VictorJuiz/thesis huggingface dataset:
Saxitoxin-derived probes for labeling voltage-gated sodium channels [electronic resource]

Voltage-gated sodium channels (NaVs) are obligatory membrane proteins responsible for the initiation and propagation of bioelectricity in excitable cells. A desire to study channel trafficking and regulatory mechanisms inspires the development of molecular tools for labeling channels patterned after the bis-guanidinium neurotoxin, (+)-saxitoxin (STX). The synthesis and electrophysiological evaluation of a novel class of cysteine-reactive, trifunctional STX-maleimide conjugates are described herein. These probes covalently inhibit wild-type NaVs, and contain a fluorophore, affinity, or bioorthogonal tag for visualizing and/or isolating toxin-bound channels. STX-maleimide derivatives were also demonstrated to covalently inhibit cysteine mutant channels, enabling the development of an orthogonal ligand-receptor pair. In addition, the preparation and characterization of reversible fluorescent STX conjugates are also described, which display excellent potency against neuronal NaV subytpes. Such reagents therefore represent valuable imaging agents for the visualization of NaVs in cultured neurons.

Keywords: Chemistry.
Advisor: Du Bois Justin primary advisor. Thesis advisor
Chen James Kenneth advisor. Thesis advisor
Wender Paul A. advisor. Thesis advisor
Scalable techniques for quantum network engineering [electronic resource]

In the quest for creating ``quantum enhanced'' systems for information processing many currently pursued design strategies are difficult to scale significantly beyond a few dozen qubits. The dominant design paradigm relies on starting with near perfect quantum components and a vast overhead of classical external control. In my thesis I present tools and methods for a more integrated framework which treats quantum and hybrid quantum-classical systems on equal footing. We have recently defined a Quantum Hardware Description Language (QHDL) capable of describing networks of interconnected open quantum systems. QHDL is compiled to symbolic and numerical system models by a custom software tool suite named QNET. This allows us to rapidly iterate over quantum network designs and derive the associated equations of motion. Building on a recently developed model reduction technique for describing networks of nonlinear oscillators in the semi-classical regime, I present a library of nonlinear optical circuit designs useful for all-optical computation. I further present an end-to-end theoretical proposal to create all-optical neuromorphic circuits capable of supervised learning. The system is hierarchically composed of tunable linear amplifiers, analog phase memories and thresholding non-linear circuits which can be used to construct more general quantum feedback networks for nonlinear information processing. Finally, I introduce a novel model transformation capable of dividing the description of quantum states into a low-dimensional quasi-classical part coupled to a lower complexity quantum state. This approach is exact and naturally tailored to simulating coupled quantum systems with varying degrees of dissipation.

Keywords: Applied Physics.
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Ganguli Surya
Hayden Patrick (Patrick M.)
Vuckovic Jelena advisor. Thesis advisor
"Se svou neúnavnou prací" [electronic resource] : Antonín Salac̆ and classics at the margins

In this dissertation, I give an account of the history of classical studies in Czechoslovakia, focalized through the life and career of the philologist, epigrapher, and archaeologist Antonín Salač (1885-1960). Salač was born, educated, and habilitated in Prague, in the center of Europe but the margins of classicism. What does the study of Graeco-Roman antiquity look like in circumstances like these? Because of the relative geopolitical marginality of Czechoslovakia, as well as the relative marginality of classical studies in Czech culture, in order to facilitate their scholarly work, Salač and his colleagues were compelled to leverage a host of strategies to which our histories of classical studies rooted in great powers and "source nations" have failed to acquaint us—strategies running the gamut from theories of "small nations" to quasi-core-periphery economic relations, subtended by historical forces like Pan-Slavism and Czech nationalism. I also integrate into my dissertation people—women, diggers, "local enablers"—and narratives—dead ends, false starts, unanswered questions—not typically accorded space in our histories of classical studies. Thus, the life and career of Antonín Salač become an opportunity for a new perspective on the people and practices that create both classical studies and its histories.

Keywords: Classics.
Advisor: Shanks Michael primary advisor. Thesis advisor
Ceserani Giovanna advisor. Thesis advisor
Parker Grant Richard
Searches for light scalar dark matter [electronic resource]

If the dark matter is made up of a bosonic particle, it can be ultralight, with a mass potentially much below 1 eV. Moduli fields, whose values could set couplings and masses of known particles, are good candidates for such light dark matter. Their abundance in our Universe would manifest itself as tiny fractional oscillations of Standard Model parameters, such as the electron mass or the fine-structure constant, in turn modulating length and time scales of atoms. Rods and clocks, used for gedanken experiments in the development of relativity theory, have since transformed into actual precision instruments. The size of acoustic resonators and the frequency of atomic transitions can now be measured to 1 part in 10^24 and 10^18, respectively, and thus constitute sensitive probes of moduli. Atomic gravitational wave detectors can have a time-domain response to modulus dark matter, and sense temporal oscillations of atomic frequencies down to 1 part in 10^25. This thesis gives an overview of the parameter space of modulus dark matter, and compares the sensitivity of various experimental proposals relative to existing constraints from searches for new forces. I will focus on two classes of experimental strategies in particular: resonant-mass detectors (rods), and atomic spectroscopy and interferometry (clocks).

