460 Works

Conformational Plasticity of HIV-1 Env and Implications for Vaccine Design

Zhi Yang
The human immunodeficiency virus (HIV) envelope glycoprotein (Env), a (gp120/gp41)₃ trimer, is present on the surface of the viral envelope membrane. Env binding to the host cell receptor, CD4, and the co-receptor, CCR5 or CXCR4, triggers a cascade of Env conformational changes and structural rearrangements which ultimately leads to the viral and host cell membrane fusion, marking the initiation of a viral infection. In this work, we present findings of the conformational changes of an...

Nanophotonic Application to Biomedical Devices

Haeri Park Hanania
Nanophotonics is the study of interactions between nanoscale structures and light. It has greatly expanded the fields of application over the past decades, taking advantage of the advancement in MEMS technology. The most common nanophotonic structures consist of either dielectrics, metals, or both. When a nanophotonic structure contains metals, it is considered as a plasmonic structure. Plasmonics is a field of light-metal interactions. Due to the negative permittivity of metals, the electromagnetic energy of light...

Nickel-Catalyzed Electroreductive Cross-Coupling Reactions of Anhydrides and Alkyl Halides

Daniel K. Chang
The formation of new carbon–carbon bonds is one of the most important transformations in organic chemistry due to its ability to build the backbone of organic molecules. Nickel-catalyzed reductive cross-coupling reactions have recently emerged as an efficient and powerful strategy for the creation of new carbon–carbon bonds. Furthermore, electrochemistry can be harnessed to overcome some of the challenges encountered in many of the reductive cross-coupling reactions in the literature. Herein, we discuss the development of...

Progress in Low-Cost Gallium Arsenide Solar Cells

Phillip R. Jahelka
In order to prevent disastrous global warming the manufacturing capacity of renewable energy power sources must grow rapidly. Solar photovoltaics will likely be one of humanity's main sources of energy in the future due to the enormous available resource but increasing the manufacturing capacity of solar panels is hamstrung by both the limited profit margins of the highly-competitive renewable energy market and the enormous capital cost of building the factories that convert sand into semiconductor-grade...

Quantum Statistical Mechanics, Noncommutative Geometry, and the Boundary of Modular Curves

Jane Mariam Panangaden
The Bost-Connes system is a C*-dynamical system whose partition function, KMS states, and symmetries are related to the explicit class field theory of the field of rational numbers. In particular, its zero-temperature KMS states, when evaluated on certain points in an arithmetic sub-algebra, yield the generators of the maximal abelian extension of the rationals. The Bost-Connes system can be viewed in terms of a geometric picture of 1-dimensional Q-lattices. The GL₂ system is an extension...

Exploration of Materials and Mesostructures Accessible via Inorganic Phototropic Growth

Kathryn Rose Hamann
Biological systems have evolved complex methods to interact with and adapt to a given environment to optimize fitness, and replication of these natural mechanisms in artificial systems has been a long-standing area of research interest with significant potential utility. Phototropic growth is a natural phenomenon wherein an organism spatially orients biomass addition to optimize light collection. An artificial analog, inorganic phototropic growth, has been demonstrated and relies on a similar process: semiconductor mass is selectively...

The Claytons

Margaret Sui
[Prologue] To the North, tucked beside the Adirondack Mountains, lay the suburban town of Bethlehem, an average town filled with ordinary people. The nearest city, Albany, was a small city with few attractions, so that natives who saw the tourist stand at the airport would wonder why tourists would ever visit. Indeed, few did. Despite the mediocrity that existed in the place, the people of Bethlehem held for it a fierce pride – they bragged...

Earthquakes and the New Paradigm of Diluted Cores in Gas Giant Planets

Benjamín Rodo Idini Zabala
In this thesis, I present results on two distinct topics within geophysics: earthquake mechanics and the core of gas giant planets. A common element connecting this work is the similar research approach that I use to address each topic. Each chapter in this thesis attempts to provide a simple physical understanding on the fundamental aspects relevant to the system in question. Further, I use numerical models to expand my arguments in some cases, while in...

