Axially symmetric rf ion traps consists of a mass analyser having three electrodes, one of which is a central ring electrode and the other two are endcap electrodes. In the ideal Paul trap mass spectrometer, the electrodes have hyperboloidal shape (March and Hughes, 1989) and in mass analyser with simplified geometry, such as the cylindrical ion trap (Wu et al.,2005) the central electrode is a cylinder and the two endcap electrode and flat plates. rf-only or rf/dc potential is applied across the ring electrode and the grounded endcap electrodes for conducting the basic experiments of the mass spectrometer. In recent times, the miniaturisation of ion trap is one of the research interests in the field of mass spectrometry. The miniaturisation has the advantages of compactness, low power consumption and portability. However, this is achieved at the cost of the overall performance of the mass spectrometer with its deleterious effect on resolution. Research groups study the field distribution in the trap for better understanding of ion dynamics in the direction of achieving improved performance with the miniaturised traps. One aspect which has not received any attention in research associated with quadrupole ion traps is the possible role of the magnetic field in improving performance of these traps. Since in the quadrupole ion trap mass analyser ion is confined by an oscillating (rf) field, magnetic fields have been considered superfluous. The motivation of the thesis is to understand the dynamics of ions in axially symmetric rf ion traps, in the presence of the magnetic field. The axially symmetric rf ion trap geometries considered in this thesis are the Paul trap and the cylindrical ion trap (CIT). The changes incurred to the ion motion and Mathieu stability diagram in the presence of magnetic field is observed in this work. Also, the relation between the magnetic field and the Mathieu parameter is shown. The thesis contains 4 chapters: Chapter 1 provides the basic back ground of mass spectrometry and the operating principles. The equations of ion motion in the Paul trap is derived and also the solution to Mathieu equation is provided. The solution to the Mathieu equation are the Mathieu parameters and , when plotted with on the x-axis and on the y-axis, results in the Mathieu stability plot, the explanation of which is also given in the chapter. A brief description of the secular frequency associated with the ion dynamics is given in this chapter. The popular experiments conducted (i.e. the mass selective boundary ejection and resonance ejection) with a mass spectrometer is described here. Finally at the end of the chapter is the scope of the thesis. Chapter 2 facilitates with the preliminary study required fort he accomplishment of the task. The Paul trap and the CIT are the rf ion traps considered in this work. The geometries of these two traps are described in this chapter. The computational methods used for the analysis of various aspects of mass spectrometer is introduced. The computational methods used involve the methods used for calculating the charge distribution on the electrodes, potentials, multipole co-efficients and trajectory calculations. The boundary element method(BEM), calculation for Potentials and the Runge-Kutta method used for the trajectory calculations are introduced in this chapter. The expressions for calculating the multipole co-efficients are also specified. Chapter 3 presents the results obtained. The equations of ion motion in a quadrupole ion trap in the presence of magnetic field is derived here. Verification of numerical results with and without the magnetic field are presented at the end of this chapter. The chapter also presents various graphs showing the impact of magnetic field on the ion dynamics in the Paul trap and the CIT. The impact of the presence of magnetic field on the micro motion in -, -and -directions of the rf ion traps are shown in this chapter. Also the figures showing the variation in the Mathieu stability plots, with varying magnetic field intensity are presented in the chapter. At the end of this chapter the relation between the magnetic field and the Mathieu parameter is derived and plotted. Chapter 4 explains the various observations made from the results obtained. This chapter also highlights the future scope of the work for making this a more applicable one. References in the text have been given by quoting the author’s name and year of publication. Full references have been provide, in an alphabetic order, at the end of the thesis.

A mix of physics, mathematics, and computer science, the study of quantum information seeks to understand and utilize the information that can be held in the state of a quantum system. Quantum cryptography is then the study of various cryptographic protocols on the information in a quantum system. One of the goals we may have is to verify the integrity of quantum data, a process called quantum message authentication. In this thesis, we consider two quantum message authentication schemes, the Clifford code and the trap code. While both of these codes have been previously proven secure, they have not been proven secure in the simulator model, with an efficient simulation. We offer a new class of simulator that is efficient, so long as the adversary is efficient, and show that both of these codes can be proven secure using the efficient simulator. The efficiency of the simulator is typically a crucial requirement for a composable notion of security. The main results of this thesis have been accepted to appear in the Proceedings of the 9th International Conference on Information Theoretic Security (ICITS 2016).

