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The OMFIT (One Modeling Framework for Integrated Tasks) modeling environment and the BRAINFUSE module have been deployed on the PPPL (Princeton Plasma Physics Laboratory) computing cluster with modifications that have rendered the application of artificial neural networks (NNs) to the TRANSP databases for the JET (Joint European Torus), TFTR (Tokamak Fusion Test Reactor), and NSTX (National Spherical Torus Experiment) devices possible through their use. This development has facilitated the investigation of NNs for predicting heat transport profiles in JET, TFTR, and NSTX, and has promoted additional investigations to discover how else NNs may be of use to scientists at PPPL. In applying NNs to the aforementioned devices for predicting heat transport, the primary goal of this endeavor is to reproduce the success shown in Meneghini et al. in using NNs for heat transport prediction in DIII-D. Being able to reproduce the results from is important because this in turn would provide scientists at PPPL with a quick and efficient toolset for reliably predicting heat transport profiles much faster than any existing computational methods allow; the progress towards this goal is outlined in this report, and potential additional applications of the NN framework are presented.
ContributorsLuna, Christopher Joseph (Author) / Tang, Wenbo (Thesis director) / Treacy, Michael (Committee member) / Orso, Meneghini (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2015-05
Description
The central goal of this thesis is to develop a practical approach to validating the correctness of SSA forms. Since achieving this goal is very involved for a general program, we restrict our attention to simple programs. In particular, the programs we consider are loop-free and are comprised of simple assignments to scalar variables, as well as input and output statements. Even for such a simple program, a full formal treatment would be very involved, extending beyond the scope of an undergraduate honors thesis.
ContributorsLusi, Dylan Patrick (Author) / Bazzi, Rida (Thesis director) / Fainekos, Georgios (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Microwave hydrolysis of egg-white lysozyme was optimized using 1H liquid-state nuclear magnetic resonance (NMR) spectroscopy experiments for amino acid analysis (AAA). Time held under microwave hydrolysis was arrayed for 2, 4, 6, 8, 10, and 15 minutes. Correlations from gCOSY 2D NMR experiments combined with 1H assignments in the one-dimensional chemical shift spectra identified 18 of the 20 amino acids found in lysozyme. Comparison with Uniprot database amino acid composition values revealed the optimal microwave hydrolysis time lies between 4 and 6 minutes. Identification of lysozyme was confirmed with the ExPASy online database search tool AACompIdent. The microwave hydrolysis procedure presented is a simple analytical technique allowing quick and reliable sample preparation in less than one hour that requires no separation or derivation of amino acids residues prior to detection.
ContributorsEdwards, Maximillian Ashur (Author) / Yarger, Jeff (Thesis director) / Marzke, Robert (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
In this paper, I analyze representations of nature in popular film, using the feminist / deconstructionist concept of a dualism to structure my critique. Using Val Plumwood’s analysis of the logical structure of dualism and the 5 ‘features of a dualism’ that she identifies, I critique 5 popular movies – Star Wars, Lord of the Rings, Brave, Grizzly Man, and Planet Earth – by locating within each of them one of the 5 features and explaining how the movie functions to reinforce the Nature/Culture dualism . By showing how the Nature/Culture dualism shapes and is shaped by popular cinema, I show how “Nature” is a social construct, created as part of this very dualism, and reified through popular culture. I conclude with the introduction of a number of ‘subversive’ pieces of visual art that undermine and actively deconstruct the Nature/Culture dualism and show to the viewer a more honest presentation of the non-human world.
ContributorsBarton, Christopher Joseph (Author) / Broglio, Ron (Thesis director) / Minteer, Ben (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Geographical Sciences and Urban Planning (Contributor)
Created2015-05
Description
Twitter, the microblogging platform, has grown in prominence to the point that the topics that trend on the network are often the subject of the news and other traditional media. By predicting trends on Twitter, it could be possible to predict the next major topic of interest to the public. With this motivation, this paper develops a model for trends leveraging previous work with k-nearest-neighbors and dynamic time warping. The development of this model provides insight into the length and features of trends, and successfully generalizes to identify 74.3% of trends in the time period of interest. The model developed in this work provides understanding into why par- ticular words trend on Twitter.
ContributorsMarshall, Grant A (Author) / Liu, Huan (Thesis director) / Morstatter, Fred (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
Description
This project discusses simulation results of star formation by Active Galactic Nuclei (AGN) jets using the WENO method. A typical AGN jet with velocity uj=0.3c, density ρj=10^(-2) H/cm3, and temperature Tj=10^(7) K was injected into a 425 light years square region. The jet passes through a stationary inhomogeneous ambient background of temperature Ta=5x10^4 K and density ρa= 2 H/cm^3 to test if AGN jets, by creating bow shocks propagating through the interstellar medium and molecular clouds, can form stars in the densest regions. According to the star formation criteria for gravitational collapse of Cen and Ostriker, the resulting simulations indicate the presence of star formation via AGN jets (1992). The parameters are tuned to match Centaurs A to identify star formation in this galaxy. The simulations will also be run in three dimensions in the future and for longer time intervals to gain a better understanding of the star formation process via AGN jets.
