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Orbitofrontal Cortex And The Decision-Making Process, Youran Wu
Orbitofrontal Cortex And The Decision-Making Process, Youran Wu
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Orbitofrontal cortex (OFC) is situated at the ventral floor of the prefrontal cortex region. OFC and some of its related structure (ventral striatum, ventral tegmental area, basolateral amygdala) are considered to be part of the valuation system that is essential to the decision-making process. In order to understand the exact role OFC plays in the decision-making process, we sought to find out how decision variables are represented in different OFC projections, and what will happen if OFC projections were disrupted. The first specific aim of this project is to find out whether projections to OFC related structures are originated from …
Development Of A Line-Scanned Dual-Axis Confocal Microscope For Video-Rate Diagnostic Imaging, Danni Wang
Development Of A Line-Scanned Dual-Axis Confocal Microscope For Video-Rate Diagnostic Imaging, Danni Wang
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
The prevalence of oral cancer has been increasing at an alarming rate in recent years. Due to a limited understanding of the cause and progression of this disease, patient prognosis remain poor, and the mortality and morbidity of the disease remain significant. The need to diagnose cancerous regions early is key to patient survival. However, the high cost and invasive nature of standard pathological analysis motivates the search for an alternative real-time imaging technology that provides accurate non-invasive early diagnosis of the disease. The goal of this thesis is to develop a line-scanned dual-axis confocal (LS-DAC) microscope for high-resolution, high-contrast, …
Enhanced Backbone Dihedral Parameters For Protein Simulations, Carmenza Martinez
Enhanced Backbone Dihedral Parameters For Protein Simulations, Carmenza Martinez
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Molecular Dynamics (MD) and Monte Carlo (MC) simulations of biomolecules have become a supportive tool to experimental methods for structure refinement, protein folding, drug discovery and many more applications. This is due to the increase in computational power and necessity of finding a method capable of describing the forces at work in chemical systems without the need to do extensive quantum calculations. All of these are possible because of the classical definition of the potential force field function. The force field function is essential to perform MD simulations, since this equation carries the physical description of the molecules being studied. …
Improved Generalized Born Solvent Model Parameters For Protein And Nucleic Acid Simulations, Hai Minh Nguyen
Improved Generalized Born Solvent Model Parameters For Protein And Nucleic Acid Simulations, Hai Minh Nguyen
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Generalized Born solvent model offers inexpensive approach for solvation energy calculation as compared to explicit solvent and Poisson-Boltzmann (PB) method. Thanks to its speed, GB models have been widely used in molecular dynamics (MD) simulations. However the speed comes with tradeoffs. Literatures have pointed out the weaknesses of GB models in inaccurately calculating solvation energy that leads to helical bias in protein simulation or unstable DNA/RNA duplex in nucleic acid simulation. Here we introduced the reparameterization of the recently developed GB-Neck model to improve its accuracy. Compared to other pairwise GB models (e.g. GB-OBC and GB-Neck) the new GB models …
Synthesis And Characterization Studies Of Li-Fe-In-(Po4) Phases: Chemical Relatives Of Battery Cathode Material Lithium Iron Phosphate, Michael Richard Saccomanno
Synthesis And Characterization Studies Of Li-Fe-In-(Po4) Phases: Chemical Relatives Of Battery Cathode Material Lithium Iron Phosphate, Michael Richard Saccomanno
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Lithium iron(II) phosphate, also known as lithium ferrophosphate (LiFePO4, LFP), has been the subject of many recent energy storage studies. As a battery cathode material, LFP has many advantages for commercial applications. Compared to its competitors like LiMn2O4 and the ubiquitous but carcinogenic LiCoO2, LFP (specific energy = 600 Wh/kg) exhibits low toxicity, low cost, good thermal stability, and excellent electrochemical performance at high charge/discharge rates. As part of the efforts to understand and improve LFP, a great amount of research has been committed towards developing, characterizing, and electrochemically testing chemical relatives of …
The Impact Of Children With And Without Developmental Disabilities On Relationship Satisfaction And The Parenting Alliance, Caitlin E. Walsh
The Impact Of Children With And Without Developmental Disabilities On Relationship Satisfaction And The Parenting Alliance, Caitlin E. Walsh
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Studies have shown that parents of children with ASD report greater negative impact of the child on family adaptation including financial stability, sibling relationships, and parents' social lives than parents of children with other chronic problems (e.g. | Down syndrome, ADHD, ODD). Parents of children with ASD also report increased marital discord and parent stress. Currently there are no studies examining differences in parent perceptions of child impact and how this factor may influence parental relationships, particularly parents' spousal relationships and agreement on co-parenting. In this study, 157 mothers of children with an Autism Spectrum Disorder (ASD), Down syndrome (DS), …
