This PhD dissertation reports the development of miniature ion optics components of a mass spectrometer (MS) with the ultimate goal to lay the foundation for a compact low-power micromachined MS (µMS) for broad-range chemical analysis. Miniaturization of two specific components a) RF ion traps and b) an ion funnel have been investigated and miniature low-power versions of these components have been developed and demonstrated successfully in lab experiments. Power savings, simpler electronics and packaging schemes required to operate the micro-scale RF cylindrical ion traps have been the key motivation driving this research. Microfabricated cylindrical ion traps (µCITs) and arrays in silicon, silicon-on-insulator and stainless steel substrates have been demonstrated and average power of as low as 55 mW for a low mass range (28 to 136 amu) and mass spectra with better than a unit-mass-resolution have been recorded. For the ion funnel miniaturization effort, simple assembly, small form factor and ease of integration have been emphasized. A simplification of the conventional 3D ion funnel design, called the planar ion funnel, has been developed in a single plate and has been tested to demonstrate ion funneling at medium vacuum levels (1E-5 Torr) using DC voltages and power less than 0.5 W. Miniaturization of these components also enables use of other novel ion optics components, packaging and integration, which will allow a new class of µMS architectures amenable for radical miniaturization.

Ion traps are an incredibly versatile tool which have many applications throughout the physical sciences, including such diverse topics as mass spectrometry, precision frequency metrology, tests of fundamental physics, and quantum computing. In this thesis, experiments are presented which involve trapping and measuring properties of Th³⁺. Th³⁺ ions are of unique interest in part because they are a promising platform for studying an unusually low-lying nuclear transition in the 229Th nucleus which could eventually be used as an exceptional optical clock. Here, experiments to measure electronic lifetimes of Th³⁺ are described. A second experimental topic explores the production of sympathetically cooled molecular ions. The study of cold molecular ions has a number of applications, some of which include spectroscopy to aid the study of astrophysical objects, precision tests of quantum electrodynamics predictions, and the study of chemical reactions in the quantum regime. The experiments presented here involve the production of barium monohalide ions, BaX⁺ (X = F, Cl, Br). This type of molecular ion proves to be particularly promising for cooling to the rovibrational ground state. The method used for producing BaX⁺ ions involves reactions between cold, trapped Ba⁺ ions and neutral gas phase reactants at room temperature. The Ba⁺ ion reaction experiments presented in this thesis characterize these reactions for producing Coulomb crystals composed of laser cooled Ba⁺ ions and sympathetically cooled BaX⁺ ions.

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In the normal operation of quadrupole ion trap mass spectrometers, the trapped ions are ejected symmetrically through both the upper (detector) and lower(source) endcap electrodes during mass selective boundary ejection experiment. This reduces the sensitivity of the instrument by almost 50%. In this preliminary study, we altered the geometry parameters of the quadrupole ion traps to introduce asymmetry. The asymmetry displaced the ion cloud towards the detector endcap which resulted in a preferential ejection through this endcap, thus imparting directionality to the ejected ions and hence to the sensitivity enhancement. Two symmetrical mass analyzers have been taken up for numerical study. They include the Paul trap(QIT) and the cylindricaliontrap(CIT). Asymmetry to these geometries is introduced in two ways, one by varying the upper endcap hole radius alone and in other by stretching the trap along the upper endcap only. The escape velocity plots and mass selective boundary ejection simulations are used to demonstrate the directionality of ion ejection for these geometries. The simulations revealed a significant increase in the number of ions getting ejected in the direction of asymmetry.

The Orbitrap is a mass analyzer that employs an electrostatic field to confine ions. The mass of an ion is determined from the frequency of its axial oscillations in the Orbitrap. The Orbitrap has high resolving power and accuracy. However, the electrodes of the Orbitrap have complicated curved shapes. As a consequence the Orbitrap is not easy to miniaturize. In this thesis we have proposed a class of easily machinable cylindrical-electrode structures to mimic the behavior of an Orbitrap. The proposed structure consists of a single cylinder and many coaxial equally spaced thick rings. A detailed numerical simulation of the cylindrical-electrode structure reveals that axial ion oscillations in it have many spurious frequency components in addition to the dominant frequency component. We have carried out a systematic shape optimization that adjusts the dimensions of the structure to minimize the amplitudes of the spurious frequency components of ion motion in the axial direction. The performance of the optimized structure was found to rival that of a practical Orbitrap.

