The dynamics of individual DNA molecules were analyzed under the nonhomogeneous shear flow in a rectangular microchannel. The effects of a complex flow field on individual molecular behavior have never before been experimentally studied. Understanding the specific behavior of complex fluids in flow can lead to enhanced control of applications from synthetic polymer coatings to microfluidics and DNA microarrays. The molecular dynamics were measured though fluorescence microscopy with digital image acquisition. The flow channel, which was plasma etched into a silicon wafer for precise control of features, allowed for visualization of molecules in the plane defined by the velocity and velocity gradient. The extension of each DNA molecule in the ultra-dilute solution was measured in flow as a function of its position in the channel, which was then related to the Weissenberg number (Wi = lambdagamma). Wi values ranging from 0 to 30 were simultaneously studied in this work. Even at relatively high Wi, the molecules stretched to less than 50% of their full contour length because shear flow is a combination of elongation and rotation. The combination of these two forces caused partially extended molecules to tumble onto themselves before reaching maximum extension. These results were found to be in good agreement with data previously acquired for molecules in homogeneous shear flow. The molecules were not evenly distributed across the channel width or depth while flowing. Regions devoid of molecules extended 7 mum from each wall due to hydrodynamic interactions between the DNA molecules and the walls of the channel. Molecules also moved away from the centerline of the channel in both width and depth due to normal stresses. After cessation of flow, the depletion region in the middle of the channel disappeared and the width of the depletion regions adjacent to the walls was reduced to 4 mum because weaker static boundary layer effects replaced the flow-induced hydrodynamic interactions. This research brings us closer to fully understanding how individual molecules in solution respond to nonhomogeneous shear flow.

To better understand hydrate formation and dissociation mechanisms, Nuclear Magnetic Resonance (NMR), Magnetic Resonance Imaging (MRI), and viscosity measurements were employed to examine the hydrate transition processes of tetrahydrofuran (THF) - water (D2O or H2O) solution. Specifically, Spin-Lattice Relaxation Time (T1) and Spin-Spin Relaxation Time (T2) of THF in D2O were measured before hydrate formation, during hydrate formation, during hydrate dissociation, and after hydrate dissociation to probe the local molecular ordering changes around THF molecules. Hydrate formation and dissociation patterns were imaged using MRI. The viscosity of THF/H2O solution was monitored before hydrate formation and after hydrate dissociation using Champion Technologies Hydrate Rocking Cell (CTHRC) to investigate the residual viscosity phenomenon. NMR relaxation time results demonstrated that the presence of hydrate phase strongly influences the fluid structure of the coexisting liquid phase. T2 distribution technique was proven to be an effective tool in measuring the dynamic behavior of THF molecules in the hydrate phase and the liquid phase independently and concurrently. Comparison of T1's of THF in D2O solution during hydrate formation with that during dissociation revealed evidence of residual hydrate structures remaining in the liquid phase. Residual viscosity (as measured by CTHRC) was absent after THF hydrate dissociation. It was suggested that the residual viscosity observed by other groups after natural gas hydrate dissociation was more likely due to higher than equilibrium gas concentration than residual hydrate clathrate structures. To enable direct and accurate measurements of gas hydrate behavior in black oil, liquid-state proton NMR spectroscopy was innovatively applied to monitor the water peak area change in the NMR spectrum of water-in-oil emulsion during hydrate formation and dissociation. Because water in the hydrate phase does not contribute to the water peak area in such a spectrum, as water is being converted into hydrate, the water peak area would decrease. Results validated that it is feasible to directly and accurately monitor hydrate behavior in black oil using this technique.

