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Publication The Role of Tidal Interactions and Mergers on the Evolution of Intermediate Redshift Galaxies(University of Kansas, 2019-12-31) Deger, Sinan; Rudnick, Gregory H.; Blumenstiel, Justin; Cravens, Thomas E.; Feldman, Hume A.; Twarog, Bruce A.In this work, we present our analysis attempting to constrain the prevalence of tidal interaction and merger (TIM) events on the evolution of intermediate redshift galaxies. The main focus of this work is the effect of such events on the star formation properties of galaxies. Such an undertaking requires the precise selection of tidal interactions and mergers (TIMs), in a wide range of environments to account for environmental effects. As such, in the first part of this work we study the fraction of tidal interactions and mergers with well identified observability timescales ($f_{\rm TIM}$) in group, cluster, and accompanying field galaxies and its dependence on redshift ($z$), cluster velocity dispersion ($\sigma$), and environment. We analyze images from the Hubble Space Telescope (HST), and catalogs from the ESO Distant Cluster Survey (EDisCS) for our work. Our data sample consists of 11 clusters, 7 groups, and accompanying field galaxies at $0.4 \leq z \leq 0.8$. We select our TIM sample using both a visual classification of galaxy morphologies and an automated method, the $G-M_{20}$ method. We calibrate this method using the visual classifications that were performed on a subset of our sample. After this calibration, we label visual TIMs also picked by our $G-M_{20}$ selection criterion as \textquotedblleft $G-M_{20}$ TIM \textquotedblright, and gather our visually undisturbed galaxies plus the visual TIMs that are not $G-M_{20}$ selected under the \textquotedblleft undisturbed \textquotedblright label. Our tests indicate that these subpopulations are well-seperated in the $G-M_{20}$ space, and that our results are robust against different $G-M_{20}$ TIM selection criteria. Next, we investigate whether the fraction of $G-M_{20}$ TIMs, or $f_{\rm TIM}$, shows any strong trends with redshift ($z$), cluster velocity dispersion ($\sigma$), and the global environment the in which our galaxies reside. We find marginal evidence for a trend between $f_{\rm TIM}$ and $z$, in that higher $z$ values correspond to higher $f_{\rm TIM}$. However, we also cannot rule out the null hypothesis of no correlation at higher than 68\% confidence. No trend is present between $f_{\rm TIM}$ and $\sigma$. We find that $f_{\rm TIM}$ shows suggestive peaks in groups, and tentatively in clusters at $R > 0.5\times R_{200}$, implying that $f_{\rm TIM}$ gets boosted in these intermediate density environments. However, our analysis of the local densities of our cluster sample does not reveal a trend between $f_{\rm TIM}$ and density, except for a potential enhancement at the very highest densities. We also perform an analysis of projected radius-velocity phase space for our cluster members. Our results reveal that tidal interactions and mergers (TIM), and undisturbed galaxies only have a 6\% probability of having been drawn from the same parent population in their velocity distribution and 37\% in radii, in agreement with the modest differences obtained in $f_{\rm TIM}$ at the clusters. After classifying our sample into $G-M_{20}$ TIMs and undisturbed galaxies, we investigate the stellar populations of our sample. To this purpose, we perform a full spectral fitting on the deep EDisCS spectroscopy data. We use the publicly available pPXF code for the spectral fitting, obtaining the details of the stellar populations, and the gas present in our sample, as results of our spectral fitting. We extract the fraction of the total stellar mass contained in stellar populations of different ages in our sample from this information. We also derive age-sensitive spectral indices, the strength of the narrow 4000$\mbox{\AA}$ break strength, $D_{n,4000}$, and the Balmer H$\mathrm{\delta}$ absorption line index using the results of the spectral fitting. The final part of our analysis attempts to combine our morphological analysis, and our stellar population analysis. We search for trends in our $G-M_{20}$ TIMs and undisturbed galaxies with respect to the ages of their stellar populations. We find that our $G-M_{20}$ TIM galaxies are predominantly star-forming, as derived from multi-band photometric data. A larger fraction of the $G-M_{20}$ TIM galaxies also have features in their galaxy spectra indicating that their light is dominated by young stars. We then analyze the mass-weighted age fractions in the last 0.5 Gyr ($f_{Age 0.5\times R_{200}$, implying that $f_{\rm TIM}$ gets boosted in these intermediate density environments. However, our analysis of the local densities of our cluster sample does not reveal a trend between $f_{\rm TIM}$ and density, except for a potential enhancement at the very highest densities. We also perform an analysis of projected radius-velocity phase space for our cluster members. Our results reveal that tidal interactions and mergers (TIM), and undisturbed galaxies only have a 6\% probability of having been drawn from the same parent population in their velocity distribution and 37\% in radii, in agreement with the modest differences obtained in $f_{\rm TIM}$ at the clusters. After classifying our sample into $G-M_{20}$ TIMs and undisturbed galaxies, we investigate the stellar populations of our sample. To this purpose, we perform a full spectral fitting on the deep EDisCS spectroscopy data. We use the publicly available pPXF code for the spectral fitting, obtaining the details of the stellar populations, and the gas present in our sample, as results of our spectral fitting. We extract the fraction of the total stellar mass contained in stellar populations of different ages in our sample from this information. We also derive age-sensitive spectral indices, the strength of the narrow 4000$\mbox{\AA}$ break strength, $D_{n,4000}$, and the Balmer H$\mathrm{\delta}$ absorption line index using the results of the spectral fitting. The final part of our analysis attempts to combine our morphological analysis, and our stellar population analysis. We search for trends in our $G-M_{20}$ TIMs and undisturbed