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Title: Fabrication and Characterization of High Aspect Ratio Hard X-ray Zone Plates with Ultrananocrystalline Diamond Molds
Creator: Wojcik, Michael J.
Date: 2013, 2013-05
Description: Hard x-ray zone plate development has played an important role in improving x-ray microscopy through ner resolution and greater functional X...
Show moreHard x-ray zone plate development has played an important role in improving x-ray microscopy through ner resolution and greater functional X-ray energy. Similar to circular di raction gratings except with changing period as a function of radius, zone plates are di ractive focusing optics with resolution determined by the outer most zone width (OZW). Hard X-ray zone plates are mostly phase zone plates with a limited e ciency that peaks when the zone material causes a -phase shift on the x-ray, and the zone thickness required can be multiple microns dependent on x-ray energy. The combination of sub-100-nm resolution and peak e ciency for hard xrays requires very high aspect ratio zones. In this dissertation, two materials were used to fabricate high aspect ratio zone plates in a single layer mold and a two layer mold process. Ultrananocrystalline diamond (UNCD) is composed of 2-5 nm diamond grains bounded together with graphitic bonds. This form of diamond can be deposited onto substrates with thickness greater than a micron and with physical properties similar to bulk diamond. Hydrogen silsesquioxane (HSQ) is a spin on glass that is also a high contrast electron beam lithography resist. A thick layer of HSQ can be patterned into high aspect ratio structures and could be used as a pattern transfer mask for several etch recipes. Both of these materials were used to fabricate up to 25 aspect ratio zone plates and with OZW of 60 and 80 nm. Zone plates fabricated with UNCD were the rst high aspect ratio zone plates using a diamond like material and this technique was leveraged into a new fabrication method using two layers as an electroplating mold. Fabricated zone plates were characterized to measure the optical properties to compare with the fabrication properties. After characterization, several zone plate models based on fabricated zone plates were developed and simulated using a wave propagation technique to compare with the characterization data. The results xiii from fabrication, characterization, and simulation of zone plates with 25 aspect ratio will be presented as well as future possibilities for the techniques used.
PH.D in Physics, May 2013
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Title: Leader-Member Exchange as A Mediator Between Negative Affectivity and Work-Family Conflict
Creator: Pugliese, Stephanie
Date: 2012-04-11, 2012-05
Description: The purpose of this study was to investigate the relationship between work-family conflict, negative affectivity, and leader-member exchange....
Show moreThe purpose of this study was to investigate the relationship between work-family conflict, negative affectivity, and leader-member exchange. Survey data was collected from a sample of union employees (n = 358). As hypothesized, leader-member exchange significantly mediated the relationship between negative affectivity and work interfering with family conflict (WIF). Contrary to prediction, leader-member exchange did not mediate the relationship between negative affectivity and family interfering with work conflict (FIW). Discussion of results and implications for practice are provided. In conclusion, this study highlights the importance of leaders in helping employees manage work-family conflict.
M.S. in Psychology, May 2012
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Title: SIMULTANEOUS INJECTION OF STABLE AND RADIOACTIVE IONS INTO UPGRADED MULTI-USER ATLAS
Creator: Perry, Amichay
Date: 2015, 2015-12
Description: Argonne Tandem Linac Accelerator System (ATLAS) is a Department of Energy (DOE) national user research facility, located at Argonne National...
Show moreArgonne Tandem Linac Accelerator System (ATLAS) is a Department of Energy (DOE) national user research facility, located at Argonne National Laboratory (ANL). Presently, Radioactive Ion Beams (RIBs) produced in the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility are charge bred in an Electron Cyclotron Resonance (ECR) charge breeder prior to post acceleration in ATLAS. A new state of the art Electron Beam Ion Source charge breeder, the CARIBU-EBIS charge breeder, has been developed (not in the scope of the work presented here) at ANL to replace the existing ECR for charge breeding RIBs generated in CARIBU. The CARIBU-EBIS charge breeder is now in the final stages of offline commissioning at the Accelerator Development Test Facility (ADTF). A significant part of the commissioning effort has been devoted to testing the source by breeding singlycharged cesium ions injected from a surface ionization source. Characterization of the CARIBU-EBIS performance has been accomplished through a comparison between the measured properties of extracted beams and simulation results. Following its offline commissioning, CARIBU-EBIS will be relocated to its permanent location in ATLAS. An electrostatic transport line has been designed to transport RIBs from CARIBU and inject them into CARIBU-EBIS. In addition, modifications to the existing ATLAS Low Energy Beam Transport (LEBT) were also required in order to transport the charge bred RIBs from CARIBU-EBIS to ATLAS. A proposal for upgrading ATLAS to a multi-user facility has been explored as well. In this context, beam dynamics simulations show that further modifications to the ATLAS LEBT will enable the simultaneous injection and acceleration of RIBs and stablebeams in ATLAS. Furthermore, a novel technique proposed by Ostroumov et al. will allow for the acceleration of multiple charge states from CARIBU-EBIS, thereby increasing the intensity of available RIBs by up to 60%.
Ph.D. in Physics, December 2015
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Title: THE VERY ENERGETIC RADIATION IMAGING TELESCOPE ARRAY SYSTEM OBSERVATIONS OF THE STARBURST GALAXY M82
Creator: Ratliff, Gayle
Date: 2015, 2015-07
Description: This work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by...