Traditional metabolic engineering focused on pathway manipulation strategies like amplification addition or deletion of pathway to manipulate fluxes. However, cofactors play an essential role in cellular metabolism and their manipulation has the potential to be used, as an additional tool to achieve desired metabolic engineering goals. Coenzyme A and its derivative acetyl-CoA are important cofactors involved in many biosynthetic pathways and precursors for many industrially useful compounds. Our study focused on increasing the intracellular level/fluxes of CoA and acetyl-CoA. This was accomplished by overexpression of key rate controlling enzyme panK in the CoA biosynthesis pathway along with simultaneous supplementation of precursor pantothenic acid. The effect of such precise alteration of CoA metabolism on extracellular metabolite formation was studied. The utility of CoA manipulation system in enhancing production of isoamyl acetate, an industrially useful compound derived from acetyl-CoA was demonstrated. This novel approach of cofactor manipulation was combined with the more traditional approach of competing pathway deletion, acetate production pathway in this case, to further enhance isoamyl acetate productivity. Overexpression of panK led to a significant increase in CoA levels. Acetyl-CoA levels also increased but not as much as CoA leaving much of it in an unacetylated form. The central carbon flux was enhanced, either by overexpression of pdh or pps to increase acetyl-CoA, under elevated CoA levels. The flux through the acetyl-CoA node increased under such conditions. This enhanced carbon flux was efficiently channeled to isoamyl acetate production pathway by inactivating the acetate production pathway. The combination of these metabolic engineering strategies led to a significant increase in isoamyl acetate production. We used production of isoamyl acetate as a model system to demonstrate the beneficial effects of CoA/acetyl-CoA manipulations in enhancing product productivity. This methodology can be easily extended to any other production systems involving the cofactors CoA/acetyl-CoA. Additional studies in our lab have shown that CoA/acetyl-CoA manipulation system is useful in improving productivities of succinate and lycopene.

NMR surface relaxation mechanisms and their dependence on temperature were investigated. Paramagnetic ions are a very important factor of surface relaxation. The mechanism of the surface enhanced dipole-dipole interaction is negligible when the paramagnetic ion mechanism is strong. In such case, surface relaxivity of both water and oil depends only weakly on temperature. However, in cases when paramagnetic ion mechanism is weak, the contribution from surface enhanced dipole-dipole interaction could dominate the total surface relaxation rate. In such case, surface relaxivity of both water and oil decreases with temperature. Effects of synthetic oil base mud (OBM) surfactants on wettability alteration, NMR response and irreducible water saturation (Swir ) were systematically examined. The originally strongly water-wet Berea and limestone cores are altered to be intermediate-wet or oil-wet by OBM surfactants. As a result, Swir from NMR T 2, cutoff model with the default assumption of water-wetness generally underestimates the measured value. The magnitude of underestimation depends on the type of OBM surfactants, their concentration in the flushing fluid, and the flushing volume. The magnitude of underestimation correlates with the Amott-Harvey wettability index. These results suggest that the effects of OBM invasion on estimation of Swir can be minimized by controlling the volume of OBM invasion and the concentration of OBM surfactants. Mechanisms of Swir underestimation and modifications of NMR interpretation when wettability alteration occurs were investigated. In the case of an oil-bearing rock at Swir, OBM invasion does not significantly decrease the actual S wir, but changes the water and oil relaxation time distributions due to wettability alteration. This is visualized by the D-T 2 map. When wettability alteration occurs (water-wet to intermediate-wet or oil-wet), a T2, cutoff value larger than the one based on water-wetness is needed because the irreducible water relaxes at a longer relaxation time. Correlation between this modified T2, cutoff value and the Amott-Harvey wettability index was found. Three unusual NMR properties were observed for the filtered OBM filtrates due to the unexpected presence of trace amount of paramagnetic particulates. Interactions between the filtered OBMF and rock samples can cause wettability alteration, enhanced surface relaxation and increased internal gradient strength.

This thesis investigates the role of dispersed phase concentration on the drop deformation and breakup process of oil-in-water emulsions under flow. This work is motivated by two earlier studies: one by Mason & Bibette [4], on concentrated viscoelastic emulsions, which became monodisperse under the application of a simple shear flow, and a second, by Aronson [5], where a similar emulsion became monodisperse in a complex mixing flow. In the first part of the thesis, we study the effect of changing surfactant concentration, dispersed phase concentration and flow rate on the Aronson emulsion and two other oil-in-water emulsions. We find that emulsions in a mixing flow only become monodisperse around the close packing oil concentration of 70%. Increasing mixer speed and surfactant concentration decreases the polydispersity. Final mean drop sizes follow the same trend as the polydispersity. Qualitatively similar results are obtained by subjecting the emulsions to a simple shear flow. In the second part of the thesis, we directly visualize drop breakup in a concentrated emulsion. We used a model emulsion of castor oil in aqueous maltose in a simple shear flow, over an oil concentration range of 2--75%. Above 20% oil concentration, we observe qualitative changes in the deformation process. Instead of deforming into well-defined cylindrical threads, drops deform into convoluted shapes, with fluid accumulating unevenly along the drop length. The end-pinching instability is also suppressed with increasing concentration. The time to breakup for the drops becomes increasingly independent of initial drop size with increasing concentration until at around the close packing volume fraction, all the drops in the emulsion break together.