Keywords: Physics.
Advisor: Dimopoulos Savas
Graham Peter (Peter Wickelgren) advisor. Thesis advisor
Senatore Leonardo
Searching for heavy photons in the HPS experiment [electronic resource]

The Heavy Photon Search (HPS) is a new experiment at Jefferson Lab that searches for a massive U(1) vector boson (known as a heavy photon or A') in the MeV-GeV mass range and coupling weakly to ordinary matter through a kinetic mixing interaction. The HPS experiment seeks to produce heavy photons by electron bremsstrahlung on a fixed target, is sensitive to heavy photon decays to electron-positron pairs, and targets the range in heavy photon mass from 20 to 600 MeV, and kinetic mixing strength epsilon^2 from 1E-5 to 1E-10. HPS searches for heavy photons using two signatures: a narrow mass resonance and displaced vertices. This dissertation presents the theoretical and experimental motivations for a heavy photon, the design and operation of the HPS experiment, and the displaced vertex search. The data used in this dissertation is the unblinded fraction of the 2015 HPS run, for the period of operation where the HPS silicon vertex tracker (SVT) was operated at its nominal position. This data was recorded from May 13 to May 18, 2015, at a beam energy of 1.056 GeV and a nominal beam current of 50 nA. The integrated luminosity is 119 inverse nanobarns, which is equivalent to 0.172 days of ideal running at the nominal beam current. This dissertation presents results (signal significance and upper limits) from the displaced vertex search in the mass range from 20 to 60 MeV, and kinetic mixing strength epsilon^2 from 2E-8 to 1E-10. This search does not have sufficient sensitivity to exclude a canonical heavy photon at any combination of mass and mixing strength. The strictest limit achieved in this analysis on the production of a particle that decays like a heavy photon is 115 times the expected production cross-section for a heavy photon. Factors limiting the sensitivity of this analysis are discussed. Projections of HPS performance with the full 2015 data set, and with planned improvements to the analysis, are presented. Comparisons are also made to earlier reach estimates.

Keywords: Physics.
Advisor: Jaros John
Burchat P. (Patricia) advisor. Thesis advisor
Peskin Michael Edward
Sediment transport due to river plumes in stratified, rotationally-influenced lakes [electronic resource]

River inflows are often the dominant source of sediment, contaminants, and nutrients into an aquatic system and the dynamics of these flows dictate the fate of introduced constituents and their impact on the lake. The form of the river plume depends on the density of the river flow relative to the ambient surface waters. For instance, a dense river plume will plunge beneath the surface and, in a deep stratified system, will intrude into the water column at a depth of neutral buoyancy. While near-field (momentum-dominated) mixing between the plume and ambient water masses dictates the depth of an inflow intrusion, once the intrusion forms, the plume is influenced by buoyancy and rotational forces. The far-field plume is characterized by a balance between rotation and buoyancy forcing and the mid-field is defined as the adjustment region between the near-field momentum dominated region and the far-field geostrophic plume region. We have employed both field observations and numerical modeling to investigate sediment transport dynamics from intrusive plumes in the mid- and far-field regions. Field observations of multiple river inflows were collected in Pallanza Bay of Lake Maggiore, Italy, a stratified, rotational lacustrine system. We verified that the measured inflow intrusion speeds in Pallanza Bay were well characterized by a simple buoyancy-driven plume scaling. The effective sediment settling speed was shown to be one order of magnitude larger than the expected settling speed based on particle size, which can be due to effects such as particle flocculation and convective sedimentation. We also investigate the role of ambient stratification on the plume dynamics in the mid and far-field regions with a three-dimensional numerical model that was extensively validated with observations. An analytical expression was developed to predict the extent of sediment (in the along-plume direction) using the flow rate and ambient stratification. Finally, an idealized numerical model was employed to extend the range of conditions and to investigate the role of the lateral boundary in a lake on the plume transport dynamics. The lateral boundary modifies the amount of material that is trapped in a recirculating region near the mouth relative to the amount transported along the boundary. The plume propagation speed and thickness, which differ for buoyant and intrusive plumes, are shown to dictate the extent of sediment transport across a wide range of conditions. The timescale of sediment settling relative to the timescale of plume development will dictate sediment transport in a lake. In particular, the sediment settling timescale relative to the timescale of far-field plume development will dictate whether the sedimentation extent increases or decreases with the basin Rossby number.

