Chemical and mineralogical characterization of micro-inclusions in diamonds

Secondary-ion mass spectrometry (SIMS), electron probe analysis (EPMA), analytical scanning electron microscopy (SEM) and infrared (IR) spectroscopy were used to determine the chemical composition and the mineralogy of sub-micrometer inclusions in cubic diamonds and in overgrowths (coats) on octahedral diamonds from Zaire, Botswana, and some unknown localities.

The inclusions are sub-micrometer in size. The typical diameter encountered during transmission electron microscope (TEM) examination was 0.1-0.5 µm. The micro-inclusions are sub-rounded and their shape is crystallographically controlled by the diamond. Normally they are not associated with cracks or dislocations and appear to be well isolated within the diamond matrix. The number density of inclusions is highly variable on any scale and may reach 10^(11) inclusions/cm^3 in the most densely populated zones. The total concentration of metal oxides in the diamonds varies between 20 and 1270 ppm (by weight).

SIMS analysis yields the average composition of about 100 inclusions contained in the sputtered volume. Comparison of analyses of different volumes of an individual diamond show roughly uniform composition (typically ±10% relative). The variation among the average compositions of different diamonds is somewhat greater (typically ±30%). Nevertheless, all diamonds exhibit similar characteristics, being rich in water, carbonate, SiO_2, and K_2O, and depleted in MgO. The composition of micro-inclusions in most diamonds vary within the following ranges: SiO_2, 30-53%; K_2O, 12-30%; CaO, 8-19%; FeO, 6-11%; Al_2O_3, 3-6%; MgO, 2-6%; TiO_2, 2-4%; Na_2O, 1-5%; P_2O_5, 1-4%; and Cl, 1-3%. In addition, BaO, 1-4%; SrO, 0.7-1.5%; La_2O_3, 0.1-0.3%; Ce_2O_3, 0.3-0.5%; smaller amounts of other rare-earth elements (REE), as well as Mn, Th, and U were also detected by instrumental neutron activation analysis (INAA). Mg/(Fe+Mg), 0.40-0.62 is low compared with other mantle derived phases; K/ AI ratios of 2-7 are very high, and the chondrite-normalized Ce/Eu ratios of 10-21 are also high, indicating extremely fractionated REE patterns.

SEM analyses indicate that individual inclusions within a single diamond are roughly of similar composition. The average composition of individual inclusions as measured with the SEM is similar to that measured by SIMS. Compositional variations revealed by the SEM are larger than those detected by SIMS and indicate a small variability in the composition of individual inclusions. No compositions of individual inclusions were determined that might correspond to mono-mineralic inclusions.

IR spectra of inclusion- bearing zones exhibit characteristic absorption due to: (1) pure diamonds, (2) nitrogen and hydrogen in the diamond matrix; and (3) mineral phases in the micro-inclusions. Nitrogen concentrations of 500-1100 ppm, typical of the micro-inclusion-bearing zones, are higher than the average nitrogen content of diamonds. Only type IaA centers were detected by IR. A yellow coloration may indicate small concentration of type IB centers.

The absorption due to the micro-inclusions in all diamonds produces similar spectra and indicates the presence of hydrated sheet silicates (most likely, Fe-rich clay minerals), carbonates (most likely calcite), and apatite. Small quantities of molecular CO_2 are also present in most diamonds. Water is probably associated with the silicates but the possibility of its presence as a fluid phase cannot be excluded. Characteristic lines of olivine, pyroxene and garnet were not detected and these phases cannot be significant components of the inclusions. Preliminary quantification of the IR data suggests that water and carbonate account for, on average, 20-40 wt% of the micro-inclusions.

The composition and mineralogy of the micro-inclusions are completely different from those of the more common, larger inclusions of the peridotitic or eclogitic assemblages. Their bulk composition resembles that of potassic magmas, such as kimberlites and lamproites, but is enriched in H_2O, CO_3, K_2O, and incompatible elements, and depleted in MgO.

It is suggested that the composition of the micro-inclusions represents a volatile-rich fluid or a melt trapped by the diamond during its growth. The high content of K, Na, P, and incompatible elements suggests that the trapped material found in the micro-inclusions may represent an effective metasomatizing agent. It may also be possible that fluids of similar composition are responsible for the extreme enrichment of incompatible elements documented in garnet and pyroxene inclusions in diamonds.