Developing Dalotia coriaria, the Greenhouse Rove Beetle, as a Novel Model Organism

David Ryan Miller
This thesis deals with the development of Dalotia coriaria, the greenhouse rove beetle, as a novel model organism. A fundamental characteristic of metazoan life is inter-species interactions. Chapter 1 explores why there is a need for Dalotia as a new model organism to study these interspecies interactions in ways that are intractable with current established models. It also explores the life history characteristics of Dalotia that make it amenable to development as a novel model...

Causal Sampling, Compressing, and Channel Coding of Streaming Data

Nian Guo
With the emergence of the Internet of Things, communication systems, such as those employed in distributed control and tracking scenarios, are becoming increasingly dynamic, interactive, and delay-sensitive. The data in such real-time systems arrive at the encoder progressively in a streaming fashion. An intriguing question is: what codes can transmit streaming data with both high reliability and low latency? Classical non-causal (block) encoding schemes can transmit data reliably but under the assumption that the encoder...

The \"Interpolated Factored Green Function\" Method

Christoph Bauinger
This thesis presents a novel Interpolated Factored Green Function (IFGF) method for the accelerated evaluation of the integral operators in scattering theory and other areas. Like existing acceleration methods in these fields, the IFGF algorithm evaluates the action of Green function-based integral operators at a cost of O(N log N) operations for an N-point surface mesh. The IFGF strategy capitalizes on slow variations inherent in a certain Green function analytic factor, which is analytic up...

Methods for Control of Granular Material Attributes

Robert Andrew Buarque de Macedo
A granular material is a collection of discrete, solid particles. This substance is ubiquitous in nature and industry, with examples ranging from soils, jointed rocks, foodstuffs, ball bearings, powders, and even asteroids. As such, understanding granular materials is necessary for making sense of the physical world. Tremendous progress has been made in directly simulating granular materials in the previous decades, in particular via the discrete element method (DEM). Nevertheless, there remains ample opportunity for manipulating...

Supplemental Materials for the Atlas of Bacterial and Archaeal Cell Structure

Catherine Oikonomou & Grant Jensen
Supplemental materials (pdb files, images, and narration) for version 2.1 of "The Atlas of Bacterial & Archaeal Cell Structure" by Catherine M. Oikonomou & Grant J. Jensen

Optimisation & Generalisation in Networks of Neurons

Jeremy Bernstein
The goal of this thesis is to develop the optimisation and generalisation theoretic foundations of learning in artificial neural networks. The thesis tackles two central questions. Given training data and a network architecture: Which weight setting will generalise best to unseen data, and why? What optimiser should be used to recover this weight setting? On optimisation, an essential feature of neural network training is that the network weights affect the loss function only indirectly through...

Surveying metal antimonate photoanodes for solar fuel generation

Lan Zhou & John M. Gregoire
Data .zip file containing data tables used to generate the figures of the associated manuscript, raw photoelectrochemistry data, and .udi files that combined composition and XRD data. See the enclosed readme.txt

I. Dynamics at the Galileo Probe Site on Jupiter and II. Orbital and Thermal Evolution of Ganymede

Adam Peter Showman
The low abundances of water and H₂S measured by the Galileo probe at Jupiter sug­gest that the probe entered a downdraft where dry air from above cloud top advects to 10 bars or deeper. I use basic physical constraints to extract dynamical informa­tion from three aspects of Galileo probe data. First, I suggest that to remain dry, the downdraft must be underlain by a stable layer which inhibits mixing of volatiles from below; this requires...

Test record to confirm a behavior of Invenio-RDM

Robert Doiel
This is a test record. It should remain restricted or deleted after the test.