Show moreThis work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by documenting the analysis of 231 quality-selected hours of observational data taken between 2008 and 2014. The prototypical starburst galaxy, M82’s high supernova (SN) rate and dense central accumulation of molecular gas make it a promising candidate for studying cosmic ray (CR) acceleration and propagation with the detection of di↵use very high energy (VHE; approximately 100 GeV-100 TeV) !-ray emission. This di↵use emission is predicted to result from proton-proton interactions within the galaxy’s core that produce VHE !-rays through neutral pion decay. This work confirms the results of the initial VERITAS publication covering 137 hours of M82 observations between January 2008 and April 2009, yielding a total of 103.5 excess !-ray-like events (0.007 !/min, 5.7 pre-trial statistical significance) from a deeper exposure of 231 hours of observation. The spectral properties found are in agreement with the original detection within errors ("=2.85 ± 0.39). These results are consistent with paradigms that describe the production of CRs via the conversion of mechanical energy generated in supernovae (SNe). These findings will improve current di↵use emission models by better constraining galaxy parameters and by providing insight into CR proton loss processes and timescales, with further understanding to be gained with the introduction of the Cherenkov Telescope Array (CTA). xiiThis work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by documenting the analysis of 231 quality-selected hours of observational data taken between 2008 and 2014. The prototypical starburst galaxy, M82’s high supernova (SN) rate and dense central accumulation of molecular gas make it a promising candidate for studying cosmic ray (CR) acceleration and propagation with the detection of di↵use very high energy (VHE; approximately 100 GeV-100 TeV) !-ray emission. This di↵use emission is predicted to result from proton-proton interactions within the galaxy’s core that produce VHE !-rays through neutral pion decay. This work confirms the results of the initial VERITAS publication covering 137 hours of M82 observations between January 2008 and April 2009, yielding a total of 103.5 excess !-ray-like events (0.007 !/min, 5.7 pre-trial statistical significance) from a deeper exposure of 231 hours of observation. The spectral properties found are in agreement with the original detection within errors ("=2.85 ± 0.39). These results are consistent with paradigms that describe the production of CRs via the conversion of mechanical energy generated in supernovae (SNe). These findings will improve current di↵use emission models by better constraining galaxy parameters and by providing insight into CR proton loss processes and timescales, with further understanding to be gained with the introduction of the Cherenkov Telescope Array (CTA). xiiThis work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by documenting the analysis of 231 quality-selected hours of observational data taken between 2008 and 2014. The prototypical starburst galaxy, M82’s high supernova (SN) rate and dense central accumulation of molecular gas make it a promising candidate for studying cosmic ray (CR) acceleration and propagation with the detection of di↵use very high energy (VHE; approximately 100 GeV-100 TeV) !-ray emission. This di↵use emission is predicted to result from proton-proton interactions within the galaxy’s core that produce VHE !-rays through neutral pion decay. This work confirms the results of the initial VERITAS publication covering 137 hours of M82 observations between January 2008 and April 2009, yielding a total of 103.5 excess !-ray-like events (0.007 !/min, 5.7 pre-trial statistical significance) from a deeper exposure of 231 hours of observation. The spectral properties found are in agreement with the original detection within errors ("=2.85 ± 0.39). These results are consistent with paradigms that describe the production of CRs via the conversion of mechanical energy generated in supernovae (SNe). These findings will improve current di↵use emission models by better constraining galaxy parameters and by providing insight into CR proton loss processes and timescales, with further understanding to be gained with the introduction of the Cherenkov Telescope Array (CTA). xiiThis work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by documenting the analysis of 231 quality-selected hours of observational data taken between 2008 and 2014. The prototypical starburst galaxy, M82’s high supernova (SN) rate and dense central accumulation of molecular gas make it a promising candidate for studying cosmic ray (CR) acceleration and propagation with the detection of di↵use very high energy (VHE; approximately 100 GeV-100 TeV) !-ray emission. This di↵use emission is predicted to result from proton-proton interactions within the galaxy’s core that produce VHE !-rays through neutral pion decay. This work confirms the results of the initial VERITAS publication covering 137 hours of M82 observations between January 2008 and April 2009, yielding a total of 103.5 excess !-ray-like events (0.007 !/min, 5.7 pre-trial statistical significance) from a deeper exposure of 231 hours of observation. The spectral properties found are in agreement with the original detection within errors ("=2.85 ± 0.39). These results are consistent with paradigms that describe the production of CRs via the conversion of mechanical energy generated in supernovae (SNe). These findings will improve current di↵use emission models by better constraining galaxy parameters and by providing insight into CR proton loss processes and timescales, with further understanding to be gained with the introduction of the Cherenkov Telescope Array (CTA). xiiThis work describes the Very Energetic Radiation Imaging Telescope Array Systems (VERITAS) observations of the starburst galaxy M82 by documenting the analysis of 231 quality-selected hours of observational data taken between 2008 and 2014. The prototypical starburst galaxy, M82’s high supernova (SN) rate and dense central accumulation of molecular gas make it a promising candidate for studying cosmic ray (CR) acceleration and propagation with the detection of di↵use very high energy (VHE; approximately 100 GeV-100 TeV) !-ray emission. This di↵use emission is predicted to result from proton-proton interactions within the galaxy’s core that produce VHE !-rays through neutral pion decay. This work confirms the results of the initial VERITAS publication covering 137 hours of M82 observations between January 2008 and April 2009, yielding a total of 103.5 excess !-ray-like events (0.007 !/min, 5.7 pre-trial statistical significance) from a deeper exposure of 231 hours of observation. The spectral properties found are in agreement with the original detection within errors ("=2.85 ± 0.39). These results are consistent with paradigms that describe the production of CRs via the conversion of mechanical energy generated in supernovae (SNe). These findings will improve current di↵use emission models by better constraining galaxy parameters and by providing insight into CR proton loss processes and timescales, with further understanding to be gained with the introduction of the Cherenkov Telescope Array (CTA).