ContributorsFindley, Christina Marie (Author) / Gardner, Carl (Thesis director) / Scannapieco, Evan (Committee member) / Barrett, The Honors College (Contributor) / School of Earth and Space Exploration (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
Description
A literature review summarizing the current status of conservation efforts of the Mojave Desert tortoise (Gopherus agassizii) including a brief overview of the Endangered Species Act (ESA) and its applicability to this species' conservation. A genetic and physiological comparison of the morphologically similar Mojave species with the Sonoran (Gopherus morafkai) species proceeded by an analysis of if and how the ESA should apply to the Sonoran population. Analysis of current plans and interagency cooperations followed by a multi-step proposal on how best to conserve the Sonoran population of Desert tortoise.
ContributorsKulik, Elise Chikako (Author) / Kusumi, Kenro (Thesis director) / Tollis, Marc (Committee member) / Wilson Sayres, Melissa (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
We study an idealized model of a wind-driven ocean, namely a 2-D lid-driven cavity with a linear temperature gradient along the side walls and constant hot and cold temperatures on the top and bottom boundaries respectively. In particular, we determine numerically the response on flow field and temperature stratification associated with the velocity of the lid driven by harmonic forcing using the Navier-Stokes equations with Boussinesq approximation in an attempt to gain an understanding of how variations of external forces (such as the wind over the ocean) transfer energy to a system by exciting internal modes through resonances. The time variation of the forcing, accounting for turbulence at the boundary is critical for allowing penetration of energy waves through the stratified medium in which the angles of the internal waves depend on these perturbation frequencies. Determining the results of the interaction of two 45 degree angle wave beams at the center of the cavity is of particular interest.
ContributorsTaylor, Stephanie Lynn (Author) / Welfert, Bruno (Thesis director) / Lopez, Juan (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Economics Program in CLAS (Contributor) / W. P. Carey School of Business (Contributor)
Created2015-05
Description
Almost commuting matrices, i.e. matrices with a sufficiently small commutator, may be nearly commuting, i.e. there may exist matrices close by which do commute. By referencing current literature, this condition is studied for fixed dimension, unitary, self-adjoint, and orthogonal matrices. These proofs are made more accessible and compared to each other, providing insight to possible future progress in the field.
ContributorsMolloy, Riley Phillip (Author) / Spielberg, Jack (Thesis director) / Quigg, John (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2015-05
Exploring Structure and Function of Human Cold Sensing Protein TRPM8 with ROSETTA Comparative Models
Description
Transient Receptor Potential (TRP) channels are a diverse class of ion channels notable as polymodal sensors. TRPM8 is a TRP channel implicated in cold sensation, nociception, and a variety of human diseases, including obesity and cancer. Despite sustained interest in TRPM8 since its discovery in 2001, many of the molecular mechanisms that underlie function are not yet clear. Knowledge of these properties could have implications for medicine and physiological understanding of sensation and signaling. Structures of TRP channels have proven challenging to solve, but recent Cryoelectron microscopy (Cryo-EM) structures of TRPV1 provide a basis for homology-based modeling of TRP channel structures and interactions. I present an ensemble of 11,000 Rosetta computational homology models of TRPM8 based on the recent Cryo-EM apo structure of TRPV1 (PDB code:3J5P). Site-directed mutagenesis has provided clues about which residues are most essential for modulatory ligands to bind, so the models presented provide a platform to investigate the structural basis of TRPM8 ligand modulation complementary to existing functional and structural information. Menthol and icilin appear to interact with interfacial residues in the sensor domain (S1-S4). One consensus feature of these sites is the presence of local contacts to the S4 helix, suggesting this helix may be mechanistically involved with the opening of the pore. Phosphatidylinositol 4,5-bisphosphate (PIP2)has long been known to interact with the C-terminus of TRPM8, and some of the homology models contain plausible binding pockets where PIP2 can come into contact with charged residues known to be essential for PIP2 modulation. Future in silico binding experiments could provide testable hypothesis for in vitro structural studies, and experimental data (e.g. distance constraints from electron paramagnetic resonance spectroscopy [EPR]) could further refine the models.
ContributorsHelsell, Cole Vincent Maher (Author) / Van Horn, Wade (Thesis director) / Wang, Xu (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05