Image Reconstruction Theory And Implementation For Low-Dose X-Ray Computed Tomography, Yan Liu
Image Reconstruction Theory And Implementation For Low-Dose X-Ray Computed Tomography, Yan Liu
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
The excessive X-ray radiation exposure during clinical examinations has been reported to be linked to increase lifetime risk of cancers in patients. Directly lower computed tomography (CT) dose without improving reconstruction technique will degrade the image quality and is not acceptable. The objective of this dissertation is investigating novel reconstruction methods to improve image quality in low-dose cases. In practice, it is usually more convenient to improve the conventional analytical methods by refining projection model and designing new filters due to the fast computing time and low computational complexity. However, the reconstructions from analytical methods are still sensitive to artifacts …
Representations Of Disability In Of Mice And Men And One Flew Over The Cuckoo's Nest: Avoiding Handicapism In The Classroom, Lyndsay L. Mccabe
Representations Of Disability In Of Mice And Men And One Flew Over The Cuckoo's Nest: Avoiding Handicapism In The Classroom, Lyndsay L. Mccabe
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
In this thesis, I examine two novels that feature characters with disabilities and that are often taught in secondary English classes. These texts will be analyzed through a disability studies perspective - a form of analysis that is not often taught in schools. The disability studies perspective involves looking at disability in a critical light and examining the social, cultural, and political ramifications of assumptions that are made about those considered to be " disabled" by the able-bodied majority. Using this lens, I will explore the assumptions about disability that seem to be represented in these works through their use …
American Masculinity And Home In Antebellum Literature, Derek Scott Mcgrath
American Masculinity And Home In Antebellum Literature, Derek Scott Mcgrath
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
The conventional argument in literary and gender studies of nineteenth-century United States culture has been that the home was women's claimed sphere of influence, whereas men were excluded from the home because of their economic, cultural, and societal commitments to the public sphere. Even as Catharine Beecher, Lydia Maria Child, Sarah Josepha Hale, and other adherents to a conservative domestic ideology closely associated the private sphere with women, these same writers identified specific roles and spaces that they expected men to occupy in the home. Hardly only a woman's domain, the home was a powerful force in motivating constructions of …
Is There Room For The Modern Narrator? A Study Of Narrative Intrusion In Henry James' The Golden Bowl, Rachael Pompeii
Is There Room For The Modern Narrator? A Study Of Narrative Intrusion In Henry James' The Golden Bowl, Rachael Pompeii
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
At the turn of the twentieth century, narrative presentation saw one of the most intense transitionary movements in literary history. The instructive, omniscient authorial narrator of Victorian literature slowly faced demise as an increasing turn towards subjective, stream-of-consciousness narration dominated the literary age of twentieth century modern realism. The critical and fictional work of Henry James, literary genius who wrote across the century line, persists in the presentation of a distinctive narrating body at the same time that it encourages and anticipates the incipient effacement of such a figure. In his final completed novel, The Golden Bowl, James' narrative choices …
Pharmacological Targeting Of Mutant P53 - Hsf1 Feed Forward Circuit, Dun Li
Pharmacological Targeting Of Mutant P53 - Hsf1 Feed Forward Circuit, Dun Li
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Tumor suppressor protein p53 responds to cellular stress by activating transcriptional and transcription-independent programs that induce apoptosis, growth arrest or senescence. Given its critical tumor suppressing role, p53 is often mutated in human cancers. Once altered by missense mutations in the DNA-binding domain, mutant p53 (mutp53) protein becomes highly stabilized in tumors, which is critical for mutp53′s oncogenic gain-of function. Current insight into the mechanism of tumor-specific stabilization of mutp53 is fragmentary and largely derived from ectopically constructed cell systems. We find that in human cancer cells endogenous mutp53, despite its ability to interact with MDM2, suffers from a profound …
Polymodal Grain-Size Modes In Long Island Sands, Silts, And Weathered Bedrock, Courtney Anne Melrose
Polymodal Grain-Size Modes In Long Island Sands, Silts, And Weathered Bedrock, Courtney Anne Melrose
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