Ph.D. in Physics, July 2015
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Title: IN SITU X-RAY ABSORPTION SPECTROSCOPY STUDY OF TIN ANODE NANOMATERIALS FOR LITHIUM-ION BATTERIES
Creator: Pelliccione, Christopher J.
Date: 2015, 2015-05
Description: Tin is an attractive alternative to replace traditional carbon based anodes in lithium-ion batteries (LIBs) due to the nearly three-fold...
Show moreTin is an attractive alternative to replace traditional carbon based anodes in lithium-ion batteries (LIBs) due to the nearly three-fold increase in theoretical capacity over carbon. However, metallic tin su↵ers from volumetric expansion of the crystal structure during initial lithium insertion that quickly degrades the material and reduces the performance of the battery. Various techniques have been previously investigated with the goal of suppressing this destructive expansion by incorporating oxygen or a lithium-inactive metal into the tin to provide structural support and mitigate volumetric expansion. These materials show increased capacity retention compared to metallic tin, but still su↵er from capacity fading. The nature of these structural degradations must be fully understood to permit engineering of materials that avoid these destructive tendencies and can be considered as viable options for LIBs. In situ X-ray absorption spectroscopy (XAS) measurements were acquired on Sn, SnO2, Sn3 O2(OH)2, Cu6Sn5 and Ni3Sn4 nanoparticle anodes for LIBs. Accompanying the electrochemical characterization conducted on each material, the local atomic structure was modeled as a function of potential during the first charge and also as a function of charged/discharged states for several cycles. The extended X-ray absorption fine structure (EXAFS) theoretical modeling included the first unambiguous observation of Sn-Li coordination numbers and atomic distances in tin-based anode materials. From correlating the electrochemical performance to the EXAFS analysis, the long-term capacity retention of tin-based anodes is dependent on the structural deformations that occur during the first charge. The conversion of oxygen to amorphous Li2O, and the network that it forms, has a dramatic e↵ect on the kinetics of the system and the stability of the local metallic tin structure.
Ph.D. in Physics, May 2015
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Title: DESIGN OF A COVARIANCE MATRIX FITTER TO MEASURE THE ELECTRON ANTINEUTRINO OSCILLATION PARAMETERS USING NEUTRON HYDROGEN CAPTURE AT THE DAYA BAY EXPERIMENT
Creator: De Arcos Rodr´iguez, Jos´e Fernando
Date: 2015, 2015-12
Description: The Daya Bay experiment provided the first precision measurement of the third mixing angle of the Pontecorvo-Maki-Nakagawa-Sakata matrix (✓13)...
Show moreThe Daya Bay experiment provided the first precision measurement of the third mixing angle of the Pontecorvo-Maki-Nakagawa-Sakata matrix (✓13) using six detectors to determine the relative rates of correlated signals generated from gadolinium neutron capture and positron-electron annihilation gammas in the inverse beta decay process. An additional correlated hydrogen neutron capture signal is produced in the Daya Bay detectors. Its analysis has the potential of producing an independent measurement of the electron antineutrino oscillation parameters. In this thesis a fitter has been designed to measure ✓13 and the squared mass di↵erence (#m2 ee) using the shape information of the hydrogen neutron capture signal generated in the Daya Bay experiment detectors. The main challenges of the hydrogen capture signal are the high accidental background rates in the lower energy region, and hydrogen’s neutron capture cross-section being much lower than gadolinium’s. In order to have a significant signal, we had to use more aggressive selection cuts than those applied in the gadolinium neutron capture analysis, and the fiducial volume was expanded by including the gadolinium-free gamma catcher region. Both background and detector systematic uncertainties studies have been repeated for the new hydrogen signal conditions. The results of these studies have been used to produce the corresponding covariance matrices that account for the uncertainties in a covariance matrix fitter. The fitter is customizable, i.e., energy binning, antineutrino detector configuration, data periods to be fitted, reactor periods, detector response matrices and predictions can be configured using a graphical user interface, providing versatility for further research. The fitter performance has been tested in the two dimensional parameter space S ⇥ D, where S = !sin2(2✓13) 2 [0, 0.002, 0.004, ...0.2]} and D = {#m2 ee 2 [0.0015, 0.00152, 0.00154...0.0035]}, using nominal and statistically fluctuated antineutrino spectrum predictions.
