Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternative assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for …

The WARP code is a robust electrostatic particle-in-cell simulation package used to model charged particle beams with strong space-charge forces. A fundamental operation associated with seeding detailed simulations of a beam transport channel is to generate initial conditions where the beam distribution is matched to the structure of a periodic focusing lattice. This is done by solving for periodic, matched solutions to a coupled set of ODEs called the Kapchinskij-Vladimirskij (KV) envelope equations, which describe the evolution of low-order beam moments subject to applied lattice focusing, space-charge defocusing, and thermal defocusing forces. Recently, an iterative numerical method was developed (Lund, Chilton, and Lee, Efficient computation of matched solutions to the KV envelope equations for periodic focusing lattices, Physical Review Special Topics-Accelerators and Beams 9, 064201 2006) to generate matching conditions in a highly flexible, convergent, and fail-safe manner. This method is extended and implemented in the WARP code as a Python package to vastly ease the setup of detailed simulations. In particular, the Python package accommodates any linear applied lattice focusing functions without skew coupling, and a more general set of beam parameter specifications than its predecessor. Lattice strength iteration tools were added to facilitate the implementation of problems with …

Model heterogeneous catalysts have been synthesized and studied to better understand how the surface structure of noble metal nanoparticles affects catalytic performance. In this project, monodisperse rhodium and platinum nanoparticles of controlled size and shape have been synthesized by solution phase polyol reduction, stabilized by polyvinylpyrrolidone (PVP). Model catalysts have been developed using these nanoparticles by two methods: synthesis of mesoporous silica (SBA-15) in the presence of nanoparticles (nanoparticle encapsulation, NE) to form a composite of metal nanoparticles supported on SBA-15 and by deposition of the particles onto a silicon wafer using Langmuir-Blodgett (LB) monolayer deposition. The particle shapes were analyzed by transmission electron microscopy (TEM) and high resolution TEM (HRTEM) and the sizes were determined by TEM, X-ray diffraction (XRD), and in the case of NE samples, room temperature H2 and CO adsorption isotherms. Catalytic studies were carried out in homebuilt gas-phase reactors. For the nanoparticles supported on SBA-15, the catalysts are in powder form and were studied using the homebuilt systems as plug-flow reactors. In the case of nanoparticles deposited on silicon wafers, the same systems were operated as batch reactors. This dissertation has focused on the synthesis, characterization, and reaction studies of model noble metal heterogeneous catalysts. …

The magnetic flux structures in the intermediate state of bulk, pinning-free Type-I superconductors are studied using a high resolution magneto-optical imaging technique. Unlike most previous studies, this work focuses on the pattern formation of the coexisting normal and superconducting phases in the intermediate state. The influence of various parameters such as sample shape, structure defects (pinning) and applied current are discussed in relation to two distinct topologies: flux tubes (closed topology) and laminar (open topology). Imaging and magnetization measurements performed on samples of different shapes (cones, hemispheres and slabs), show that contrary to previous beliefs, the tubular structure is the equilibrium topology, but it is unstable toward defects and flux motion. Moreover, the application of current into a sample with the geometric barrier can replace an established laminar structure with flux tubes. At very high currents, however, there exists a laminar 'stripe pattern.' Quantitative analysis of the mean tube diameter is shown to be in good agreement with the prediction proposed by Goren and Tinkham. This is the first time that this model has been confirmed experimentally. Further research into the flux tube phase shows a direct correlation with the current loop model proposed in the 1990's by Goldstein, Jackson …

Remarkable advances have been made since rapid solidification was first introduced to the field of materials science and technology. New types of materials such as amorphous alloys and nanostructure materials have been developed as a result of rapid solidification techniques. While these advances are, in many respects, ground breaking, much remains to be discerned concerning the fundamental relationships that exist between a liquid and a rapidly solidified solid. The scope of the current dissertation involves an extensive set of experimental, analytical, and computational studies designed to increase the overall understanding of morphological selection, phase competition, and structural hierarchy that occurs under far-from equilibrium conditions. High pressure gas atomization and Cu-block melt-spinning are the two different rapid solidification techniques applied in this study. The research is mainly focused on Al-Si and Al-Sm alloy systems. Silicon and samarium produce different, yet favorable, systems for exploration when alloyed with aluminum under far-from equilibrium conditions. One of the main differences comes from the positions of their respective T{sub 0} curves, which makes Al-Si a good candidate for solubility extension while the plunging T{sub 0} line in Al-Sm promotes glass formation. The rapidly solidified gas-atomized Al-Si powders within a composition range of 15 to 50 …

Various single-molecule techniques were utilized for ultra-sensitive early diagnosis of viral DNA and antigen and basic mechanism study of enzymatic reactions. DNA of human papilloma virus (HPV) served as the screening target in a flow system. Alexa Fluor 532 (AF532) labeled single-stranded DNA probes were hybridized to the target HPV-16 DNA in solution. The individual hybridized molecules were imaged with an intensified charge-coupled device (ICCD) in two ways. In the single-color mode, target molecules were detected via fluorescence from hybridized probes only. This system could detect HPV-16 DNA in the presence of human genomic DNA down to 0.7 copy/cell and had a linear dynamic range of over 6 orders of magnitude. In the dual-color mode, fluorescence resonance energy transfer (FRET) was employed to achieve zero false-positive count. We also showed that DNA extracts from Pap test specimens did not interfere with the system. A surface-based method was used to improve the throughput of the flow system. HPV-16 DNA was hybridized to probes on a glass surface and detected with a total internal reflection fluorescence (TIRF) microscope. In the single-probe mode, the whole genome and target DNA were fluorescently labeled before hybridization, and the detection limit is similar to the flow …

Optimization techniques are finding their inroads into the field of nuclear physics calculations where the objective functions are very complex and computationally intensive. A vast space of parameters needs searching to obtain a good match between theoretical (computed) and experimental observables, such as energy levels and spectra. Manual calculation defies the scope of such complex calculation and are prone to error at the same time. This body of work attempts to formulate a design and implement it which would integrate the ab initio nuclear physics code MFDn and the VTDIRECT95 code. VTDIRECT95 is a Fortran95 suite of parallel code implementing the derivative-free optimization algorithm DIRECT. Proposed design is implemented for a serial and parallel version of the optimization technique. Experiment with the initial implementation of the design showing good matches for several single-nucleus cases are conducted. Determination and assignment of appropriate number of processors for parallel integration code is implemented to increase the efficiency and resource utilization in the case of multiple nuclei parameter search.

Angle- and time-resolved two-photon photoemission (2PPE) was used to study systems of organic semiconductors on Ag(111). The 2PPE studies focused on electronic behavior specific to interfaces and ultrathin films. Electron time dynamics and band dispersions were characterized for ultrathin films of a prototypical n-type planar aromatic hydrocarbon, PTCDA, and representatives from a family of p-type oligothiophenes.In PTCDA, electronic behavior was correlated with film morphology and growth modes. Within a fewmonolayers of the interface, image potential states and a LUMO+1 state were detected. The degree to which the LUMO+1 state exhibited a band mass less than a free electron mass depended on the crystallinity of the layer. Similarly, image potential states were measured to have free electron-like effective masses on ordered surfaces, and the effective masses increased with disorder within the thin film. Electron lifetimes were correlated with film growth modes, such that the lifetimes of electrons excited into systems created by layer-by-layer, amorphous film growth increased by orders of magnitude by only a few monolayers from the surface. Conversely, the decay dynamics of electrons in Stranski-Krastanov systems were limited by interaction with the exposed wetting layer, which limited the barrier to decay back into the metal.Oligothiophenes including monothiophene, quaterthiophene, and …