PDF version the Atlas of Bacterial and Archaeal Cell Structure

Catherine Oikonomou & Grant Jensen
PDF format of version 2.3 of "The Atlas of Bacterial & Archaeal Cell Structure" by Catherine M. Oikonomou & Grant J. Jensen

Data and code for figures of \"Nano-electromechanical spatial light modulator enabled by asymmetric resonant dielectric metasurfaces\" by Hyounghan Kwon et al

This upload contains the main dataset and codes represented in the figures of the following publication: "Nano-electromechanical spatial light modulator enabled by asymmetric resonant dielectric metasurfaces" by Hyounghan Kwon et al.

BEDMAP2 - Ice thickness, bed and surface elevation for Antarctica - standardised shapefiles and geopackages

Peter Fretwell, Hamish Pritchard, David Vaughan, Jonathan Bamber, N. Barrand, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, D. Callens, H Conway, Alison Cook, Hugh Corr, D Damaske, V. Damn, Fausto Ferraccioli, Rene Forsberg, S. Fujita, Y. Gim, P. Gogineni, J. Griggs, Richard Hindmarsh, P. Holmlund … & Julien Bodart
We present here the Bedmap2 ice thickness, bed and surface elevation aggregated points and survey lines. The aggregated points consist of statistically-summarised shapefile points (centred on a continent-wide 500 m x 500 m grid) that reports the average values of ice thickness, bed and surface elevation from the full-resolution survey data and information on their distribution. The points presented here correspond to the additional points to Bedmap1 used for the gridding of Bedmap2. The data...

Test record to confirm a behavior of Invenio-RDM

Robert Doiel
This is a test record. It should remain restricted or deleted after the test.

WennbergLab/py-ginput: ginput v1.1.7 release

Installing with `pip install` or `python setup.py install` will now correctly copy the files in `ginput/data` to the installation directory. Installing in develop mode through `make install` is still the recommended way of setting up `ginput` for normal use; however, if this is part of a larger project and you want the code to live alongside your other dependencies, that works now. Two notes: 1. `ginput` does cache look up tables in the `data` directory...

Enhanced Superconductivity in Spin-Orbit Proximitized Bernal Bilayer Graphene

Yiran Zhang
#Data for Enhanced Superconductivity in Spin-Orbit Proximitized Bernal Bilayer Graphene. This dataset contains the experimental data from the following paper: Yiran Zhang, Robert Polski, Alex Thomson, Etienne Lantagne-Hurtubise, Cyprian Lewandowski, Haoxin Zhou, Kenji Watanabe, Takashi Taniguchi, Jason Alicea, and Stevan Nadj-Perge, "Enhanced Superconductivity in Spin-Orbit Proximitized Bernal Bilayer Graphene", see also ArXiv: 2205.05087 Excel files are processed experimental data for Fig.1 to Fig.4 in the main text, please refer to Fig1.xlsx to Fig4.xlsx. Within each...

Data from: Common protein-coding variants and the racing phenotype in galloping racehorse breeds

Haige Han, Emmeline Hill, Beatrice McGivney, Lucy Allen, Dongyi Bai, Leanne Corduff, Gantulga Davaakhuu, Jargalsaikhan Davaasambuu, Dulguun Dorjgotov, Thomas Hall, Andrew Hemmings, Amy Holtby, Tuyatsetseg Jambal, Badarch Jargalsaikhan, David MacHugh, Hubert Pausch, Carol Readhead, David Warburton, Manglai Dugarjaviin, Uyasakh Jargalsaikhan & Naveen Kadri
Centuries-long selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest...

Gut Microbiota Modulation of Host Feeding Behavior

James Anthony Ousey
The rich, diverse community of microorganisms in the gastrointestinal tract of animals, or gut microbiota, regulates aspects of host metabolism, immunity, and neural function, with resulting effects on the expression of complex behaviors, including feeding. In this thesis, we sought to characterize gut microbiota influences on the behavioral response to palatable foods in mice. We discover that binge-like consumption of palatable foods, including high-sucrose pellets and a high-fat diet, is exacerbated in mice in the...

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