Ph.D. in Physics, December 2015
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Title: PHYSICS OF LIMITING PHENOMENA IN SUPERCONDUCTING MICROWAVE RESONATORS: VORTEX DISSIPATION, ULTIMATE QUENCH AND QUALITY FACTOR DEGRADATION MECHANISMS
Creator: Checchin, Mattia
Date: 2016, 2016-12
Description: Superconducting niobium accelerating cavities are devices operating in radiofrequency and able to accelerate charged particles up to energy of...
Show moreSuperconducting niobium accelerating cavities are devices operating in radiofrequency and able to accelerate charged particles up to energy of tera-electron-volts. Such accelerating structures are though limited in terms of quality factor and accelerating gradient, that translates—in some cases—in higher capital costs of construction and operation of superconducting rf accelerators. Looking forward for a new generation of more affordable accelerators, the physical description of limiting mechanisms in superconducting microwave resonators is discussed. In particular, the physics behind the dissipation introduced by vortices in the superconductor, the ultimate quench limitations and the quality factor degradation mechanism after a quench are described in detail. One of the limiting factor of the quality factor is the dissipation introduced by trapped magnetic flux vortices. The radio-frequency complex response of trapped vortices in superconductors is derived by solving the motion equation for a magnetic flux line, assuming a bi-dimensional and mean free path-dependent Lorentzian-shaped pinning potential. The resulting surface resistance shows the bell-shaped trend as a function of the mean free path, in agreement with the experimental data observed. Such bell-shaped trend of the surface resistance is described in terms of the interplay of the two limiting regimes identified as pinning and flux flow regimes, for low and large mean free path values respectively. The model predicts that the dissipation regime—pinning- or flux-flow-dominated—can be tuned either by acting on the frequency or on the electron mean free path value. The effect of different configurations of pinning sites and strength on the vortex surface resistance are also discussed. Accelerating cavities are also limited by the quench of the superconductive state, which limits the maximum accelerating gradient achievable. The accelerating field limiting factor is usually associated to the superheating field, which is intimately correlated to the penetration of magnetic flux vortices in the material. Experimental data for N-doped cavities suggest that uniform Ginzburg-Landau parameter cavities are statistically limited by the lower critical field, in terms of accelerating gradient. By introducing a Ginzburg-Landau parameter profile at the cavity rf surface—dirty layer—the accelerating gradient of superconducting resonators can be enhanced. The description of the physics behind the accelerating gradient enhancement as a consequence of the dirty layer is carried out by solving numerically the Ginzburg-Landau equations for the layered system. The enhancement is showed to be promoted by the higher energy barrier to vortex penetration, and by the enhanced lower critical field. Another serious threat to the quality factor during the cavity operation is the extra dissipation introduced by the quench. Such quality factor degradation mechanism due to the quench, is generated by the trapping of external magnetic flux at quench spot. The purely extrinsic origin of such extra dissipation is proven by the impossibility of decrease the quality factor by quenching in a magnetic field-free environment. Also, a clear relation of the dissipation introduced by quenching to the orientation of the applied magnetic field is observed. The full recover of the quality factor by re-quenching in compensated field is possible when the trapped flux at the quench spot is modest. On the contrary, when the trapped magnetic flux is too large, the quality factor degradation may become irreversible by this technique, likely due to the outward flux migration beyond the normal zone opening during the quench.
Ph.D. in Physics, December 2016
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Title: XAFS STUDIES OF RADIATION DAMAGE IN NUCLEAR MATERIALS
Creator: Olive, Daniel Thomas
Date: 2012-11-13, 2012-12
Description: The growing demand for nuclear energy places a high importance on the development of new materials capable of withstanding higher temperatures...
Show moreThe growing demand for nuclear energy places a high importance on the development of new materials capable of withstanding higher temperatures and harsher irradiation conditions than those used in existing reactors. By supporting the development of next generation reactors it also becomes possible to close the nuclear fuel cycle, greatly reducing the amount of waste sent for disposal in deep geologic repositories, where its interaction with the environment is also a matter of interest. In this thesis, X-ray absorption fine structure (XAFS) spectroscopy is used to investigate the local atomic structure of systems of interest to nuclear energy. First, two XAFS studies on environmental materials are presented. Granular activated carbon (GAC) was treated with iron to improve its water remediation properties, specifically with respect to arsenic. XAFS was used to determine the nature of iron coating on the GAC surface, and the method of arsenic bonding to the treated surface. Next, a neodymium precipitate from solubility studies carried out for the Waste Isolation Pilot Plant (WIPP) was analyzed. Neodymium was used as an analog for plutonium in brine solutions. XAFS fitting indicated that the neodymium substituted for calcium in a gypsum lattice, providing information useful for future geochemical modeling. XAFS was also used to study radiation damage in materials. A candidate material for advanced reactor structural materials, modified 9Cr–1Mo, was irradiated to 1, 4, and 10 displacements per atom (dpa). XAFS analyses were performed on the Fe, Mo, and Nb K-edges. Irradiation caused a reduction in coordination for all three elements, but the exact behavior was element specific. Damage around Fe atoms was linear with dose, while damage around xxii Mo atoms saturated at or before 1 dpa. XAFS was shown to provide a useful atomic level description of radiation damage for a complex alloy system. Finally, zirconium carbide and zirconium nitride, candidate materials for advanced fuel claddings were studied at the Zr K-edge. Samples irradiated to 1 dpa retained overall crystallinity, as indicated by transmission electron microscopy (TEM) images but were found to have an increase in dislocation loops compared to their non-irradiated counterparts. XAFS analysis was able to determine the size of the undefected regions, making it a valuable complement to other analysis techniques. xxiii
PH.D in Physics, December 2012
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Title: ACCESSIBLE, ALMOST AB INITIO MULTI-SCALE MODELING OF ENTANGLED POLYMERS VIA SLIP-LINKS
Creator: Andreev, Marat
Date: 2014, 2014-12
Description: It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to...