The origin of the fluid trapped in the micro-inclusions is still uncertain. It may have been formed by incipient melting of a highly metasomatized mantle rocks. More likely, it is the result of fractional crystallization of a potassic parental magma at depth. In either case, the micro-inclusions document the presence of highly potassic fluids or melts at depths corresponding to the diamond stability field in the upper mantle. The phases presently identified in the inclusions are believed to be the result of closed system reactions at lower pressures.

Structurally engineered cytochromes c with novel ligand-binding properties

Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S.c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O₂ binding constants ~ 3x greater than those of myoglobin. The resistance of O₂-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.

UV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH^- coordination and that below pH ~6.5, Fe(III)Ala80cyt cis high-spin with His-H₂O heme ligation. Significant differences in the pH dependence of the ¹H NMR spectra of S.c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.

¹H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S.c. Fe(III)Ala80cyt c. 82% of the resonances in the ¹H NMR spectrum of S.c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 ± 0.11 Å for the backbone and 1.32 ± 0.14 Å for all heavy atoms. The solution structure indicates that a tyrosine in the "distal" pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.

Phase conjugation via four-wave mixing in a resonant medium

This thesis describes the theoretical solution and experimental verification of phase conjugation via nondegenerate four-wave mixing in resonant media. The theoretical work models the resonant medium as a two-level atomic system with the lower state of the system being the ground state of the atom. Working initially with an ensemble of stationary atoms, the density matrix equations are solved by third-order perturbation theory in the presence of the four applied electro-magnetic fields which are assumed to be nearly resonant with the atomic transition. Two of the applied fields are assumed to be non-depleted counterpropagating pump waves while the third wave is an incident signal wave. The fourth wave is the phase conjugate wave which is generated by the interaction of the three previous waves with the nonlinear medium. The solution of the density matrix equations gives the local polarization of the atom. The polarization is used in Maxwell's equations as a source term to solve for the propagation and generation of the signal wave and phase conjugate wave through the nonlinear medium. Studying the dependence of the phase conjugate signal on the various parameters such as frequency, we show how an ultrahigh-Q isotropically sensitive optical filter can be constructed using the phase conjugation process.

In many cases the pump waves may saturate the resonant medium so we also present another solution to the density matrix equations which is correct to all orders in the amplitude of the pump waves since the third-order solution is correct only to first-order in each of the field amplitudes. In the saturated regime, we predict several new phenomena associated with degenerate four-wave mixing and also describe the ac Stark effect and how it modifies the frequency response of the filtering process. We also show how a narrow bandwidth optical filter with an efficiency greater than unity can be constructed.

In many atomic systems the atoms are moving at significant velocities such that the Doppler linewidth of the system is larger than the homogeneous linewidth. The latter linewidth dominates the response of the ensemble of stationary atoms. To better understand this case the density matrix equations are solved to third-order by perturbation theory for an atom of velocity v. The solution for the polarization is then integrated over the velocity distribution of the macroscopic system which is assumed to be a gaussian distribution of velocities since that is an excellent model of many real systems. Using the Doppler broadened system, we explain how a tunable optical filter can be constructed whose bandwidth is limited by the homogeneous linewidth of the atom while the tuning range of the filter extends over the entire Doppler profile.

Since it is a resonant system, sodium vapor is used as the nonlinear medium in our experiments. The relevant properties of sodium are discussed in great detail. In particular, the wavefunctions of the 3S and 3P states are analyzed and a discussion of how the 3S-3P transition models a two-level system is given.

Using sodium as the nonlinear medium we demonstrate an ultrahigh-Q optical filter using phase conjugation via nondegenerate four-wave mixing as the filtering process. The filter has a FWHM bandwidth of 41 MHz and a maximum efficiency of 4 x 10^-3. However, our theoretical work and other experimental work with sodium suggest that an efficient filter with both gain and a narrower bandwidth should be quite feasible.