galaxies with respect to the ages of their stellar populations. We find that our $G-M_{20}$ TIM galaxies are predominantly star-forming, as derived from multi-band photometric data. A larger fraction of the $G-M_{20}$ TIM galaxies also have features in their galaxy spectra indicating that their light is dominated by young stars. We then analyze the mass-weighted age fractions in the last 0.5 Gyr ($f_{Age < 0.5~\mathrm{Gyr}}$), and between 0.5 Gyr and 1 Gyr ($f_{0.5 < Age < 1.0~\mathrm{Gyr}}$). Our results imply an enhanced $f_{Age < 0.5~\mathrm{Gyr}}$ value for the $G-M_{20}$ TIMs. This time interval is comparable in length to merger timescales reported by many studies, thereby this result is indicative of the TIM event boosting the star formation of these galaxies.Publication Controlling Interface for Metal-Insulator-Metal Architectures with Ultrathin Dielectric Fabricated Using Atomic Layer Deposition and Sputtering(University of Kansas, 2019-12-31) Acharya, Jagaran; Wu, Judy Z; Han, Siyuan; Murray, Michael J.; Chan, Wai-Lun; Berrie, Cindy L.The miniaturization of future microelectronics demands the development of high quality ultrathin (few to sub-nm) dielectric films for application in metal-insulator-metal (MIM) architectures. Among all other approaches employed for ultrathin dielectric film fabrication, atomic layer deposition (ALD) provides a unique approach for the fabrication of ultrathin TBs with several advantages including an atomic-scale control on the TB thickness, conformal coating, and low defects density. Despite extensive efforts in ALD devices, the figure-of-merit dielectric constant (r) exhibits a significant monotonic decrease with the film thickness as compared to bulk single crystal value. Primarily, the control over metal-insulator (M-I) interface, specifically in ultrathin thickness range, remains a challenge due to the formation of defective oxides and interfacial layer (IL). This work demonstrates the development of high quality Al/ALD Al2O3/Al MIM trilayers using a unique in-house integrated in situ deposition (sputtering/ALD) method. These trilayers devices were characterization to understand and control the IL formation with atomic precision. To the best of our knowledge, high r ~8.9 that is within 3% of the bulk value ~9.2 has been achieved for the first time on the ALD Al2O3 films in thickness range ~3.3-4.4 nm. This corresponds to an effective oxide thickness ~1.4-1.9 nm comparable to High-K HfO2 of 3-4 nm. The low leakage current density (J) ~10-9 A/cm2 is an order of magnitude lower than the best previously reported values. These results suggest that the optimal ultrathin high quality ALD Al2O3 provides a much lower-cost alternative for gate dielectric. Also, ALD Al2O3 seed layer (SL) approach was used to illustrate the critical importance of control over M-I interface to obtain dense hydroxylation and reduce incubation period, improving the dielectric properties of ultrathin ALD MgO films. ALD MgO with SL demonstrated r ~8.8-9.4 in thickness range ~3.8-4.9 nm comparable to bulk MgO ~9.4. In contrast, low r ~3.6-4.7 was observed for ALD MgO without Al2O3 SL in a similar thickness range. Both the scanning tunnelling spectroscopy and ab-initio molecular dynamics studies point out that SL allows the initial dense nucleation and perfect interface resulting in a high quality dielectric with tunnel barrier height (Eb)~1.5 eV compared to 0.8 eV for MgO without SL. This result provides an approach to engineering incompatible M-I interface using a SL for obtaining high quality dielectric as required for applications in MIM tunnel junctions and CMOS. In addition, tuning thickness of Al wetting layer (t_Al) in capacitors consisting of Nb (25 nm)/Fe (20 nm)/ALD Al2O3 (2.2 nm)/ t_Al/Fe (20 nm)/Nb (50 nm) shows switching between pure dielectric behavior for t_Al >1 nm and ferroelectric/dielectric (FE/DE) bilayer at t_Al≤ 1 nm. These FE/DE bilayer gate with ultrathin DE are promising for low power microelectronic devices. This helps to realize FE/DE bilayer capacitors with a total FE/DE total thickness 1 nm and ferroelectric/dielectric (FE/DE) bilayer at t_Al≤ 1 nm. These FE/DE bilayer gate with ultrathin DE are promising for low power microelectronic devices. This helps to realize FE/DE bilayer capacitors with a total FE/DE total thickness < 3-4 nm that show a dynamic switching on/off of the negative capacitance under the application of an external force. This result not only provides a viable approach for generating ultrathin FE/DE bilayer capacitors but also offers a promising solution to low-power consumption microelectronics and piezoelectric sensors applications. Pinhole-free and defect-free ultrathin dielectric tunnel barriers (TBs) is a key to obtaining high tunnelling magnetoresistance (TMR) and efficient switching in magnetic tunnel junctions (MTJs). Motivated by this, this work explores fabrication and characterization of spin-valve Fe/ALD-Al2O3/Fe MTJs with ALD Al2O3 TB thickness of 0.55 nm using in situ ALD. Remarkably, high TMR values of ~77% and ~ 90% have been obtained respectively at room temperature and at 100 K, which are comparable to the best reported on MTJs having thermal AlOx TBs with optimized device structures. In situ scanning tunnelling spectroscopy characterization of the ALD Al2O3 TBs has revealed a higher tunnel barrier height Eb of 1.33 eV, in contrast to Eb~0.3-0.6 eV for their AlOx TB counterparts, indicative of significantly lower defect concentration in the former. This first success of the MTJs with sub-nm thick ALD Al2O3 TBs demonstrates the feasibility of in situ ALD for the fabrication of pinhole-free and low-defect ultrathin TBs for practical applications and the performance could be further improved through device optimization.Publication Controllable Self-Assembly of Nanostructured Artificial Pinning Centers (APCs) in High Temperature Superconductor Epitaxial Thin Films(University of Kansas, 2019-08-31) Gautam, Bibek; Wu, Judy; Murray, Michael J.; Han, Siyuan; Chan, Wai-Lun; Berrie, Cindy L.A Superconductor exhibits dc zero-resistance below a critical temperature (Tc). The possible uses of superconductors in a high temperature range of 50-77 K are greatly expanded by the discovery of high temperature superconductors (HTS) in 1986. One of the most important parameters for the industrial applications of high temperature superconductors (HTS) is a high value of critical current density Jc, in applied magnetic fields (H) up to tens of Teslas. In HTS, magnetic flux would be expected to penetrate the superconductor in the form of filaments containing one flux quantum (Φo) in each filament. These flux lines are surrounded by circulating current that acts as screening current and give rise to the mixed state known as vortex state. Application challenges involve preventing vortex motion in HTS and determining the high value of Jc at the high magnetic field (H). The vortex motion increases with increasing applied field and hence decreases the Jc due to dissipation induced by the vortex motion. Obtaining a high Jc(H) requires stoppage of vortex motion in HTS. This can be done using pinning centers which capture the vortices and prevent their motion. Therefore, reaching high Jc(H) in HTS requires the insertion of strong pinning centers of dimension comparable to the superconducting coherence length on the order of few nanometers. Such pinning centers improve the critical current density and strengthen the pinning force density. Various innovative approaches have been developed in the last decade to generate optimally efficient artificial pinning centers (APCs) in YBa2Cu3O7-x (YBCO) nanocomposite films. However, controllable generation of self-assembled nanostructures during sample growth stage remains a challenge. Therefore, in this study, we generate a landscape of one-dimensional (1D) plus three-dimensional (3D) APCs of flexible elastic materials to improve strong and isotropic pinning which is beneficial for many industrial applications such as motors and generators. Specifically, a study of 3 vol.% Y2O3+2-6 vol.% BaHfO3 (BHO) double doped YBa2Cu3O7-x epitaxial thin films is carried out and compared to the same concentration of BaZrO3 (BZO) doping materials to explore the morphologic adaptation of the c-axis aligned 1D APCs to the 3D APCs. A significant reduction of Jc anisotropy is found for low doping BaHfO3 and 3 vol.% Y2O3 doped YBCO nanocomposite films (BHO double doped films). The self-assembly of 1D APCs in YBCO film matrix driven by the strain field is influenced by the lattice mismatch at the APC/YBCO interface. To answer the fundamental question on how the pinning efficiency of 1D APCs is affected by the APC/YBCO interface, electrical transport properties Jc (H, T) of the comparable diameter of BaZrO3 and BaHfO3 1D APCs on single doped YBCO nanocomposite films have been studied. The pinning force density is found to be significantly larger for a coherent, a less defective, BHO 1D APC/YBCO interface compared to a semicoherent, defective and oxygen deficient, BZO 1D APC/YBCO interface of epitaxial YBCO nanocomposite thin films. Transmission Electron Microscopy (TEM) images are utilized to study the difference of the nanostructures’ morphology, and 1D APC/YBCO interface of single and double doped nanocomposite thin films. It is found that less rigid BHO material forms a mixed APCs morphology reducing Jc anisotropy to about 20 % for 2 vol.% BHO double doped YBCO thin film at temperature of 65 K and at magnetic field of 9.0 T. A coherent APC/YBCO interface enhances the pinning efficiency of 1D APCs in BHO doped YBCO thin films. Significantly reduced pinning efficiency of BZO 1D APCs is observed for a defective BZO/YBCO interface. A method of repairing defective APC/YBCO interface through calcium doping is explored and recommended to enhance the pinning efficiency of one-dimensional APCs.Publication Supernova triggers for end-Devonian extinctions(National Academy of Sciences, 2020-08-18) Fields, Brian D.; Melott, Adrian L.; Ellis, John; Ertel, Adrienne F.; Fry, Brian J.; Lieberman, Bruce S.; Liu, Zhenghai; Miller, Jesse A.; Thomas, Brian C.The Late Devonian was a protracted period of low speciation resulting in biodiversity decline, culminating in extinction events near the Devonian–Carboniferous boundary. Recent evidence indicates that the final extinction event may have coincided with a dramatic drop in stratospheric ozone, possibly due to a global temperature rise. Here we study an alternative possible cause for the postulated ozone drop: a nearby supernova explosion that could inflict damage by accelerating cosmic rays that can deliver ionizing radiation for up to ∼100 ky. We therefore propose that the end-Devonian extinctions were triggered by supernova explosions at ∼20pc, somewhat beyond the “kill distance” that would have precipitated a full mass extinction. Such nearby supernovae are likely due to core collapses of massive stars; these are concentrated in the thin Galactic disk where the Sun resides. Detecting either of the long-lived radioisotopes Sm146 or Pu244 in one or more end-Devonian extinction strata would confirm a supernova origin, point to the core-collapse explosion of a massive star, and probe supernova nucleosynthesis. Other possible tests of the supernova hypothesis are discussed.Publication A study of the propagation of large Barkhausen discontinuities as a function of longitudinal field, circular field, and intensity of magnetization(University of Kansas, 1933-05-31) Reinhart, Raymond E.Publication The optical constants of liquid sodium, liquid sodium amalgams, liquid thallium, and liquid thallium-bismuth alloys(University of Kansas, 1935-05-31) Friesen, Abraham PennerPublication The role of spatial size and orientation of electronic wavefunction in exciton dissociation at van der Waals interfaces(University of Kansas, 2019-12-31) Kafle, Tika Ram; Chan, Wai-Lun; Besson, Dave Z.; Zhao, Hui; Wu, Judy; Caricato, MarcoOrganic photovoltaic (OPV) devices are environmental-friendly, lightweight, flexible and inexpensive. However, one of the setbacks for commercial application is its relative low performance in solar to electrical energy conversion compared to inorganic counterparts such as Si solar cells. Unlike typical inorganic materials in which free carriers are generated directly by the light absorption, excitons, Coulombic bound electron-hole pairs, are created upon light absorption in OPV materials. The performance of OPVs depends on how effective the bound charge