Show moreIt is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most–detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least–detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.
Ph.D. in Physics, December 2014
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Title: P-DOPED STRONTIUM TITANATE GROWN USING TWO TARGET PULSED LASER DEPOSITION FOR THIN FILM SOLAR CELLS
Creator: Man, Hamdi
Date: 2015, 2015-12
Description: Thin-film solar cells made of Mg-doped SrTiO3 (STO) p-type absorbers are promising candidates for clean energy generation. This material shows...
Show moreThin-film solar cells made of Mg-doped SrTiO3 (STO) p-type absorbers are promising candidates for clean energy generation. This material shows p-type conductivity and also demonstrates reasonable absorption of light. In addition, p-type SrTiO3 can be deposited as thin films so that the cost can be lower than the competing methods. In this work, Mg:SrTiO3 (Mg:STO) thin-films were synthesized and analyzed in order to observe their potential to be employed as the base semiconductor in photovoltaic applications. Mg:STO thin-films were grown with pulsed laser deposition (PLD) using a frequency quadrupled Yttrium Aluminum Garnet (YAG) laser and with a substrate that was heated by back surface absorption of infrared (IR) laser light. The samples were characterized using X-ray photoelectron spectroscopy (XPS) and it was observed that Mg atoms were incorporated in the STO films. Reflection high energy electron diffraction (RHEED) spectroscopy proved that the thin films were polycrystalline. Calculations showed that the lattice constant of Mg:STO/SSF is slightly greater than that of STO/SSF, therefore, the conservation of the characteristic ring pattern for STO suggests of doping by substitution, which is consistent with the examples in literature. Kelvin Probe work function measurements indicated that the work function of the films were 4.167 eV after annealing. EDS spectroscopy showed that Mg was present in the thin films.
M.S. in Physics, December 2015
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Title: SIMULATION OF H2A.B CONTAINING HISTONE VARIANT NUCLEOSOME
Creator: Kohestani, Havva
Date: 2019
Description: The H2A.B histone is a highly evolving vertebrate specific variant of the H2A histone family. It has been implicated in increased gene...
Show moreThe H2A.B histone is a highly evolving vertebrate specific variant of the H2A histone family. It has been implicated in increased gene expression, and experiments have shown that incorporation of H2A.B into nucleosomes results in more extended structures with fewer wrapped DNA base pairs. To study the molecular mechanisms of H2A.B, we have performed a series of conventional and enhanced sampling molecular dynamics simulation of H2A.B and canonical H2A containing nucleosomes.Results of adaptively biased molecular simulations show that substitution of canonical H2A with H2A.B results in geometrical changes such as unwrapping of 10 to 15 base pairs of DNA on each side of the nucleosome and an increase in the diameter and radius of gyration, which is in agreement with previous AFM, FRET, and SAXS experiments. DNA unwinding is energetically favorable in H2A.B containing compared to canonical nucleosomes, while in both systems we observe a wide range of sampling over various structures of DNA. H3 histone tails excluded simulations, show the importance and effect of N-terminal residues of H3 histones on attachment of DNA at the entry/exit sites to nucleosome protein core. Clustering and hydrogen bond analysis suggest that introduction of H2A.B to nucleosome systems triggers mechanisms leading to rearrangement of hydrogen bond network which may influence the pattern and intensity of interactions between DNA-protein and protein-protein complexes.
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Title: Doing physics : a festschrift for Thomas Erber
Creator: Johnson, Porter Wear
Date: 2010, 2010
Publisher: IIT Press, Chicago, IL
Description: Doing Physics is a festschrift (collection of articles, essays, and rememberances) published in honor of Illinois Tech Physics professor...
Show moreDoing Physics is a festschrift (collection of articles, essays, and rememberances) published in honor of Illinois Tech Physics professor Thomas Erber's 80th birthday. Selections were authored by Erber's colleagues, former stduents, and fellow scholars. This book was released in print form, this file was the original pdf assembled by editor Porter Johnson and submitted for printing with the front and rear covers added.
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Title: EARLY PHYSICS OF THE DAYA BAY REACTOR ANTINEUTRINO EXPERIMENT
Creator: Seilhan, Brandon
Date: 2011-07, 2011-07
Description: The Daya Bay reactor antineutrino experiment is designed to measure the last unknown neutrino mixing angle to less than 0.01 in sin2 2 13 at...
