Confocal and two-photon microscopy : image enhancement /

Confocal and two-photon microcopy have become essential tools in biological research and today many investigations are not possible without their help. The valuable advantage that these two techniques offer is the ability of optical sectioning. Optical sectioning makes it possible to obtain 3D visuahzation of the structiu-es, and hence, valuable information of the structural relationships, the geometrical, and the morphological aspects of the specimen. The achievable lateral and axial resolutions by confocal and two-photon microscopy, similar to other optical imaging systems, are both defined by the diffraction theorem. Any aberration and imperfection present during the imaging results in broadening of the calculated theoretical resolution, blurring, geometrical distortions in the acquired images that interfere with the analysis of the structures, and lower the collected fluorescence from the specimen. The aberrations may have different causes and they can be classified by their sources such as specimen-induced aberrations, optics-induced aberrations, illumination aberrations, and misalignment aberrations. This thesis presents an investigation and study of image enhancement. The goal of this thesis was approached in two different directions. Initially, we investigated the sources of the imperfections. We propose methods to eliminate or minimize aberrations introduced during the image acquisition by optimizing the acquisition conditions. The impact on the resolution as a result of using a coverslip the thickness of which is mismatched with the one that the objective lens is designed for was shown and a novel technique was introduced in order to define the proper value on the correction collar of the lens. The amoimt of spherical aberration with regard to t he numerical aperture of the objective lens was investigated and it was shown that, based on the purpose of our imaging tasks, different numerical apertures must be used. The deformed beam cross section of the single-photon excitation source was corrected and the enhancement of the resolution and image quaUty was shown. Furthermore, the dependency of the scattered light on the excitation wavelength was shown empirically. In the second part, we continued the study of the image enhancement process by deconvolution techniques. Although deconvolution algorithms are used widely to improve the quality of the images, how well a deconvolution algorithm responds highly depends on the point spread function (PSF) of the imaging system applied to the algorithm and the level of its accuracy. We investigated approaches that can be done in order to obtain more precise PSF. Novel methods to improve the pattern of the PSF and reduce the noise are proposed. Furthermore, multiple soiu'ces to extract the PSFs of the imaging system are introduced and the empirical deconvolution results by using each of these PSFs are compared together. The results confirm that a greater improvement attained by applying the in situ PSF during the deconvolution process.

Phonon spectra and thermal properties of some fcc metals using embedded-atom potentials /

By employing the embedded-atom potentials of Mei et ai.[l], we have calculated the dynamical matrices and phonon dispersion curves for six fee metals (Cu,Ag,Au,Ni,Pd and Pt). We have also investigated, within the quasiharmonic approximation, some other thermal properties of these metals which depend on the phonon density of states, such as the temperature dependence of lattice constant, coefficient of linear thermal expansion, isothermal and adiabatic bulk moduli, heat capacities at constant volume and constant pressure, Griineisen parameter and Debye temperature. The computed results are compared with the experimental findings wherever possible. The comparison shows a generally good agreement between the theoretical values and experimental data for all properties except the discrepancies of phonon frequencies and Debye temperature for Pd, Pt and Au. Further, we modify the parameters of this model for Pd and Pt and obtain the phonon dispersion curves which is in good agreement with experimental data.

A fast atom bombardment mass spectrometry study of tris (3, 6-dioxaheptyl) amine-alkali metal halide complexes and hydrogen bonded complexes

The objective of this thesis was to demonstrate the potential of fast atom bombardment mass spectrometry (FABMS) as a probe of condensed phase systems and its possible uses for the study of hydrogen bonding. FABMS was used to study three different systems. The first study was aimed at investigating the selectivity of the ligand tris(3,6-dioxaheptyl) amine (tdoha) for the alkali metal cations. FABMS results correlated well with infrared and nmr data. Systems where a crown ether competed with tdoha for a given alkali metal cation were also investigated by fast atom bombardment. The results were found to correlate with the cation affinity of tdoha and the ability of the crown ether to bind the cation. In the second and third studies, H-bonded systems were investigated. The imidazole-electron donor complexes were investigated and FABMS results showed the expected H-bond strength of the respective complexes. The effects of concentration, liquid matrix, water content, deuterium exchange, and pre-ionization of the complex were also investigated. In the third system investigated, the abundance of the diphenyl sulfone-ammonium salt complexes (presumably H-bonded) in the FABMS spectrum were found to correlate with qualitative considerations such as steric hindrance and strength of ion pairs.