transfer (CT) exciton, an exciton with its electron and hole spatially separated by the donor-acceptor interface, can dissociate to generate free charge carriers. In this thesis, the roles of the orientation of the delocalized electron wavefunction and the interfacial energy landscape in the exciton dissociation (ED) process are studied in order to understand mechanisms that control the ED efficiency. A number of donor–acceptor interfaces including organic/organic and organic/transition metal dichalcogenides (TMDs) interfaces with different molecular orientations were prepared, and exciton dynamics at these interfaces were probed. We employed time-resolved photoemission spectroscopy to measure the CT exciton dynamics, by which we were able to track the temporal evolution of the energy and the size of CT excitons. Our results on the organic-organic donor-acceptor interfaces show that the relative orientation of the delocalized electron and hole wavefunction within the CT exciton plays an important role in determining whether free carriers can be generated effectively from the CT exciton. Energy uphill, spontaneous exciton dissociation (SED) was observed on the few picosecond (ps) timescale at the zinc phthalocyanine (ZnPc)/fluorinated zinc phthalocyanine (F8ZnPc) interface with a face-on molecular orientation, at which both the electron and hole wavefunctions delocalize in the direction perpendicular to the interface. By contrast, cooling of hot CT excitons to lower energy bound CT excitons (cold excitons) was observed at the ZnPc/fullerene (C60) interface with an edge-on ZnPc orientation, at which the hole wavefunction in the CT exciton delocalizes in a direction parallel to the interface. The difference in the CT exciton dynamics suggests that free charges can be generated more effectively at the ZnPc/F8ZnPc interface with a face-on orientation. In addition, two very similar organic-TMD interfaces (ZnPc/bulk-MoS2 and ZnPc/monolayer (ML) MoS2) were studied and distinctly different CT exciton dynamics were observed. At the ZnPc/bulk-MoS2 interface, after the formation of the CT exciton, back electron transfer occurs which results in the formation of triplet excitons in the ZnPc. On the other hand, at the ZnPc/ML MoS2 interface, free carriers are generated effectively from CT excitons. This difference in the CT exciton dynamics is explained by the difference in the extent of the interfacial band bending found at the two interfaces. Overall, our study demonstrates that whether free carriers can be generated from the CT exciton depends sensitively on the local energy landscape around the interface and the electron delocalization within the CT exciton at the nanoscale. Understanding how the interfacial structure would affect the temporal evolution of the CT exciton is important for designing interfaces for effective charge generation.Publication Comprehensive Model of Jupiter's Polar Aurora(University of Kansas, 2019-05-31) Houston, Stephen Jeffrey; Cravens, Thomas E; Twarog, Bruce A; Besson, David Z; Lewis, Ian M; Ackley, BrianThe source of auroral X-ray emission from the Jovian polar caps, whether from electron bremsstrahlung or heavy ion precipitation, has been a topic of debate for the past 40 years, beginning with the Einstein Observatory's first measurement of X-ray emission in 1979. Since then the Roentgen satellite, Chandra X-ray Observatory, and XMM-Newton have distinguished heavy ion (oxygen and sulfur) line emission in the X-ray spectrum and measure a total power of about 1 GW. There have been many attempts to model both bremsstrahlung and ion precipitation with the goal of reproducing what is being seen; however, both have encountered push back. Electron bremsstrahlung modeling has fallen short of producing the total overall power output being observed by our earth-orbiting X-ray observatories. Whereas heavy ion precipitation has been able to reproduce strong X-ray fluxes, but the proposed incident ion energies seemed to likely be much higher (1 MeV/nucleon) than what was thought to be present above Jupiter's polar caps. Now with the National Aeronautics and Space Administration's (NASA's) Juno spacecraft arriving at Jupiter, there have been many measurements of heavy ion populations above the polar cap with energies up to 300-400 keV/nucleon (keV/u), well below predictions the of previous models. Meanwhile, Schultz et al. (2019) have provided a new outlook on how ion-neutral collisions in the Jovian atmosphere are occurring, providing an entirely new set of impact cross-sections and a total of 35 collision processes (prior models only account for 9). A model is described for the transport of magnetospheric oxygen and sulfur ions with low charge state and energies up to several MeV/nucleon (MeV/u) as they precipitate into Jupiter’s polar atmosphere. A revised and updated hybrid Monte Carlo model originally developed by Ozak et al. (2010) is used to model the Jovian X-ray aurora. The current model uses a wide range of incident oxygen ion energies (10 keV/u - 5 MeV/u) and the most up-to-date collision cross-sections. In addition, the effects of the secondary electrons generated from the heavy ion precipitation are included using a two-stream transport model that computes the secondary electron fluxes and their escape from the atmosphere. The model also determines H2 Lyman-Werner band emission intensities, including a predicted spectrum and the associated color ratio. I predict X-ray fluxes, efficiencies, and synthetic spectra for various initial ion energies considering opacity effects from two different atmospheres. The data is made available for quick X-ray calculations given an input ion flux. A calculation is given that demonstrates an in situ measured heavy ion flux above Jupiter's polar cap is capable of producing over 1 GW of X-ray emission. Implications of the new model results for the interpretation of data from NASA’s Juno mission are discussed.Publication The analysis of angular correlations of radiative transitions and an investigation of excited states of Cl³⁵(University of Kansas, 1965-05-31) Watson, Denny DuanePublication Disrupted Pathways: Generating Tunable Macromolecular Assembly Pathways(University of Kansas, 2018-12-31) Briggs, Koan Edward