Show moreThe Daya Bay reactor antineutrino experiment is designed to measure the last unknown neutrino mixing angle to less than 0.01 in sin2 2 13 at the 90% con dence level after 3 years of running. The fully commissioned experiment consists of three experimental halls, measuring the antineutrino ux from six reactor cores. The various subsystems of the Daya Bay experiment involved in reaching this ultimate sensitivity are discussed. With full physics running not scheduled until summer 2012, a fully functional near site with 40 tons of target mass can be used to measure sin2 2 13 to 0.08 at the 90% con dence level in less than 6 months of data taking beginning in summer of 2011. Early physics at the Daya Bay hall does not bene t from the a near detector to measure the reactor antineutrino ux. Understanding and predicting the reactor antineutrino ux is therefore extremely important for early physics. A method of predicting the time-dependent antineutrino spectrum at the Daya Bay near site using publicly available information is presented. Using the antineutrino ux predictions, early physics measurements involving fuel cycles and refueling shutdowns are explored.
Ph.D. in Physics, July 2011
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Title: CHARACTERIZATION OF SPATIALLY MODULATED MULTICOMPONENT MATERIALS DEPOSITED BY ATOMIC LAYER DEPOSITION
Creator: Becker, Nicholas
Date: 2014, 2014-07
Description: Spatially modulated multicomponent materials are used in a variety of fields and industries. In this dissertation Atomic Layer Deposition (ALD...
Show moreSpatially modulated multicomponent materials are used in a variety of fields and industries. In this dissertation Atomic Layer Deposition (ALD) will be used to create two types of spatially modulated multicomponent materials: Erbium doped Yttrium Oxide (Er+3:Y2O3) for high energy lasers and standard reference materials for Synchrotron based X-ray Fluorescence (SXRF) and Scanning Transmission X-ray Microscopy (STXM). Er+3:Y2O3 was produced and the inter- and intra-layer doping of each film was controlled by the cycle ratio of ALD grown Er2O3:Y2O3 and by the steric hinderance of erbium precursor ligands, respectively. Photolumenescent Spectroscopy and X-ray di↵raction measurements showed that all films of Er+3:Y2O3 were crystalline as deposited, with no evidence of amorphous, or glassy, emission lines in the PLS spectra. Photoluminescent Lifetime (PLL) measurements were performed to prove that ALD can be used to control both inter- and intra-layer doping. PLL was shown to vary with both Er2O3:Y2O3 cycle ratio and with Erbium precursor growth rate, increasing to a maximum of 6.5ms. This is the longest PLL reported for ALD grown Er+3:Y2O3. Results from Rutherford backscattering spectroscopy, X-ray absorption fine structure spectroscopy, and ultraviolet to visible light spectroscopy are presented to verify inter- and intra-layer doping control. Standard reference materials for SXRF and STXM were produced via ALD on transmission electron microscopy windows and native oxide silicon. Materials produced were Fe2O3, TiO2 , ZnO, Al2O3, and Y2O3. Films were analyzed with SXRF, and SXTM to determine the optical density and from this the areal density was calculated using preexisting standard reference materials and absorption value charts. It was found that the RBS measurements were more precise, and were within the error associated with the SXRF and STXM measurements.
Ph.D. in Physics, July 2014
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Title: HIGH PRESSURE GAS FILLED RF CAVITY BEAM TEST AT THE FERMILAB MUCOOL TEST AREA
Creator: Freemire, Ben
Date: 2013, 2013-05
Description: The high energy physics community is continually looking to push the limits with respect to the energy and luminosity of particle accelerators...
Show moreThe high energy physics community is continually looking to push the limits with respect to the energy and luminosity of particle accelerators. In the realm of leptons, only electron colliders have been built to date. Compared to hadrons, electrons lose a large amount of energy when accelerated in a ring through synchrotron radiation. A solution to this problem is to build long, straight accelerators for electrons, which has been done with great success. With a new generation of lepton colliders being conceived, building longer, more powerful accelerators is not the most enticing option. Muons have been proposed as an alternative particle to electrons. Muons lose less energy to synchrotron radiation and a Muon Collider can provide luminosity within a much smaller energy range than a comparable electron collider. This allows a circular collider to be built with higher attainable energy than any present electron collider. As part of the accelerator, but separate from the collider, it would also be possible to allow the muons to decay to study neutrinos. The possibility of a high energy, high luminosity muon collider and an abundant, precise source of neutrinos is an attractive one. The technological challenges of building a muon accelerator are many and diverse. Because the muon is an unstable particle, a muon beam must be cooled and accelerated to the desired energy within a short amount of time. This requirement places strict requisites on the type of acceleration and focusing that can be used. Muons are generated as tertiary beams with a huge phase space, so strong magnetic fields are required to capture and focus them. Radio frequency (RF) cavities are needed to capture, bunch and accelerate the muons. Unfortunately, traditional vacuum RF cavities have been shown to break down in the magnetic fields necessary for capture and focusing. To successfully operate RF cavities in strong magnetic fields, the idea of filling xv them with a high pressure gas in order to mitigate breakdown was proposed. The gas has the added benefit of providing cooling for the beam. Experiments were successfully performed using different gas species in a test cell cavity placed in a multi-Tesla magnetic field. These encouraging results lead to the necessity of a test closer to actual accelerator conditions, namely sending a beam of particles through the cavity. The electron-ion plasma created in the cavity by the beam absorbs energy and can degrade the accelerating electric field of the cavity. Electrons can recombine with hydrogen ions, however this process is slow compared to the bunch length and spacing. As electrons account for the majority of the energy loss in the cavity, their removal in a short time is highly desirable. The addition of an electronegative dopant gas can greatly decrease the lifetime of an electron in the cavity. The results of two beam tests will be presented. The experimental variables cover a wide range of gas pressure, beam intensity, and cavity electric field. Measurements in pure hydrogen of the power consumption of electrons in the cavity indicate a range of energy loss between 10−18 and 10−16 joules per RF cycle per electron. When hydrogen doped with dry air is used, measurements of the power consumption indicate an energy loss range of 10−20 to 10−18 joules per RF cycle per ion, two orders of magnitude improvement over non-doped measurements. The rate at which electrons recombine with positively charged hydrogen ions ranges from 10−7 to 10−5 cm3 s . The lifetime of electrons in a mixture of hydrogen gas and dry air has been measured from <1 ns, up to 200 ns. Finally, the ion-ion recombination rate falls between 10−8 and 10−7 cm3 s . The results extrapolated to the parameters of a Neutrino Factory and Muon Collider indicate that a high pressure gas filled RF cavity will work in a coolingchannel for either machine. A demonstration experiment is warranted to prove this technology’s validity.