Properties of α-monoclinic selenium

The growth of bulky and platelet shaped α-monoclinic crystals is discussed. A simple method is devised for identifying and orienting them.

The density, previously in disagreement with the value calculated from x-ray studies, is carefully redetermined, and found to be in good agreement with the latter.

The relative dielectric constant is determined, an effort being made to eliminate errors inherent in previous measurements, which have not been in agreement. A two parameter model is derived which explains the anisotropy in the relative dielectric constant of orthorhombic sulfur, which is also composed of 8-atom puckered ring molecules. The model works less well for α-monoclinic selenium. The relative dielectric constant anisotropy is quite noticeable, being 6.06 along the crystal b axis, and 8.52-8.93 normal to the axis.

Thin crystal platelets of α-monoclinic selenium (less than 1µ thick) are used to extend optical transmission measurements up to 4.5eV. Previously the measurements extended up to 2.1 eV, limited by the thickness of the available crystals. The absorption edge is at 2.20 eV, with changes in slope of the absorption coefficient occurring at 2.85 eV and 3.8 eV. Measurement of transmission through solutions of selenium in CS_2 and trichlorethylene yield an absorption edge of 2.75 eV. There is evidence the selenium exists in solution partly as Se_8 rings, the building block of monoclinic selenium. Transmission is measured at low temperatures (80°K and 10°K) using the platelets. The absorption edge is at 2.38 eV and 2.39 eV, respectively, for the two temperatures. Measurements at low temperatures with polarized and unpolarized light reveal interesting absorption anisotropy near 2.65 eV.

Innovations of wide-field optical-sectioning fluorescence microscopy : toward high-speed volumetric bio-imaging with simplicity

Optical microscopy has become an indispensable tool for biological researches since its invention, mostly owing to its sub-cellular spatial resolutions, non-invasiveness, instrumental simplicity, and the intuitive observations it provides. Nonetheless, obtaining reliable, quantitative spatial information from conventional wide-field optical microscopy is not always intuitive as it appears to be. This is because in the acquired images of optical microscopy the information about out-of-focus regions is spatially blurred and mixed with in-focus information. In other words, conventional wide-field optical microscopy transforms the three-dimensional spatial information, or volumetric information about the objects into a two-dimensional form in each acquired image, and therefore distorts the spatial information about the object. Several fluorescence holography-based methods have demonstrated the ability to obtain three-dimensional information about the objects, but these methods generally rely on decomposing stereoscopic visualizations to extract volumetric information and are unable to resolve complex 3-dimensional structures such as a multi-layer sphere.

The concept of optical-sectioning techniques, on the other hand, is to detect only two-dimensional information about an object at each acquisition. Specifically, each image obtained by optical-sectioning techniques contains mainly the information about an optically thin layer inside the object, as if only a thin histological section is being observed at a time. Using such a methodology, obtaining undistorted volumetric information about the object simply requires taking images of the object at sequential depths.

Among existing methods of obtaining volumetric information, the practicability of optical sectioning has made it the most commonly used and most powerful one in biological science. However, when applied to imaging living biological systems, conventional single-point-scanning optical-sectioning techniques often result in certain degrees of photo-damages because of the high focal intensity at the scanning point. In order to overcome such an issue, several wide-field optical-sectioning techniques have been proposed and demonstrated, although not without introducing new limitations and compromises such as low signal-to-background ratios and reduced axial resolutions. As a result, single-point-scanning optical-sectioning techniques remain the most widely used instrumentations for volumetric imaging of living biological systems to date.

In order to develop wide-field optical-sectioning techniques that has equivalent optical performance as single-point-scanning ones, this thesis first introduces the mechanisms and limitations of existing wide-field optical-sectioning techniques, and then brings in our innovations that aim to overcome these limitations. We demonstrate, theoretically and experimentally, that our proposed wide-field optical-sectioning techniques can achieve diffraction-limited optical sectioning, low out-of-focus excitation and high-frame-rate imaging in living biological systems. In addition to such imaging capabilities, our proposed techniques can be instrumentally simple and economic, and are straightforward for implementation on conventional wide-field microscopes. These advantages together show the potential of our innovations to be widely used for high-speed, volumetric fluorescence imaging of living biological systems.