Keywords: Civil and Environmental Engineering.
Advisor: Fringer Oliver B. (Oliver Bartlett) primary advisor. Thesis advisor
Fong Derek advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
SEDIMENTOLOGY AND STRATIGRAPHY OF A PART OF THE UPPER CRETACEOUS PIGEON POINT FORMATION, SAN MATEO COUNTY, CALIFORNIA

The Upper Cretaceous Pigeon Point Formation (PPF) is exposed for 16 km along the Pacific coast of San Mateo County, California, from just south of Pescadero Beach to just north of Año Nuevo Point. This study focuses on the area from Pescadero Point to Pebble Beach and explores the stratigraphy, process sedimentology and the depositional environments of the formation. The PPF is part of the Salinian terrane, the basement block of granitoid and metasedimentary rocks lying immediately west of the San Andreas Fault in central California. The Salinian block is thought to be the major source of the PPF sediments. The study area includes a stratigraphic section about 500 meters in thickness that is composed of three main lithofacies: thick-bedded sandstone, interbedded mudstone and sandstone, and mudstone. The formation has both syn-depositional (planar lamination, cross sets, ripples) and post-depositional (soft sediment deformation such as water escape structures, dish structures, flame structures and a sandstone dike) sedimentary structures. S3/Ta divisions form the most of the sedimentation units in the thick-bedded sandstone units, which were deposited by high-density turbidity currents, whereas thin-bedded sandstone and mudstone beds are interpreted as partial or complete Bouma sequences deposited by low-density flows. The facies associations suggest that the overall depositional setting of Pigeon Point rocks in the study area was a channel mouth or upper splay for the thick-bedded sandstones and a laterally related levee-overbank and possible lobe fringe areas for the interbedded sandstone and mudstone and mudstone lithofacies.

Keywords:  Department of Geological and Environmental Sciences
School of Earth Energy &amp; Environmental Sciences
Pigeon Point Formation
sedimentology
stratigraphy
Thesis
Advisor: Lowe Donald
Graham Stephan
Selecting the dimension of a subspace in principal component analysis and canonical correlation analysis [electronic resource]

It is common practice in statistical data analysis to perform dimension reduction, as modern data sets grow larger and more complex. Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA) are two of the most popular methods for dimension reduction. Despite the popularity of these methods, there is no widely adopted standard approach to select the proper dimension of the subspace to be obtained by PCA or CCA. To address this issue, we propose a novel method utilizing the hypothesis testing framework and test whether the currently selected subspace via PCA or CCA captures all the statistically significant signals in the given data set. While existing hypothesis testing approaches do not enjoy the exact type 1 error property and lose power under some scenarios, the proposed method provides exact type 1 error controls along with decent size of power in detecting signals. Central to our work is the post-selection inference framework which facilitates valid inference after data-driven model selection; the proposed hypothesis testing method provides exact type 1 error controls by conditioning on the selection event which leads to the inference.

Keywords: Statistics.
Advisor: Taylor Jonathan
Tibshirani Robert primary advisor. Thesis advisor
Johnstone Iain advisor. Thesis advisor
Self interferometry [electronic resource] : self interference cancellation and its applications

Wireless radios are typically half-duplex radios, and hence, the current wireless networks are Time Division Duplex(TDD) or Frequency Division Duplex (FDD). Full-duplex for wireless communications is considered impossible i.e. radios cannot transmit and receive at the same frequency at the same time. If we could achieve full duplex radios we won't need TDD or FDD strategy, we could potentially double the spectral efficiency. The fundamental challenge in achieving full duplex radios, when a radio is transmitting while simultaneously trying to receive (hear another radio) on the same frequency, it cannot. It's own transmission acts as a very strong self-interference. In this dissertation, we present the design, prototype and implementation of full duplex mimo radios. In particular, we built the first single antenna per chain full-duplex MIMO radios for 2.4 GHz WiFi-PHY i.e. to achieve an m-chain MIMO transceiver we need only m antenna. We design novel cancellation algorithms and circuits that reduce all self-interference to the noise floor and enable full-duplex MIMO PHY with almost no loss. The cancellation algorithms designed for full duplex themselves are of independent interest and apply to many other interference problems in wireless. We exploit this to build a full duplex relay which is the first one to provide both range extension and increase the capacity, is oblivious to ongoing transmission the source and the destination don't even realise that relay exist. Further, we build on top of the cancellation BackFi; a system that provides high throughput connectivity using backscatter to IoT devices at a very lower power. BackFi backscatters all ubiquitous ongoing WiFi signals to provide connectivity. Thus, providing connectivity without using extra spectrum just leveraging full duplex link. The cancellation, in essence, cancels all the reflections from the environment of self transmitted signal, inferring the reflection from cancellation provides us information about the environment. Towards the end, we abstract this information with a platform of Self-Interferometry, which provides with a unique way of looking at environment using wireless signals instead of light. Thus building a camera with wireless radios.