The purpose of this study is to determine if grain size modes already present in weathered bedrock sediments can be retained and inherited in derived, or processed sediments. To test this theory, weathered bedrock sediment, as well as Cretaceous aged sands and silts, Glacial sands and silts, Loess-like silt sediment, and glacially transported granitic gneisses were collected and analyzed for grain size. This study is based on the implicit assumption that grain size modes are indicative only of process, and are not reflective of modes present in the parent material of the sediment. A distinct pattern of grain size modes …
Using Seismic Observations And Modeling To Place Constraint On The Structure Beneath Japan And Central America, Hui Long
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Understanding Earth's internal structure by seismic observations, both temporally and spatially, is key in seismology. In this thesis, I constrained structural changes beneath the Japan subduction zone based on a newly developed theory, and detailed mid to lower mantle structure beneath Central America by waveform and travel time observations and modeling. A newly developed theory states that the differential wave field of two repeated sources in a temporally changed medium can be equivalently treated as wave fields propagating from virtual point sources or volumetric sources. The virtual point sources or volumetric sources are located at the place of temporal changes, …
High-Throughput Single-Cell Copy Number Profiling For Cancer Heterogeneity Analysis, Taimour Baslan
High-Throughput Single-Cell Copy Number Profiling For Cancer Heterogeneity Analysis, Taimour Baslan
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Intra-tumoral genetic heterogeneity has long been recognized, yet remains poorly understood. This has primarily been due to the lack of sensitive technologies to measure it. Genome wide analysis at the level of single cells has recently emerged as a powerful tool to dissect cancer genome heterogeneity. However, to be truly transformative, single cell approaches must accommodate the analysis of large numbers of single cells. Here, using integrative informatics and molecular biology approaches this study presents a robust, low-cost, and high-throughput method to retrieve the genome-wide copy number landscape of hundreds of single cancer cells. Application of the method to human …
The Role Of Tolc In Francisella Tularensis Virulence, Christopher Richard Doyle
The Role Of Tolc In Francisella Tularensis Virulence, Christopher Richard Doyle
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Francisella tularensis is a Gram-negative, facultative intracellular pathogen and the causative agent of tularemia. F. tularensis is a Tier 1 agent of bioterrorism that is highly lethal via the pulmonary route of infection. F. tularensis invades host cells, escapes the phagosome, and replicates in the cytosol prior to being released upon host cell death. The molecular mechanisms behind the virulence of F. tularensis are largely unknown. Among the described virulence factors of F. tularensis is a functional type I secretion system (T1SS). The T1SS is important for the secretion of virulence factors from the bacterial cytoplasm to the extracellular environment. …
Identification Of Sporulation-Defective Genes And A Rab-Cascade Model For The Formation Of The Forespore Membrane In Schizosaccharomyces Pombe, Esma Ucisik-Akkaya
Identification Of Sporulation-Defective Genes And A Rab-Cascade Model For The Formation Of The Forespore Membrane In Schizosaccharomyces Pombe, Esma Ucisik-Akkaya
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
In the fission yeast, Schizosaccharomyces pombe, environmental stress conditions such as nitrogen starvation induce mating of two haploid cells. The newly formed diploid cells immediately undergo meiosis and form spores, which are equivalent to gametes in higher organisms. The packaging of the haploid nuclei, which are formed after two rounds of meiosis, is achieved by the de novo formation of double membranes called forespore membranes, which form adjacent to the meiotic spindle pole bodies (SPBs). This work focuses on the initiation of the forespore membrane at the SPB and the genes that are required for the proper formation of the …
Democracy And Its Others, Jeffrey Harry Epstein
Democracy And Its Others, Jeffrey Harry Epstein
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Today's unprecedented levels of human migration present urgent challenges to traditional conceptualizations of national identity, nation-state sovereignty, and democratic citizenship. The instrumental valorization or vilification of foreignness for nationalistic ends has long-determined who is to be included within or excluded from " the people" of the democratic state. Against this instrumentalization, I argue that foreignness is an originary and constitutive element of democratic political identity which severs the links among nationality, citizenship, and democratic rights. Accordingly, a re-conceptualization of democratic rights is required that reflects the structural necessity of foreignness to democratic political identity. | 225 pages
Propaedeutic To Philosophy: Dialogue And Truth In Philosophical Practice, Lauren Nelson Hesse
Propaedeutic To Philosophy: Dialogue And Truth In Philosophical Practice, Lauren Nelson Hesse
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