Michael; Fischer, Christopher J; Deeds, Eric J; Hawley, Steven A; Murray, Michael J; Shi, JiCongWhat follows is a pathway; a sequence of individual events, which together form a story. Yet it is still only a small part of what has come before. Biological structures also have individual stories; each composed of simple events in sequence. One story does not tell the whole, for that we must observe many stories, sample them if you will. Together, they bring understanding. Assembly is an emergent property of many individual binding events. Through this, all of the structures that make up life are created. Understanding the regime of possibilities provides insight into both the breadth and tendencies of the system. Cells contain numerous types of individual proteins many of which come together to form larger complexes. I will begin by introducing the elementary building blocks of those protein complexes. An introductory example will provide the first perspective, it will form common ground and allow the telling of the larger story with a shared perspective. Then a case study, a real biological complex and how understanding the progression of its pathways provided insight into the states which it reached. With the elementary operations described, I will move on to laying out the landscape of possible pathways; first for a specific case and then the structure of the assembly pathways themselves. Thus, providing a novel framework for the understanding of the stochastic space of protein complex assembly. Finally, I will provide an example of how making changes in the possible assembly pathways leads to non-intuitive changes in the conclusion of the protein complexes’ stories.Publication Bulk and Surface Radio-Frequency Response of Ice(University of Kansas, 2018-12-31) Stockham, Mark; Besson, David; Allen, Christopher; Cravens, Thomas; McKay, Douglas; Ralston, JohnThe flux and cross section of high energy neutrinos is an active area of research. Due to the expected low flux and cross section, interactions are rare and direct detection is ruled out. Large detector volumes with detection signals that can be observed from far away represent a reasonable and economical way to combat this problem. A currently popular detection strategy is to use a large, dense medium -- such as ice -- for the detector volume and radio antennas as the detectors. These radio antennas are sensitive to Cherenkov radiation produced via the Askaryan effect when a neutrino interacts in the detector volume. To determine the absolute amplitude of radio frequency (RF) emissions from high energy physics processes observed by Antarctic detectors, the bulk attenuation and surface reflection properties of Antarctic ice must be estimated. Neutrino experiments that intend to use polar ice as the detector volume must consider the depth-dependent attenuation length of the ice. Airborne experiments, such as the balloon-borne ANtarctic Impulsive Transient Antenna (ANITA), additionally need to consider the effects of the ice-air transition for both refracted signals produced by neutrino collisions in ice and reflected signals generated by cosmic ray-induced extensive air showers (EAS). Combining radar depth sounding (RDS) data for the estimation of attenuation length with radar scatterometer measurements for the estimation of surface roughness, we seek to create Antarctica-wide attenuation models. Though models and estimates for attenuation and reflection are motivated by ANITA analysis, the methods and results should have general use for the treatment of radio frequency signals interacting with ice and similar media.Publication Design, Implementation and First Results of the ANITA-HiCal Experiment(University of Kansas, 2018-12-31) Stockham, Jessica; Besson, David Z; Allen, Christopher; Feldman, Hume; Lewis, Ian; Zhao, HuiThe ANITA (ANtarctic Impulsive Transient Antenna) experiment is a balloon-borne suite of radio frequency antennas deployed during the austral summers in 2006, 2011, 2014, and 2016 to travel on the circumpolar winds over the ice sheets of Antarctica. The goal of the ANITA experiment is to detect UHE (Ultra-High Energy) neutrinos $(10^9$ to $10^{13}$ GeV) and cosmic rays through the RF (Radio-Frequency) emission of in-ice and atmospheric particle showers initiated, respectively, by these two types of particles. Radio detection of ultra-high energy cosmic ray (UHECR) extensive air showers (EAS) above the Antarctic continent has been demonstrated by the four flights of the ANITA experiment. The majority of the detected events were received as reflections from the ice surface. In order to reconstruct the energy of these reflected events, it is necessary to quantify any decoherence in the ANITA frequency band (180-1200 MHz) due to roughness of the ice surface. The purpose of this work is to provide details on the HiCal (High-altitude Calibration) experiment implemented to measure surface reflectivities of the Antarctic ice as a part of the ANITA experiment. The first HiCal payload flew in conjunction with the ANITA-3 flight in 2014 and provided a set of direct and reflected event pairs from which an inclination angle dependent measurement of the surface reflection coefficients was determined. It was found that at the highest incidence angles (most skimming) this coefficient deviates significantly both from the Fresnel predicted coefficients and from the model derived coefficients currently used in the ANITA analysis reconstruction of UHECR events.Publication Radar detection of cosmic-ray and neutrino induced cascades(University of Kansas, 2018-12-31) Prohira, Steven; Besson, David; Ralston, John P; Kong, KC; Bean, Alice; McKay, Doug; Allen, ChristopherAn ultra high energy particle, incident upon the earth, will produce a cascade of particles upon interaction. Detection of this cascade holds the key to understanding the properties of the primary-what it was, how much energy it carried, and maybe even where it came from. Of the many strategies developed over the course of the last century to detect such cascades, the radar technique is one of the latest to be explored with interest. For high enough incident energies, the relativistic progression of the cascade through a medium will produce a cloud of ionization that may become