Keywords: Electrical Engineering.
Advisor: Katti Sachin primary advisor. Thesis advisor
Prabhakar Balaji
Weissman Tsachy advisor. Thesis advisor
Sensing using ubiquitous wireless communication infrastructure [electronic resource]

An estimated 12 billion connected devices exist today and this number is expected to grow to 30 billion by 2020. These connected devices will be used to control everyday objects like thermostat, light bulb, or even our coffee machines. Sensors and network connectivity are two very important enablers for these devices. Most of these devices will be connected via ubiquitous wireless networks like WiFi, Bluetooth, and ZigBee. Despite their widespread deployment, these wireless networks so far have been used solely for the purpose of transferring digital data between radios. In this thesis, we will describe how we can overload functionalities to these ubiquitous wireless networks by adding novel sensing modalities into them. We first describe the design and implementation of a localization system that can pinpoint radios to sub-meter accuracy in an indoor environment. This system provides localization by simply analyzing the wireless signal that is used for communication. Such a localization system can help network managers to identify and locate unauthorized interferers. At the same time, such a localization technique can also enable navigation of large indoor spaces like airports and malls using smartphones. Next, we describe a technique that allows a wireless Access Point (AP) to detect and analyze reflections of wireless signal from its own transmission. In particular, we demonstrate how it enables a WiFi AP to trace human motion by simply listening to and analyzing reflections from its own transmission. But this technique also has many more applications beyond motion tracing. As an example, we describe design and implementation of a system which allows us to passively read data from Internet of Things (IoT) sensors using ambient WiFi signals. Such a system can prolong life of battery operated sensors or even pave path for RF powered sensors in the future.

Keywords: Electrical Engineering.
Advisor: Katti Sachin primary advisor. Thesis advisor
Montanari Andrea advisor. Thesis advisor
Wetzstein Gordon advisor. Thesis advisor
Shock tube studies of kinetics of conventional and alternative engine fuels [electronic resource]

Experiments were performed using shock tube and laser absorption methods to investigate the oxidation and pyrolysis systems of conventional and alternative fuels, and fuel components, under engine-relevant conditions. Ignition delays were measured during fuel oxidation and several stable intermediates were measured during fuel pyrolysis. Ignition delay times were measured in the gas-phase for several engine fuels in various oxidizers behind reflected shock waves in a heated high-pressure shock tube. Initial reflected shock conditions were as follows: temperatures of 1000 - 1500 K, pressures of 2 - 60 atm, equivalence ratios of 0.2 - 2, and oxygen concentrations of 4% and 21% with argon and 21% in synthetic air. Ignition delay times were measured using sidewall pressure, OH* emission at 306 nm as well as 3.39 µm mid-infrared He-Ne laser absorbance. The new experimental results were modeled using several kinetic mechanisms with the most current jet fuel surrogate mixtures as well as with a new hybrid model currently in development at Stanford. Measurements of stable decomposition products of engine fuel pyrolysis were performed behind reflected shock waves at temperatures from 1100 to 1600 K and pressure of 12 atm for all engine fuels tested. Species time-history measurements of ethylene and methane were made in pyrolysis experiments using laser absorption. Similar product yields were found for conventional fuels but not for alternative fuels at current conditions. These data provide needed input for the development and validation of a new compact hybrid kinetic model under development at Stanford. A traditional jet fuel chemical kinetics model using surrogate fuel compounds and combined detailed mechanisms of these surrogates was also discussed and compared with the hybrid model. The performance of the hybrid model appears better than that of the surrogate model, but still needs improvement. Finally, we applied a new driven-gas loading method that constrains the volume of reactive gases, thereby producing near-constant-pressure test conditions for reflected shock measurements. The near-constant-pressure ignition delay times provide a new database for low-temperature 1-butanol mechanism development independent of non-idealities caused by either shock attenuation or pre-ignition perturbations. Comparisons of these near-constant-pressure measurements with predictions using several reaction mechanisms available in the literature were performed. All current studies of kinetics of conventional engine fuels, engine fuel component (decalin), alternative engine fuels, and alternative fuel component (butanol) provide useful kinetic targets for the development, validation, and refinement of combustion kinetics models, and provide valuable insights on the pre-ignition phenomenon typically observed in shock tube ignition delay experiments.

Keywords: Mechanical Engineering.
Advisor: Hanson Ronald primary advisor. Thesis advisor
Bowman Craig T. (Craig Thomas)
Wang Hai