This dissertation advocates a model of dialogue as an approach to education and to philosophical discourse itself that is capable of acknowledging and accommodating the manifold possibilities for human thought. Contemporary philosophy is permeated by a loss of certainty and the increasingly problematic nature of the concept of truth, and the complication of these concepts exposes significant limitations in the ways we conceptualize thought itself. Working in this vein, Gilles Deleuze identifies what he calls an " image of thought," which characterizes the forms we have traditionally allowed thinking to take. His critique of this image, along with its subsequent …
A Comprehensive Investigation And Coupler Design For Higher-Order Modes In The Bnl Energy Recovery Linear Accelerator, Carlos Marques
A Comprehensive Investigation And Coupler Design For Higher-Order Modes In The Bnl Energy Recovery Linear Accelerator, Carlos Marques
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
A next generation Energy Recovery Linac (ERL) is under development in the Collider-Accelerator Department at Brookhaven National Laboratory (BNL). This ERL uses a superconducting radio frequency (SFR) cavity to produce an electric field gradient ideal to accelerate charged particles. As with many accelerators, higher-order modes (HOMs) can be induced by a beam of charged particles traversing the linear accelerator cavity. The excitation of these modes can result in problematic single and multi-bunch effects and also produce undesirable heat loads to the cryogenic system. Understanding HOM prevalence and structure inside the accelerator cavity is crucial for devising a procedure for extracting …
Towards Single Photon Nonlinearities Using Cavity Eit, Zakary Burkley
Towards Single Photon Nonlinearities Using Cavity Eit, Zakary Burkley
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
In third order nonlinear mediums, the intensity of one optical field can modify the phase of another optical field. This is known as cross-phase modulation (XPM) and is important for Quantum Information Processing (QIP) as phase shifts of single-photons that exceed π rad can be used to implement two-qubit quantum logic gates. For a conventional XPM scheme, the Kerr nonlinearity responsible for XPM is too small for appreciable phase shifts to be achieved with low intensity optical fields. However, Electromagnetically Induced Transparency (EIT) can increase this nonlinearity by several orders of magnitude. This thesis discusses the experimental construction of a …
Optical Forces On Metastable Helium, Christopher Scott Corder
Optical Forces On Metastable Helium, Christopher Scott Corder
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Optical forces using lasers allow precise control over the motion of atoms. The bichromatic optical force (BF) is unique in its large magnitude and velocity range, arising from the absorption and stimulated emission processes. These properties were used to transversely collimate a beam of metastable helium (He∗ ) using the 2^{3}S − 2^{3}P transition. The collimation created a very bright beam of He∗ , allowing experiments of neutral atom lithography. The He∗ beam was used to pattern material surfaces using a resist-based lithography technique, where the pattern was determined by either mechanical or optical masks. The optical masks produced features …
Exploring Warped Compactifications Of Extra Dimensions, Sujan P. Dabholkar
Exploring Warped Compactifications Of Extra Dimensions, Sujan P. Dabholkar
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
In 1920s, the concept of extra dimensions was considered for the first time to unify gravity and electromagnetism. Since then there have been many developments to understand the unification of fundamental forces using extra dimensions. In this thesis, we study this idea of extra dimensions in higher dimensional gravity theories such as String Theory or Supergravity to make connections with cosmology. We construct a family of non-singular time-dependent solutions of a six-dimensional gravity with a warped geometry. The warp factor is time-dependent and breaks the translation invariance along one of the extra directions. Our solutions have the desired property of …
Measurement Of Direct Photons In Ultra-Relativistic Au+Au Collisions, Haijiang Gong
Measurement Of Direct Photons In Ultra-Relativistic Au+Au Collisions, Haijiang Gong
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Direct photons provide a tool to study the different stages of a heavy ion collision, especially the formation of the quark-gluon-plasma (QGP), without being influenced by the strong reaction and hadronization processes. The yield of direct photons can be determined from the inclusive photon yield and the photon yield from hadronic decays. At low pT, where a significant fraction of direct photon is expected to come from the thermalized medium of deconfined quarks and gluons and interacting hadrons, the measurement is very challenging. These so-called thermal photons carry information about the initial temperature of the medium. We present …
Observation Of $\Nu_E$ Appearance From An Off-Axis $\Nu_{\Mu}$ Beam Utilizing The Neutrino Energy Spectrum, Joshua Michael Hignight
Observation Of $\Nu_E$ Appearance From An Off-Axis $\Nu_{\Mu}$ Beam Utilizing The Neutrino Energy Spectrum, Joshua Michael Hignight
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