abstract: Land use change driven by human population expansion continues to influence the integrity and configuration of riparian corridors worldwide. Wildlife viability in semi-arid regions depend heavily on the connectivity of riparian corridors, since water is the primary limiting resource. The Madrean Archipelago in northern Mexico and southwestern United States (US) is a biodiversity hotspot that supports imperiled wildlife like jaguar (Panthera onca) and ocelot (Leopardus pardalis). Recent and ongoing infrastructure developments in the historically understudied US-México borderlands region, such as the border wall and expansion of Federal Highway 2, are altering wildlife movement and disconnecting essential habitat. I used wildlife cameras to assess species occupancy, abundance, and related habitat variables affecting the use of washes as corridors for mammals in semi-arid Los Ojos (LO), a private ranch within a 530 km2 priority conservation area in Sonora, México located south of the border and Federal Highway 2. From October 2018 to April 2019, I deployed 21 wildlife cameras in five different riparian corridors within LO. I used single- season occupancy models and Royal Nichols abundance models to explore the relationship between habitat variables and use of riparian corridors by mammal communities of conservation concern within this region. Twenty-one mammal species were recorded in the study area, including American black bear (Ursus americanus), white-tailed deer (Odocoileus virginianus) and the first sighting of jaguar (Panthera onca) in this region in 25 years. For the 11 medium- and large-bodied mammals recorded, habitat variables related to perennial river characteristics (distance to river, weekly water, and site width) and remoteness (distance from highway, elevation, and NDVI) were important for occupancy, but the direction of the relationship varied by species. For commonly observed species such as mountain lion (Puma concolor) and white-nosed coati (Nasua narica), topographic variety was highly informative for species abundance. These results highlight the importance of habitat diversity when identifying corridors for future protection to conserve wildlife communities in semi-arid regions. Additionally, this study provides robust evidence in support of mitigation measures (e.g. funnel fencing, over- or under- passes) along Federal Highway 2, and other barriers such as the border wall, to facilitate wildlife connectivity. / Dissertation/Thesis / Masters Thesis Biology 2020

<p>Advances in mass spectrometry (MS) instrumentation and techniques have provided approaches for complementing current biochemical research. Native mass spectrometry, which aims to analyze intact biomolecules and biomolecular complexes, has become a powerful tool for identifying and measuring different units of complex structures as well as probing interactions among the different units. Ion traps generally are important in native MS workflows because of their ability to accumulate ions and perform multi-stage analyses including fragmentation, photoreactions, and gas-phase reactions with reagent molecules or ions. Native MS, however, has shortcomings primarily due to the preferred ionization technique, electrospray ionization (ESI). ESI tends to distribute signal from a single analyte among a range of charge states. Additionally, the ions generated from droplets tend to carry adducted molecules and ions proportional to the size of the analyte. For analysis of high mass and heterogeneous biomolecular complexes, these shortcomings lead to wide overlapping charge states for different components that might be difficult to interpret correctly. Charge reduction via gas-phase ion/ion reactions facilitates interpretation of native mass spectra by generating product ions that are well separated in <i>m/z</i>. Current sine wave technology limits the upper <i>m/z</i> range of ion traps required for stabilizing and measuring high mass ion/ion reaction products. Digital ion trapping (DIT) technology circumvents the voltage limitations of sine wave technology by varying frequency to achieve high <i>m/z</i>. The combination of ion/ion reactions and DIT operation facilitates further unique probing reactions such as fragmentation reactions of charge reduced biomolecular complexes via neutral collisions and photoreactions. DIT operation also provides a straightforward approach for isolation of high <i>m/z</i> ions using duty cycle modulation to further facilitate analysis of heterogeneous mixtures. This work highlights developments of a home-built 3D ion trap mass spectrometer as a viable native MS platform.</p>

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This project is a master’s thesis in collaboration with Nomor, a company that offers pest control services. They had the need for the development of an automated mechanical rat trap for sewage systems. Brown rats populate the sewage systems in many cities, as it offers shelter and abundant food resources. Rats have been observed carrying various zoonotic diseases which are a health risk to people and animals, as rats may enter households via the sewage system. This report details the design and development process for a prototype for a striking mechanism, which will act as the foundation for a future trap. The process follows the theory described by Ulrich and Eppinger. The project resulted in the generation of 8 different concepts, which were screened down to a final pneumatic concept. The selected concept was then developed into a physical prototype, able to detect heat sources. A Simulink model was developed to support the detail design. The model calculates resulting impact energy from various input parameters, such as working pressure and moving mass. The prototype functions up to 3 bar with an impact energy of approximately 6 Joules.

Organic co-solvent-induced secondary conformation of α17-40 of human hemoglobin facilitates the splicing of E30-R31 in a mixture of its complementary segments by V8 protease. The amino acid sequence of α17-40 has been conceptualized by the general structure FR1-EALER-FRII and the pentapeptide sequence EALER playing a major role in inducing the α-helical conformation. The primary structure of α17-40 has been engineered in multiple ways to perturb one, two, or all three regions and the influence of the organic co-solvent-induced conformation and the concomitant resistance of E30-R31 peptide bond to V8 protease digestion has been investigated. The central pentapeptide (EALER), referred to here as splicedon,3 appears to dictate a primary role in facilitating the splicing reaction. When the same flanking regions are used, (1) splicedons that carry amino acid residues of low α-helical potential, for example G at position 2 or 3 of the splicedon, generate a conformational trap of very low thermodynamic stability, giving an equilibrium yield of only 3%-5%; (2) splicedons with amino acid residues of good α-helical potential generate a conformational trap of medium thermodynamic stability and give an equilibrium yield of 20%-25%; (3) the splicedons with amino residues of good α-helical potential and also an amino acid that can generate an i, i + 4 side-chain carboxylate-guanidino (amino) interaction, a conformational trap of maximum thermodynamic stability is generated, giving an equilibrium yield of 45%-50%; and (4) the thermodynamic stability of the conformational trap of the spliced peptide is also influenced by the amino acid composition of the flanking regions. The V8 protease resistance of the spliced peptide bond is not a direct correlate of the amount of α-helical conformation induced into the product. The results of this study reflect the unique role of the splicedon in translating the organic co-solvent-induced product conformation as a site-specific stabilization of the spliced peptide bond. It is speculated that the splicedon with higher α-helical potential as compared to either one of the flanking regions achieves this by integrating its potential with that of the flanking region(s). Exchange of flanking regions with the products of other V8 protease-catalyzed splicing reactions will help to establish the general primary structural requirements of this class of splicing reactions and facilitate their application in modular construction of proteins.