Part I. ab initio Molecular Dynamics of Interaction of Fe Atoms with Single-Wall Carbon Nanotubes. The interaction of Fe atoms with a single-wall carbon nanotube is investigated using the ab initio molecular dynamics method of Car and Parrinello. The variations in stability, band gap, Fermi energy, and total magnetic moment of the Fe-single wall carbon nanotube systems are found to depend on the location of the Fe atoms relative to the carbon nanotube surface. Noteworthy is that the Fe atoms in the Fe-carbon nanotubes systems are coupled ferromagnetically. The curvature effects on the interaction of Fe atoms with carbon nanotubes are also studied by comparing with the Fe-graphite systems. Part II. Phase Transitions and Long-Range Order of Magnetic Carbon Nanotubes. The magnetic coupling between single-wall carbon nanotubes filled with magnetic transition metals, which is assumed to be of the indirect type, is shown to lead to long-ranged ferromagnetic order for arrays of both metallic and semiconducting carbon nanotubes. The critical temperature and spontaneous magnetization are determined. It is found that metallic and semiconducting carbon nanotubes filled with magnetic elements can be turned into magnetic materials. Part III. Computer Simulation of Depletion Effects in Three-Dimensional Colloid-Polymer Systems. The phase behavior of three-dimensional colloid-polymer systems with purely depletion-induced attractions (hard chain polymer and hard sphere colloid) is studied using finite-size scaling and histogram-reweighting Monte Carlo simulations. The nature of the coexisting phases and the phase diagrams are found to depend on the polymer-to-colloid size ratio q. The threshold values of q where liquid-liquid coexistence disappears are found to differ significantly from the value predicted by mean-field theories. Phase separation is found to occur at the "protein limit" of very large polymer and small colloids, in contrast to de Gennes' prediction. Part IV. Depletion Interaction in One Dimension: Short-Range Order. For one-dimensional systems in the continuum in which the particles interact with nearest-neighbor forces, the pair correlation function at short distances can be expressed exactly in a simple form. Results are given for the hard-core interaction potential in which the attractive potential is linear, which represents the depletion interaction potential in one dimension.

Nuclear Magnetic Resonance (NMR) well logging is finding wide use in formation evaluation. In most cases, it is adequate to use default parameters and interpretation methods to get formation properties. In this work, we will investigate three exceptional cases: The departure of the hydrogen index ( HI) of live crude oils from unity due to high solution gas:oil ratio; The wettability alteration from water-wet condition to some degree of mixed wettability for sandstones; Significant diffusion effect on NMR spin-spin relaxation time (T2) measurements due to internal field gradients. A new correlation is proposed to express HI as a function of density and hydrogen:carbon ratio. The HI of live crude oils can be calculated from PVT data and ambient measurements. Wettability alteration is interpreted for sandstones from NMR analysis. Bentheim and Berea were water-wet with refined oil but became mixed-wet with SMY crude oil and brine at Swir after aging. North Burbank sandstones were even mixed-wet with refined oil due to the pore lining chlorite clay flakes. NMR wettability analysis is consistent with other quantitative wettability alteration indicators. Strong internal field gradients are measured for both chlorite-coated North Burbank sandstones and chlorite slurries. The distributions of internal field gradients are analytically solved through potential theory. High gradients are concentrated around the tips of the clay flakes. Mean gradient values from analytical solutions using a clay width of 0.2 mum are close to the experimental results. The combined effects of diffusion, constant gradient, and restricted 1-D geometry on Carr-Purcell_Meiboom_Gill (CPMG) measurement are evaluated numerically. The parameter space that defines the relaxation process is reduced to only two dimensionless groups: D* and tau*. The hypothesis that the dimensionless normalized magnetization relaxes as a single exponential with a constant dimensionless relaxation time T*2 is justified for most regions of the parameter space. The location of the boundaries between different relaxation regimes defined in the analytical analysis is challenged by the numerical results. After adjustment of boundaries, numerical simulation results and analytical solutions match each other for every relaxation regime except for near the boundaries. A procedure to estimate fluid diffusivity and system length is illustrated.