<p>Mass spectrometry has become the premium chemical identification method. The next advancement for mass spectrometry is the widespread use of mass spectrometers for on-site chemical/biological identification. Ion trap mass spectrometers have emerged as powerful on-site analytical platforms, in spite of limited mass resolution, due to their compatibility with ambient ionization methods and ready implementation of tandem mass spectrometry (MS/MS). However, conventionally operated ion traps are inefficient in accessing the entire tandem mass spectrometry dataspace. By operating the ion trap at a constant trapping voltage, more efficient tandem mass spectrometry scan modes are accessible. The most efficient is to acquire the entire tandem mass spectrometry data space and this work demonstrates three different methods of acquiring this data domain. These methods acquire the data in under a second and the best performing method was implemented in a miniature mass spectrometer without performance decrease. The impact of this device is most powerful when analysis requires the entire ionized sample be considered to determine the identity of the sample. This was shown to be useful for monitoring the lipid metabolism in a model microorganism. </p>

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This thesis is a numerical study of fields within ion traps having segmented electrodes1. The focus is on two cylindrical ion trap structures, two Orbit rap structures and one planar structure which mimics the field of the Orbit rap. In all these geometries, the segments which comprise the electrodes are easily Machin able rings and plates. By applying suitable potential to the different segments, the fields within these geometries are made to mimic the fields in the respective ideal structures. This thesis is divided into 6 chapters. Chapter 1 presents introduction and background information relevant to this work. A brief description of the Quadrupole Ion Trap (QIT) and the Orbit rap is given. The role of numerical simulations in the design of an ion trap geometry is briefly outlined. The motivation of this thesis is presented. The chapter ends by describing the scope of the thesis. Chapter 2 presents a general description of computational methods used throughout this work. The Boundary Element Methods (BEM) is first described. Both 2D and 3D BEM are used in this work. The software for 3D BEM is newly developed and hence 3D BEM is described in more detail. A verification of 3D BEM is presented with a few examples. The Runge-Kutta method used to compute the trajectory of ion is presented. A brief overview of the Nelder-Mead method of function minimization is given. The computational techniques specifically used to obtain the results in Chapter 3, 4 and 5 are presented in the respective chapters. Chapter 3 presents segmented electrode geometries of the Cylindrical Ion Trap (CIT). In these geometries, the electrodes of the CIT are split into number of mini-electrodes and different voltages are applied to these segmented electrodes to achieve the desired field. Two geometries of the segmented electrode CIT will be investigated. In the first, we retain the flat end cap electrodes of the CIT but split the ring electrode into five mini-rings. In the second configuration, we split the ring electrode of the CIT into three mini-rings and 1The term ‘segmented electrode’ used in this thesis has the same connotation as the term ‘split-electrode’ used in Sonalikar and Mohanty (2013). also divide the end caps into two mini-discs. By applying different potentials to the mini-rings and mini-discs of these geometries we will show that the field within the trap can be optimized to desired values. Two different types of fields will be targeted. In the first, potentials are adjusted to obtain a linear electric field and, in the second, a controlled higher order even multipole field are obtained by adjusting the potential. It will be shown that the different potentials to the segmented electrodes can be derived from a single RF generator by connecting appropriate capacitor terminations to segmented electrodes. The field within the trap can be modified by changing the value of the external capacitors. Chapter 4 presents segmented electrode geometries which are possible alternatives for the Orbitrap. Two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap, will be investigated. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap are replaced by rings and discs of fixed radii, respectively. In this structure two segmented end cap electrodes are added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap are replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies will be undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) measurement of image currents. These studies will be carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM is developed specifically for this study. It will be seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It will be shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analysers. A novel technique of optimization of the electric field is proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode trap having the same design as ORB1 show that it can provide accurate mass analysis. Chapter 5 presents a segmented electrode planar geometry named as PORB used to mimic the electric field of the Orbit rap. This geometry has two planes, each plane consisting of 30 concentric ring electrodes. Although the geometry of PORB does not have conventional inner and outer electrodes of the Orbit rap, it will be shown that by selecting appropriate geometry parameters and suitable potentials for the ring electrodes, this geometry can trap the ions into an orbital motion similar to that in the Orbit rap. The performance of the planar geometry is studied by comparing the variation of potential, ion trajectories and image current in this geometry with that in the Orbit rap. The optimization of applied potentials is performed to correct the errors in the electric field so that the variation of axial frequency of ions with their initial position is minimized. Chapter 6 presents the summary and a few concluding remarks

This thesis investigates the loss of high mass ions due to the initial thermal energy in ion trap mass analyzers. It provides an analytical expression for estimating the percentage loss of ions of a given mass at a particular temperature, in a trap operating with a set of conditions. The investigations have been carried out on quadrupole and cylindrical ion trap geometries. The three-dimensional Maxwellian velocity distribution function has been assumed to derive an expression for the percentage of ions lost. Adopting an approximation based on the observed escape velocity profiles of ions, an expression for the percentage loss of ions of a given mass has been derived as a function of the temperature for an ensemble of ions, its mass and its escape velocity. An analytical expression for the escape velocity has also been developed. It is seen that the escape velocity is a function of the trapping field, drive frequency and ion mass. Because the trapping field is determined by trap design parameters and operating conditions, it has been possible to study the influence of these parameters on ion loss. The parameters investigated include ion temperature, magnitude of the initial potential applied to the ring electrode (which determines the low mass cut-off), trap size, dimensions of apertures in the endcap electrodes and RF drive frequency. The studies demonstrate that ion loss due to initial thermal energy increases with increase in mass and that ion escape occurs in the radial direction. Reduction in the loss of high mass ions is favoured by lower ion temperatures, increasing low mass cut-off, increasing trap size, and higher RF drive frequencies. The dimensions of the apertures in the endcap electrodes do not influence ion loss in the range of aperture sizes considered.