dense enough to reflect incident radio-frequency (RF) fields. If so, a broadcasting transmitter and distant receiver could feasibly detect cascades at very long baselines, thereby converting a massive volume of air or ice or sand or salt into a sensitive detector. Such an increase in volume opens up possibility of detecting events which occur on the order of 1km −2 yr −1 or less. In this dissertation, we present a detailed discussion of the radar detection method, focusing specifically on the detection of ultra high energy cosmic rays in the atmosphere, and ultra high energy neutrinos in dense material, such as ice. We will present the history and experimental efforts to date, and include the latest results from recent models and experiments seeking to address the radar problem. Ultimately, we suggest that the radar method is a promising one for the detection of 10 15 eV neutrinos which have interacted in a dense medium, such as the Antarctic ice.Publication Mathematical Modeling of Length Control in the Type III Secretion System(University of Kansas, 2018-12-31) Nariya, Maulik; Shi, Jack J; Deeds, Eric J; Shi, Jack J; Deeds, Eric J; Fischer, Christopher; Baringer, Philip; De Guzman, RobertoType III secretion secretion (T3SS) system is a protein export pathway that helps bacterial cells construct many structures, like the flagellar hook and the injectisome, that aid in crucial physiological processes such as locomotion and pathogenesis. Both, the flagellar hook and the injectisome, involve long extracellular channels and the length of these channels is highly regulated to allow these structures to perform their intended functions. Numerous experiments have been performed to understand the structural details of this nanomachine during the past decade. Despite the concerted efforts of molecular and structural biologists, several crucial aspects of the assembly of these structure, such as the regulation of the length of the needle and the flagellar hook, remain unclear. There are two leading models for how length control is achieved in the flagellar hook and T3SS needle: the substrate switching model, where the length is controlled by assembly of an inner rod, and the ruler model, in which a molecular ruler controls the length. While there is qualitative experimental evidence to support both models, there is a lack of detailed quantitative characterization of these models that could be used to unambiguously test these mechanisms experimentally. In this work, we used a combination of mathematical and computational techniques to better understand these length control mechanisms. Based on a set of straightforward assumptions, we constructed a mathematical model for length control based on the timing of substrate switching. Our model made predictions about commonly measured quantities such as the average needle lengths and the variance in lengths. In particular our model predicted for the substrate switching mechanism that the variance scales quadratically with the average length. Our model also predicted the form of the needle length distribution based on this mechanism, and found excellent agreement with available experimental data from Salmonella typhimurium with only a single free parameter. We also constructed a mathematical model of length control based on the ruler mechanism, and found that the predictions of this model are consistent with experimental data not just for the scaling of the average length with the ruler protein length, but also the variance. Interestingly, we found that the ruler mechanism allows for the evolution of needles with large average lengths without the concomitant large increase in variance that occurs in the substrate switching mechanism. In addition to making further predictions that can be tested experimentally, these findings shed new light on the trade-offs that may have lead to the evolution of different length control mechanisms in different bacterial species.Publication Topology, Geometry and Morphology of the Dark Matter Web(University of Kansas, 2018-08-31) Ramachandra, Nesar Soorve; Shandarin, Sergei F; Feldman, Hume; Anthony-Twarog, Barbara; Twarog, Bruce; Shontz, SuzanneSpatial distribution of dark matter displays a variety of intricate three dimensional structures on the largest scales in the Universe, notably the massive haloes, long tubular filaments, flattened walls and the vast under-dense voids. Galaxies embedded in the dark matter structures have illuminated the rich geometry of these structures currently known as the cosmic web. Cosmological N-body simulations are indispensable tools for understanding the evolution of the dark matter web. Recent developments in the numerical analysis of these simulations have hinted towards incorporating the dynamical information of gravitational clustering of collisionless dark matter. This is inferred from a six-dimensional Lagrangian sub-manifold -- comprising of initial and final coordinates of the dark matter particles. Velocity multistream field derived from this sub-manifold sheds new light on the nature of gravitational collapse. Geometrical, topological, morphological and heuristic diagnostic tools used in this novel parameter space reveal features of the dark matter distribution. For instance, a single void structure not only percolates the multistream field in all the directions, but also occupies over 99 per cent of all the single-streaming regions. On the other hand, connected filaments display a rapid topological transition to isolated islands at high multistream values. Hessian analysis delineates structures with different shapes: tubular, sheet-like, or globular -- enabling detection of the dark matter haloes without ad hoc parameters related to matter density or distance field.Publication The Lithium Plateau in Super Metal-Rich Stars(University of Kansas, 2018-08-31) Lee-Brown, Donald; Twarog, Bruce; Anthony-Twarog, Barbara; Rudnick, Gregory; Sanders, Stephen; Mechem, DavidI present a study of the lithium abundances for a sample of super metal-rich (SMR, [Fe/H] > + 0.20) main sequence dwarfs in the solar neighborhood. The SMR stars were selected to have surface temperatures in the region of the lithium plateau, a narrow region in temperature space where stars are predicted by models to preserve their initial surface Li abundances while on the main sequence. Despite these predictions, observations of lower-metallicity stars indicate that significant depletion occurs during the first few Gyr of stellar evolution. SMR stars, which represent the extreme end of Galactic chemical evolution, present an opportunity to constrain proposed mechanisms to explain this depletion. 