PH.D in Physics, May 2013
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Title: Analysis of the Prompt Energy and Ab Initio Spectra with the Daya Bay Reactor Neutrino Experiment
Creator: Asimacopoulos, Leia
Date: 2019
Description: Theorized in the 1930s and discovered in the 1950s, neutrinos have puzzled physicists for decades. One method of studying neutrinos and their...
Show moreTheorized in the 1930s and discovered in the 1950s, neutrinos have puzzled physicists for decades. One method of studying neutrinos and their properties is measuring energy spectra produced by interactions of antineutrinos which come from beta decays of isotopes in nuclear reactors. With precise enough detectors, the antineutrino spectra of specific isotopes, also referred to as fine structure, may be observed. In this study, theoretical models of antineutrino energy spectra are compared with measured energy spectra from the Daya Bay Reactor Neutrino Experiment to test if the resolution of Daya Bay's detectors is precise enough to measure fine structure.
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Title: Toward a Comprehensive Atomistic View of Bacterial Outer Membrane Remodeling and Antimicrobial Peptide Susceptibility
Creator: Rice, Amy
Date: 2019
Description: The cell membrane is arguably one of the most important and complex features of a cell, serving to demarcate “self” from “environment” and...
Show moreThe cell membrane is arguably one of the most important and complex features of a cell, serving to demarcate “self” from “environment” and selectively controlling the flow of material in and out of the cell. Bacterial cell membranes are of additional interest since they serve as the first point of contact for antibiotic drugs or other antimicrobial agents. In this work, I use atomistic molecular dynamics simulations to study factors that alter bacterial susceptibility to antimicrobial agents and their environment, with the goal of better understanding how bacteria are able to modulate their sensitivity.First, I present results from a series of simulations of antimicrobial peptides (AMP) interacting with phospholipid bilayers to elucidate the observed interaction differences between arginine and lysine-containing AMPs. Simulations show that the extensive interaction with arginine is due in part to arginine's strong atomic charge distribution, rather than being purely an effect of the greater hydrogen bond capacity. These results highlight the role of charge and hydrogen bond strength in peptide bilayer insertion, and offer potential insights for designing more potent analogues in the future.Next, the effects of bacterial lipopolysaccharide (LPS) modifications are examined, first to understand study how three key modifications observed in S. enterica affect bilayer properties, as well as to examine the role these modifications play in AMP resistance. We hypothesize that defects at the crystalline/liquid-ordered boundary facilitate LL-37 intercalation into the outer membrane, whereas LPS modification protects against this process by having already increased crystallinity and packing efficiency. These results further improve our understanding of outer membrane chemical properties and help elucidate how outer membrane modification systems are able to alter bacterial virulence and susceptibility. Lastly, I investigate the effects of ion type and phosphate charge on four distinct LPS types. Simulations show that bilayer properties are highly influenced by the choice of cation type, ion parameterization, and phosphate group charges. Additional free energy perturbation simulations predict that the protonated LPS state should dominate at physiological pH, in contrast to the deprotonated state utilized by many LPS force fields. Overall, these results reveal inaccuracies in the existing LPS force fields and establish guidelines to better reproduce experimental LPS membrane properties.
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Title: SEARCH FOR STERILE NEUTRINO OSCILLATIONS WITH THE PROSPECT EXPERIMENT
Creator: Surukuchi, Pranava Teja
Date: 2019
Description: Neutrinos have been one of the most interesting particles to study for the best part of the last century. Ever since the first discovery of...