Arsenic speciation by ion-exchange chromatography with on- line determination by hydride generation: electronic modification of the D.C. plasma by photon counting

A method using L-cysteine for the determination of arsenous acid (As(III)), arsenic acid (As(V)), monomethylarsonic acid (MMAA), and dimethylarsinic acid (DMAA) by hydride generation was demonstrated. The instrument used was a d.c. plasma atomic emission spectrometer (OCP-AES). Complete recovery was reported for As(III), As(V), and DMAA while 86% recovery was reported for MMAA. Detection limits were determined, as arsenic for the species listed previously, to be 1.2, 0.8, 1.1, and 1.0 ngemL-l, respectively. Precision values, at 50 ngemL-1 arsenic concentration, were f.80/0, 2.50/0, 2.6% and 2.6% relative standard deviation, respectively. The L-cysteine reagent was compared directly with the conventional hydride generation technique which uses a potassium iodide-hydrochloric acid medium. Recoveries using L-cysteine when compared with the conventional method provided the following results: similar recoveries were obtained for As(III), slightly better recoveries were obtained for As(V) and MMAA, and significantly better recoveries for DMAA. In addition, tall and sharp peak shapes were observed for all four species when using L-cysteine. The arsenic speciation method involved separation by ion exchange .. high perfonnance liquid chromatography (HPLC) with on-line hydride generation using the L.. cysteine reagent and measurement byOCP-AES. Total analysis time per sample was 12 min while the time between the start of subsequent runs was approximately 20 min. A binary . gradient elution program, which incorporated the following two eluents: 0.01 and 0.5 mM tri.. sodium citrate both containing 5% methanol (v/v) and both at a pH of approximately 9, was used during the separation by HPLC. Recoveries of the four species which were measured as peak area, and were normalized against As(III), were 880/0, 290/0, and 40% for DMAA, MMAA and As(V), respectively. Resolution factors between adjacent analyte peaks of As(III) and DMAA was 1.1; DMAA and MMAA was 1.3; and MMAA and As(V) was 8.6. During the arsenic speciation study, signals from the d.c. plasma optical system were measured using a new photon-signal integrating device. The_new photon integrator developed and built in this laboratory was based on a previously published design which was further modified to reflect current available hardware. This photon integrator was interfaced to a personal computer through an AID convertor. The .photon integrator has adjustable threshold settings and an adjustable post-gain device.

Comparative electron impact and fast atom bombardment mass spectrometric studies of some HMPA adducts of phenyltin and phenyllead halides and studies of strong hydrogen bonding by FAB-MS

The fragmentation patterns and mass spectra of some phenyl tin and -lead halide adducts with hexamethylphosphoramide are compared by subjecting them t~ electron impact and fast atom bombardment ionization in a mass spectrometer. This comparison is restricted to the metal-containing ions. Ligand-exchange mechanisms of some of the metal-containing species are explored by FAB-MS. Several moisturesensitive organo-metallics and H-bonded systems have been examined by FAB for attempted characterization, but without any success. Scavenging and trapping of water molecules by complex aggregates in solutions of quaternary ammonium fluorides and hydroxides are investigated by FAB to complement previous NMR-studies.

Fast atom bombardment and electron impact mass spectrometry studies of some aryltin compounds and ferrocenes

Both El MS and FAB MS behavior of two groups of compounds, aryltin and ferrocene compounds, have been studied. For the aryltin compounds, the effect of substituent group position, substituent group type and ligand type on the El spectra have been explored in the El MS studies. The fragmentation mechanism has been investigated under El with linked scans, such as fragment ion scans(BJE), parent ion scans(B2JE) and constant neutral radical loss scans(B2(1-E)JE2). In the FAB MS studies, matrix optimization experiments have been carried out. The positive ion FAB MS studies focused on the effect of substituent group position, substituent group type and ligand type on the spectra. The fragmentation mechanisms of all the samples under positive ion FAB have been studied by means of the linked scans. The CA positive ion FAB fragmentation studies were also carried out for a typical sample. Negative ion FAB experiments of all the compounds have been done. And finally, the comparison of the El MS and FAB MS has been made. For ferrocenes, the studies concentrated on the fragmentation mechanism of each compound under El with linked scan techniques in the first field-free region and the applicability of positive/negative ion FAB MS to this group of compounds. The fragmentation mechanisms under positive ion FAB of those ferrocenes which can give positive ion FAB MS spectra were studied with the linked scan techniques. The CA +ve F AB fragmentation studies were carried out for a typical sample. Comparison of the E1 MS and FAB MS has been made.

Fast atom bombardment mass spectrometry of the coordination complexes of the ligand 5, 5, 7, 12, 12, 14- hexamenthyl-1, 4, 8, 11-tetraazacycloteradecane

A number of metal complexes containing the ligand 5,5,7,12,12,14-hexamethyl-l,4,8,11-tetra-azatetradecane were synthesized and analyzed using electron impact (EI) and fast atom bombardment (FAB). The FAB mass spectra were obtained in positive and negative ion mode. FAB in the positive ion mode proved to be the most successful technique for the identification of these compounds. In the majority of cases the spectra obtained using positive ion FAB were structurally informative, although not all showed molecular (M+) or quasimolecular ([M+H]+) ions. The fragmentations observed were characteristic of the ligands, and were interpreted based on the chemistry of these compounds.