100 SMR candidates were selected from existing surveys and followed up with spectroscopic observations using the Hydra spectrograph on the WIYN 3.5m telescope at Kitt Peak National Observatory, as well as photometric observations using the 0.9m WIYN and 40” telescopes at Kitt Peak and Mount Laguna Observatory, respectively. Using the results from ANNA, a new tool that uses a neural network to parameterize stellar spectra, as well as a more traditional equivalent width based analysis, 44 single stars with [Fe/H] > + 0.20 were identified and Li was measured for each star. Consistent with previous studies, the SMR stars can be divided into a sample of stars with measurable Li and a sample with upper limits only. Examining the low-Li stars’ evolutionary states reveals that they are consistent with being evolved Li dip stars and therefore depleted their surface Li while on the main sequence before evolving to the cooler temperatures of the Li plateau. Considering only the high-Li sample, the stars are all consistent with having ages in the range 3 – 4.5 Gyr, indicating that they have already significantly depleted their Li. We find no young (age + 0.20) main sequence dwarfs in the solar neighborhood. The SMR stars were selected to have surface temperatures in the region of the lithium plateau, a narrow region in temperature space where stars are predicted by models to preserve their initial surface Li abundances while on the main sequence. Despite these predictions, observations of lower-metallicity stars indicate that significant depletion occurs during the first few Gyr of stellar evolution. SMR stars, which represent the extreme end of Galactic chemical evolution, present an opportunity to constrain proposed mechanisms to explain this depletion. 100 SMR candidates were selected from existing surveys and followed up with spectroscopic observations using the Hydra spectrograph on the WIYN 3.5m telescope at Kitt Peak National Observatory, as well as photometric observations using the 0.9m WIYN and 40” telescopes at Kitt Peak and Mount Laguna Observatory, respectively. Using the results from ANNA, a new tool that uses a neural network to parameterize stellar spectra, as well as a more traditional equivalent width based analysis, 44 single stars with [Fe/H] > + 0.20 were identified and Li was measured for each star. Consistent with previous studies, the SMR stars can be divided into a sample of stars with measurable Li and a sample with upper limits only. Examining the low-Li stars’ evolutionary states reveals that they are consistent with being evolved Li dip stars and therefore depleted their surface Li while on the main sequence before evolving to the cooler temperatures of the Li plateau. Considering only the high-Li sample, the stars are all consistent with having ages in the range 3 – 4.5 Gyr, indicating that they have already significantly depleted their Li. We find no young (age + 0.20 were identified and Li was measured for each star. Consistent with previous studies, the SMR stars can be divided into a sample of stars with measurable Li and a sample with upper limits only. Examining the low-Li stars’ evolutionary states reveals that they are consistent with being evolved Li dip stars and therefore depleted their surface Li while on the main sequence before evolving to the cooler temperatures of the Li plateau. Considering only the high-Li sample, the stars are all consistent with having ages in the range 3 – 4.5 Gyr, indicating that they have already significantly depleted their Li. We find no young (age < 1 Gyr) SMR stars in the sample, which may explain an observed turnover in the positive correlation between [Fe/H] and initial Li abundance at super-solar metallicities – the only SMR stars in the solar neighborhood are already too old to measure initial Li as they have depleted down to the 2-3 Gyr plateau value. The Li plateau for the SMR sample was measured to be A(Li) = 2.55 dex, which agrees with observations of the similarly-aged super metal-rich cluster NGC 6253 as well as more metal-poor clusters, confirming that the Li plateau abundance in stars older than 2-3 Gyr is apparently insensitive to stellar metallicity. Examining the kinematics and available elemental abundances of the SMR stars, they are shown to be indistinguishable from lower-metallicity thin disk stars aside from their high [Fe/H], consistent with an origin in the inner thin disk.Publication Measuring Dijets From Ultra-Peripheral Heavy Ion Collisions(University of Kansas, 2018-08-31) BOWEN, JAMES LEE SMITH; Murray, Michael J.; Baringer, Philip S.; Fischer, Christopher; Lerner, David; Tapia Takaki, DanielThe Compact Muon Solenoid Experiment measured dijets produced in photon-nuclear collisions using data taken at the Large Hadron Collider in late 2015. Dijet measurements are potentially useful in constraining the gluon density over a wide range of x and Q, which is needed in order to measure the quark-gluon plasma viscosity and to search for the color-glass condensate. Recently it has been suggested by several theoretical groups that photon induced dijets can also be used to examine the correlation between the gluons in the nucleus. This analysis focused on the latter, examining azimuthal correlations between the total transverse momentum of the dijets and the momentum difference of the dijets. Following the prescription suggested by theorists, a positive correlation was found.Publication Angular correlations of dijets in ultra-peripheral Pb+Pb collisions at sqrt(s[NN])=5.02 TeV(University of Kansas, 2018-08-31) Boren, Samuel Steed; Takaki, Daniel T.; Takaki, Daniel T.; Baringer, Phil S.; Gavosto, Estela A.; Ralston, John P.; Sanders, Stephen J.One of the most remarkable predictions of the physics of strong interactions, and quantum chromodynamics (QCD) in particular, is gluon saturation. It is observed that the gluon