture, perceived cultural needs, and the efficacy of Head Start in meeting those needs. The questions are as follows. In the minds of parents and teachers, how relevant is teaching Native American culture at the pre-school? What are the cultural needs, as perceived by parents and teachers, of the children within the Head Start program? How do parents and teachers perceive the efficacy of Head Start’s approach to teaching culture within the classroom? Through this research I hope to contribute to a growing body of literature on culturally-minded teaching and Native American identity formation.

Keywords: Graduate School of Education
Stanford University
Education honors
Head Start
Native American culture
Thesis