Fast atom bombardment mass spectrometry studies of ruthenium (II) polypyridy coordination complexes and of group V Triptycenes and related complexes

In order to investigate the use of Fast Atom Bombardment Mass Spectrometry (FAB-MS) as a tool for structural characterization, two groups of complexes are analyzed. The first group is a set of ruthenium(II) coordination complexes containing bidentate polypyridyl ligands. The positive and negative ion FAB-MS spectra are found to be sufficient to allow for an almost complete characterization of the central metal atom, the ligands and the counter anions contained in the intact complex. An unusual observation of mUltiply charged ions in the positive ion FAB-MS spectra (i.e. [RUL 3 ]2+) is explained to be as a result of the oxidative quenching of the excited state of the doubly charged ion by the matrix, 3-nitrobenzyl alcohol. An analysis of a mixture shows that the technique is a good one for identifying components therein. A group of triptycene and related complexes containing Group V elements is also analyzed by FAB-MS and the results. in terms of relative abundances of fragment ions, are found to be consistent with known metal-carbon bond strengths.

Selected topics in fast atom bombardment (FAB) mass spectrometry a)specially designed probe tips and ion generation, b)structures of vitamin B6 schiff base complexes

This thesis can be broken down into two sections. Section one is a study . of the ionization mechanisms and the ion source optimization for Fast Atom Bombardment (FAB) ionization. For this study, several specially designed probe tips were created and tested under various experimental conditions. The aIm of this section is to understand the operating characteristics of a FAB IOn source better. The second section involves the study of several Vitamin B6 Schiff Base complexes using both positive and negative ion FAB MS. This section is an exploration of the usefulness of FAB MS as a structure probe for the metalcoordination complexes of Vitamin B6.

The fast atom bombardment mass spectrometric analysis of the carbamate pesticide carbaryl

The carbamate pesticide, carbaryl, was quantitatively studied using fast atom bombardment mass spectrometry (FAB-MS). Mass spectra were obtained in the positive ion-mode using both 2-nitrophenyloctyl ether (NPOE) and 3-nitrobenzyl alcohol (NBA) as matrix liquids. The sample was applied by three different techniques; simple mixing, solvent mixing and surface precipitation. Smaller volumes of matrix liquid were found to produce more favourable ion currents. Detection limits were largely independent of the matrix or application technique used. The relationship between ion current and the mass of analyte was found to be intricately related to the choice of matrix liquid.

Bis-and tris (amidine) fluoroboron cations and related systems studies by Multinuclear NMR and fast atom bombardment mass spectometry

The formation and the isolation of fluoroboron salts, (D2BF2+)(PF6-), (DD'BF2+)(PF6-) and (D3BF2+)(PF6-)2, have been carried out. 1,8-Diazabicyclo [5,4.0]undec-7-ene (DBU) and 1,5-diazabicyclo[4,3,O]non-5-ene (DBN), extremely strong organic bases, were introduced into the fluoroboron cation systems and induced a complicated redistribution reaction in the D/BF3/BC13 systems. The result was the formation of all BFnCI4-n-, D.BFnCI3-n and fluoroboron cation species which were detected by 19p and 11B NMR spectrometry. The displacement reaction of CI- from these D.BFnCI3-n (n = 1 and 2) species by the second entering ligand is much faster than in other nitrogen donor containing systems which have been previously studied. Tetramethylguanidine, oxazolines and thiazolines can also produce similar reactions in D/BF3/BCI3 systems, but no significant BFnC4-n- species were observed. As well as influences of their basicity and their steric hindrance, N=C-R(X) (X = N, 0 or S) and N=C( X)2 (X = N or S) structures of ligands have significant effects on the fonnationof fluoroboron cations and the related NMR parameters. D3BF2+ and some D2BF2+ show the expected inertness, but (DBU)2BF2+ shows an interestingly high reactivity. (D2BF2+)(X-) formed from weak organic bases such as pyridine can react with stronger organic bases and form DD'BF2+ and D'2BF2+ in acetone or nitromethane. Fast atom bombardment mass spectrometry is doubly meaningful to this work. Firstly, FABMS can be directly applied to the complicated fluoroboron cation containing solution systems as an excellent complementary technique to multinuclear NMR. Secondly, the gas-phase ion substitution reaction of (D2BF2+)(PF6-) with the strong organic bases is successfully observed in a FABMS ion source when the B-N bond is not too strong in these cations.