Algae “super blooms” are a commonly encountered environmental issue in fresh and brackish water that occurs due to the buildup of cyanobacteria. Many of the commonly encountered cyanobacteria such as Mycrocystis aeruginosa (M. aeruginosa) produce potent cyanotoxins (microcystins) that pose serious health threats and even death to local wild life and humans. Microcystin contaminated fresh-water that empties into the ocean has been shown to lethally affect marine life in the area of contamination. Human consumption of tainted sea life and other routes of mycrocystin exposure can lead to serious liver damage and even death. Thus, a method was developed for forensic postmortem analysis of microcystins RR, LR and YR by Two-Dimensional (2D) Liquid Chromatography (LC) - tandem Mass Spectrometry (MS/MS). A final 2D LC-MS/MS method was selected from 6x6 automated method development experiments. Each microcystin were subjected to a total of 36 methods, which were completed over an 18hr period. The extraction process was performed using a reverse-phase sorbent (Oasis HLB, Waters Corporation, Milford, MA) with a 3cc solid phase extraction (SPE) barrel using sequential elution. From acetonitrile (ACN) and methanol (MeOH) stock solutions, 10 μL of the internal standard (IS) Nodularin was added to the final extract. The concept of sequential micro extraction was designed to capture the retention behaviour of the target analyte in response to various extraction parameters (sorbent strength, elution polarity, and solubility). Therefore, optimized conditions were selected to excise the region of interest during extraction. The elution solvents chosen for the microcystins were acetonitrile, methanol and acetone with 10 % sequential increments. Since microcystins exhibit a zwitterionic structure, three sets of elution solutions were created to evaluate their elution profile (pH 3, pH 7, pH 10). When the elution profile for low pH and high pH are compared, microcystin RR was eluted over the 40% to 70% methanol fractions under low pH conditions with a slight shift towards higher organic % (50%-70% fractions) under high pH. This elution behaviour suggests that the basic moieties of the structure demonstrate a stronger retention for the stationary phase. Microcystin LR and YR however, eluted at a higher organic solvent percentage under low pH conditions and at a lower organic solvent percentage under high pH conditions, indicates that the acidic moieties of the structures have stronger retention. The urine sample gave recovery values for all three microcystins in the 80-90% range, as to be expected with type of complexity associated with biological samples. The sequential extraction protocol produced an extraction method that delivered a clean extract after a 30 min workflow using a single and optimized 2D LC-MS/MS method. The total analytical run time was set at 10 minutes.

This thesis investigates ion-molecule reaction studies with the use of an apparatus with a cryogenic 22-pole RF ion trap. In the introduction, we explain the suitability of an ion trap technique for measurements with conditions replicating interstellar medium. We created a technical draft by which we propose an upgrade of ion optics in a region between a mass analyser and a detector. The draft consists of a set of electrostatic electrodes. The proper effect on the ion optics was theoretically tested by multiple simulations in a programmed model of the detection system. We installed the set of electrodes into the apparatus. The new configuration was optimized by using an algorithm for finding extremes of a function. Finally, we tested the upgraded apparatus on a study of an ion- molecule reaction. The new configuration shows stability and greater control over the trajectory of an ion beam. The study's results are being prepared for publication in an impacted journal. 1

The ability to produce power during competition is essential. Football requires explosive power in order to get off the ball faster, increase speed of the first step, and increase the height of the vertical jump. Most strength training professionals use the back squat to increase power of the lower extremities; however, as large forces are placed on the back, athletes are at greater risk for injury. The trap bar dead lift is similar to the back squat in movement and form, but the trap bar dead lift reduces the force on the lower back. After testing for maximum vertical jump,athletes at Timpview High School participated in a strength program using either back squats or trap bar dead lift for seven weeks. A pre-test, mid-test and post-test were performed to calculate the increase in maximum vertical jump, if any. It was found that neither lift was significantly different than the other when testing for maximum vertical jump. These results will allow strength training professionals to use the trap bar dead lift instead of the back squats in subjects similar to those participating in the study.