T2K (Tokai to Kamiokande) is a long baseline neutrino experiment located in Japan. It uses a 30 GeV proton beam at the J-PARC accelerator in Tokai to produce an intense off-axis muon neutrino beam that travels 295 km through the Earth to Super-Kamiokande. One of its primary goals is to measure neutrino oscillation parameters by directly detecting $\nu_e$ at Super-Kamiokande that have oscillated from the $\nu_{\mu}$ beam. The measurement of $\nu_{\mu} \rightarrow \nu_{e}$ oscillations are of a particular interest because this mode is sensitive to both mixing angle $\theta_{13}$ and CP phase $\delta_{CP}$ of the PMNS matrix. Precise measurement of …
The Case Of Extended Supersymmetry And A Study In Superspace, Dharmesh Jain
The Case Of Extended Supersymmetry And A Study In Superspace, Dharmesh Jain
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
In this dissertation we study quantum field theories with extended supersymmetry in four and three dimensions. In d=4 we study N=2 supersymmetric theories using projective superspace formalism extensively. We discover the full non-Abelian action for super Yang-Mills (SYM) theory in projective superspace by studying its relation to harmonic superspace under a suitable Wick rotation of the latter's internal two-dimensional sphere. We also show that a Chern-Simons action for SYM in ‘ full‘ N=2 superspace can be written down that reproduces both the harmonic and projective SYM actions. The projective formalism allows simplifications in computing Feynman supergraphs because the N=2 rules …
Phase Separation And Neighboring Ground States Of Superconductivity In Kxfe2− Yse2, Hyejin Ryu
Phase Separation And Neighboring Ground States Of Superconductivity In Kxfe2− Yse2, Hyejin Ryu
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Iron-based superconductor KxFe2-ySe2 has generated considerable attention having higher critical temperature (~31 K)* than previously reported FeSe series (~8 K) and showing a unique phase separation with Fe vacancy order. We investigate the effect of the chemical substitution to the ground state and report various ground states such as spin glass phase and superconductor-insulator transition (SIT) under high-magnetic field by substitution of Na, Te, and Ni on KxFe2-ySe2 single crystal. The normal-state in-plane resistivity below Tc and the upper critical field for KxFe2-ySe1.85Te0.15 and K0.50Na0.24Fe2-ySe2 are measured by suppressing superconductivity in pulsed magnetic fields. The normal-state resistivity is found to …
Measurement Of The Ww And Wz Production Cross Section In The Semi-Leptonic Final State Using Sqrt(S)=7 Tev Pp Collisions With The Atlas Detector, David Puldon
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Presented is a measurement of the WW+WZ production cross section in proton-proton collisions at sqrt(s) = 7 TeV using data produced by the Large Hadron Collider and recorded with the ATLAS detector in 2011. The measurement tests understanding of the electroweak sector of the Standard Model at high energies and is potentially sensitive to new physics models that go beyond the Standard Model. The production cross section is measured in the WW/WZ semi-leptonic decay channel where one W boson decays into a lepton (either an electron or muon) and a neutrino, and the other W or Z boson decays hadronically …
Aspects Of Perturbative Quantum Field Theory, Stanislav Srednyak
Aspects Of Perturbative Quantum Field Theory, Stanislav Srednyak
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
This thesis consists of three parts. The first is devoted to the calculation of multiplicity of two-gluon production in heavy ion collisions in the framework of Colour Glass Condensate. The second exhibits a finite basis for the perturbative correlation functions at a given loop order. The third demonstrates that the number of integrations in a perturbative amplitude can be reduced in half in even dimensions, and provides explicit formula for such a reduction in the (2,2) signature. | 79 pages
Nuclear Quantum Effects In Ice Phases And Water From First Principles Calculations, Betul Pamuk
Nuclear Quantum Effects In Ice Phases And Water From First Principles Calculations, Betul Pamuk
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Despite the simplicity of the molecule, condensed phases of water show many physical anomalies, some of which are still unexplained to date. This thesis focuses on one striking anomaly that has been largely neglected and never explained. When hydrogen (1H) is replaced by deuterium (2 D), zero point fluctuations of the heavy isotope causes ice to expand, whereas in normal isotope effect, heavy isotope causes volume contraction. Furthermore, in a normal isotope effect, the shift in volume should decrease with increasing temperature, while, in ice, the volume shift increases with increasing temperature and persists up to the melting temperature and …
Shape-Based Analysis, Krishna Chaitanya Gurijala
Shape-Based Analysis, Krishna Chaitanya Gurijala
Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)
Shape analysis plays a critical role in many fields, especially in medical analysis. There has been substantial research performed for shape analysis in manifolds. On the contrary, shape-based analysis has not received much attention for volumetric data. It is not feasible to directly extend the successful manifold shape analysis methods, such as heat diffusion, to volumes due to the huge computational cost. The work presented herein seeks to address this problem by presenting two approaches for shape analysis in volumes that not only capture the shape information efficiently but also reduce the computational time drastically. The first approach is a …