Show moreNeutrinos have been one of the most interesting particles to study for the best part of the last century. Ever since the first discovery of neutrinos, various experiments using both natural and artificial neutrino sources have helped in determining the nature of neutrinos. In particular, experiments in the last two decades helped determine the neutrino oscillation parameters. Although three neutrino picture is well established, discrepancies have been observed in some recent reactor, accelerator, and source neutrino experiments hinting at the existence of a fourth weakly non-interacting neutrino called a sterile neutrino. Additional experimental investigation is needed to test the sterile neutrino hypothesis and identify the source of discrepancies. PROSPECT is a short-baseline reactor antineutrino experiment designed to search for sterile neutrinos and make a precise measurement of 235U reactor antineutrino spectrum from the High Flux Isotope Reactor at Oak Ridge National Laboratory located in Tennessee. The PROSPECT detector is segmented with 6Li-loaded liquid scintillator as the target. The design and development of the PROSPECT detector started in 2014 and the assembly and installation have finished by early 2018. PROSPECT detector has been collecting data since March 2018. The design, development, and installation of the detector is discussed with a particular emphasis on the components designed and developed at Illinois Institute of Technology. The detector calibration, event reconstruction, and data quality are also discussed. Finally, the sterile neutrino search using 33 days of reactor on data and 29 days of reactor off data is presented.
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Title: SPIN TRANSPORT AND SPIN-ORBIT TORQUES IN ANTIFERROMAGNETS
Creator: Saglam, Hilal
Date: 2019
Description: The electron has two fundamental degrees of freedom, i.e., charge and spin. Existing semiconductor electronics utilizes the charge degree of...
Show moreThe electron has two fundamental degrees of freedom, i.e., charge and spin. Existing semiconductor electronics utilizes the charge degree of freedom in its functionalities. Spintronics seeks, in addition, to exploit the spin degree of freedom, which can suggest promising pathways for low-power and faster operations. In conventional spintronics devices, ferromagnetic materials (FMs) have been employed as active components. However, it has recently been recognized that antiferromagnetic materials (AFMs) can also play an active role in spintronic devices. Antiferromagnets have several advantages over ferromagnets; for instance, they have net zero magnetization so that they are invisible to external magnetic fields. Also, they show resonances in the terahertz frequency range. Towards this end, this thesis focuses on spin transport and spin-orbit torques in various antiferromagnetic materials. With respect to the former, I demonstrated that spin currents can be transmitted efficiently through a metallic antiferromagnet FeMn. I detect two distinctly different spin transport regimes, which can be associated with electronic and magnonic spin currents. With respect to the latter, I investigated a possible correlation between two important spintronics concepts, i.e., spin-orbit torques and exchange bias since the ferromagnetic/antiferromagnetic interface is crucial for both phenomena. The measured spin Hall angles suggest that these two effects are independent of each other, although it is worthy to mention that there are still strong spin-orbit torques even when the antiferromagnet is directly exchange coupled to the ferromagnet. Furthermore, I discuss anomalous Hall effect (AHE) and anomalous Nernst effect (ANE) in another metallic antiferromagnet, FeRh, which undergoes a temperature driven antiferromagnetic-to-ferromagnetic phase transition. The temperature dependent results show a drastic suppression of both AHE and ANE signals in the antiferromagnetic phase. Interestingly, these non-vanishing signals are opposite in sign compared to their ferromagnetic counterparts, which can suggest changes of inherent symmetries in the electronic structure of FeRh across its magnetic phase transition.
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Title: Beam Line Design for Fully Staged Two Beam Acceleration at the Argonne Wakefield Accelerator Facility
Creator: Neveu, Nicole
Date: 2018
Description: Two beam acceleration (TBA) is a candidate for future high energy physics machines and FEL user facilities. This is a scheme in which an...
Show moreTwo beam acceleration (TBA) is a candidate for future high energy physics machines and FEL user facilities. This is a scheme in which an electron accelerator uses a ``drive'' beam to transport and supply the RF power needed for acceleration on a secondary and independent 'witness' accelerator. This technology is attractive for its potential to improve the efficiency and simplicity of large scale machines. At the Argonne Wakefield Accelerator Facility (AWA), research into this potential accelerator scheme is ongoing. Completed experiments include a simplified staging set up, where high-charge, 65 MeV drive bunch trains were injected from the RF photoinjector into decelerating structures to generate a few hundred MW's of RF power. This RF power was transferred through an RF waveguide to accelerating structures that were used to accelerate the witness beam. Staging refers to the sequential acceleration (energy gain) in two or more structures on the witness beam line. The main limitation in past experiments was difficulty achieving 100\% transmission in the second stage which resulted in lower power generation. AWA plans to demonstrate fully staged TBA, which requires a separate beam line for each decelerating/accelerating pair. In this thesis, design specifications and initial hardware tests needed for a new, independent beam line for TBA was done. Simulations of the drive line were done using the code OPAL. Since OPAL was new to the AWA group, a benchmark comparison with ASTRA and GPT was done to validate initial results. Then two optimization algorithms were investigated and used to optimize the drive line at 40 nC. Comparison of results between the two algorithms were done, with no major discrepancies found. Then large scale and parallel optimizations were done for the optics configuration in the fully staged TBA beam line design. A kicker was designed and incorporated into the drive beam line to accomplish a modular design so that each accelerating structure can be independently powered by a separate drive beam. Experimental measurements of the kicker indicate the angle increases linearly with the supplied voltage, and the angle achieved meets the design requirements for fully staged TBA. Optics optimization was done to minimize the beam size at the center of the decelerating structures to ensure good charge transmission. The resulting design will be the basis for proof of principle experiments that will take place at the AWA facility.
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