density in hadrons, such as the proton, grows with energy, or equivalently with decreasing Bjorken-$x$ (the fraction of the hadron momentum carried by the parton). At some point this growth exceeds the unitarity limit and some new phenomena such as non-linear effects must set in. Data on the proton structure function, and on exclusive vector-meson photoproduction from the electron-proton collider HERA, which ended operations in 2007, have been inconclusive on whether or not gluon saturation has been observed. The search for non-linear QCD effects such as gluon saturation in both the proton and the nucleus is one of the main lines of research in high energy nuclear physics today. In nuclei the quantum fluctuations ought to be stronger than in protons. Recently, it has been found that the Quark Gluon Plasma (QGP) created in nucleus-nucleus collisions at RHIC and LHC expands with very little dissipation. The quantum fluctuations of the initial state described by the overlap of two highly Lorentz-contracted nuclei traveling on light-cone trajectories are probably imprinted upon the distribution of particles created in the QGP. Without assessing these quantum fluctuations in nuclei, fundamental properties of the QGP such as its viscosity-to-entropy ratio cannot be determined to a high precision. In this thesis we have studied, for the first time, the angular correlations of photoproduced dijets in ultra-peripheral Pb+Pb collisions at $\sqrt{s_{NN}} = 5.02$ TeV. This process has been suggested as a way to extract information of the nuclear gluon density in the Pb target, and thus provide information about the initial state of high energy nucleus-nucleus collisions.Publication Charge and Energy Transfer in Different Types of Two-Dimensional Heterostructures(University of Kansas, 2018-05-31) Bellus, Matthew Zetah; Zhao, Hui; Wu, Judy; Han, Siyuan; Chan, Wai-Lun; Hui, RongqingIn the last decade or so, layered materials have attracted significant attention due to their promise for tailoring electronic properties at an atomic level. Individually, these materials have exhibited strong attributes, relevant for both electronic and optoelectronic applications. However, the real world implementation of semiconducting materials is often derived from the junctions they form with other semiconductors. Thus, much of the interest in 2D materials arises from exploiting their ability to form low dimensional heterostructures. From a structural stand point, there are two ways these heterostructures can be formed, either vertically or laterally. The more common, vertical heterostructures, are intriguing due to their van der Waals adhesion, which eliminates many of the constraints attributed to lattice matching between materials. Lateral heterostructures, on the other hand, provide the unique opportunity to form in-plane junctions within a 2D sheet, creating novel 1D interfaces. To better understand these various heterostructures, this dissertation aims to explore photocarrier dynamics, using ultrafast laser spectroscopy techniques, in several types of structures yet to be extensively studied. First, charge and energy transfer mechanisms in vertical heterostructures formed between various transition metal dichalcogenide monolayers are studied, highlighting the addition of type-I band alignment to the discussion. Next, the extent to which materials can interact electronically through van der Waals adhesion is explored at the interface between amorphous and crystalline layers. From there, the focus shifts slightly to carrier dynamics across lateral junctions formed within monolayer sheets of transition metal dichalcogenides. This includes a discussion on lateral heterostructures, formed between different materials, as well as homostructures where an electronic junction can be induced in a single material. All of these studies will provide a unique overview on the possible directions and applications for which two dimensional materials can be facilitated. This dissertation includes previously published authored material.Publication Cosmogenic nuclide production within the atmosphere and long period comets(University of Kansas, 2013-05-31) Overholt, Andrew; Melott, Adrian L; Lieberman, Bruce; Thomas, Brian; Twarog, Bruce; Wilson, GrahamThe Earth is constantly bombarded by cosmic rays. These high energy particles collide with target nuclei, producing a shower of secondary particles. These secondaries contribute significantly to the radiation background at sea level and in the atmosphere, as well as producing rare cosmogenic nuclides. This contribution is variable over long time scales as astrophysical events change the cosmic ray flux incident on the Earth. Our work re-examines a previously proposed climate effect of increased cosmic ray flux due to galactic location. Although our work does not support this effect, cosmic ray secondaries remain a threat to terrestrial biota. We calculate the cosmogenic neutron flux within the atmosphere as a function of primary spectrum. This work is pivotal in determining the radiation dose due to any arbitrary astrophysical event where the primary spectrum is known. Additionally, this work can be used to determine the cosmogenic nuclide production from such an event. These neutrons are the fundamental source of cosmogenic nuclides within our atmosphere and extraterrestrial matter. We explore the idea that excursions in 14C and 10Be abundances in the atmosphere may arise from direct deposition by long-period comet impacts, and those in 26Al from any bolide. We find that the amount of nuclide mass on large long-period comets entering the Earth's atmosphere may be sufficient for creating anomalies in the records of 14C and 10Be from past impacts. In particular, the estimated mass of the proposed Younger Dryas comet is consistent with its having deposited sufficient isotopes to account for recorded nuclide increases at that time. The 26Al/10Be ratio is much larger in extraterrestrial objects than in the atmosphere, and so, we note that measuring this ratio in ice cores is a suitable further test for the Younger Dryas impact hypothesis. This portion of our work may be used to find possible impact events in the geologic record as well as determination of a large bolide impact rate.