Metabolic engineering studies have generally focused on manipulating enzyme levels. However, cofactors play a major role in the production of fermentation products. This thesis provides the first systematic study of cofactor manipulations for the NADH/NAD+ cofactor pair and establishes these manipulations as an additional tool for metabolic engineering. This work investigates external and genetic means of increasing the availability of NADH and the total levels of NADH/+) and examines the effect of these manipulations on the distribution of metabolites in Escherichia coli. These strategies include feeding carbon sources with different oxidation states, overexpressing an enzyme that can regenerate NADH, overexpressing an enzyme in the NAD salvage pathway (NAPRTase; pncB), and eliminating NADH competing pathways. Feeding a more reduced carbon source (sorbitol) or regenerating NADH by overexpression of a heterologous NAD+-dependent FDH increased the NADH availability and provoked a significant change in the final metabolite distribution both under anaerobic and aerobic conditions. Anaerobically, the production of reduced metabolites was favored, as evidenced by a dramatic increase in the ethanol to acetate ratio (Et/Ac) and a shift towards ethanol as the major fermentation product. Aerobically, the increased availability of NADH induced a shift to fermentation even in the presence of oxygen. The NADH regeneration system doubled the maximum yield of NADH from 2 to 4 mol NADH/mol glucose consumed. This system also allows the uncoupling of NADH generation from carbon source oxidation by formate addition. Overexpression of the pncB gene in chemostat experiments increased the total NAD levels, decreased the NADH/NAD+ ratio, and did not significantly redistribute the metabolic fluxes. However, under anaerobic tube conditions, this manipulation decreased lactate production and increased the Et/Ac ratio by 2-fold, suggesting that the higher NAD levels increase the rate of NADH-dependent pathways (ethanol). Chemostat results from all manipulations studied imply that NADH availability rather than the NADH/NAD+ ratio dictates the metabolic flux distribution. This work also investigates the effect of these cofactor manipulations on the production of a model chemical that requires NADH, 1,2-propanediol. Results showed that our current 1,2-PD pathway is not limited by the availability of NADH.

The proton nuclear spin-lattice relaxation times and self-diffusion coefficients of ethane and propane were measured at elevated temperatures and pressures. It is found that pure ethane and propane depart from the linear correlations between relaxation time and viscosity/temperature and diffusivity found for pure higher alkanes and dead crude oils. The inverse relationship between the diffusion coefficient and viscosity/temperature for pure methane, pure higher alkanes, and methane-higher alkane mixtures holds for pure ethane and propane. The proton relaxation times were calculated and compared with the experimental data for ethane. The governing relaxation mechanism is shown to be the spin rotation interaction in gaseous ethane. At liquid densities, intra- and intermolecular dipole-dipole interactions and the spin rotation interaction all have significant contributions. A mixing rule was developed to estimate T 1 of gas mixtures. The estimated results by the mixing rule compared closely with experimental results for CH4-CO2 and CH 4-N2 gas mixtures. T1 and T 2 relaxation times of about 30 heavy crude oils were measured with different frequency NMR spectrometers. In addition, relaxation times of some oil samples were measured at various temperatures. Light oils have equal T 1 and T2 relaxation times. However, heavy or asphaltene crude oils have different T1 and T2 with the ratio of T1/ T2 increasing with increasing viscosity, Larmor frequency, asphaltene content and free radical content. For heavy oils, apparent T2 time constants increase and the signal amplitude decreases with increasing echo spacing. Apparent hydrogen index of heavy crude oils increases with increasing temperature. With increasing echo spacing, apparent hydrogen index of heavy oils decreases.

The system under investigation is the crude oil/brine/mineral (COBR) system. Deposition of polar asphaltenes from oil causes mineral wetting to alter from strongly water-wet to less water-wet. The degree of alteration depends on the hydrophobicity of asphaltene and the amount of deposition, which depends on many factors such as asphaltene content and solvency of the oil, acid and base content of the oil, brine pH and salinity, aging condition, and mineral type. Bulk and interfacial physico-chemical properties that affect mineral surface wetting are examined. Acid and base content are determined by potentiometric titration. Asphaltene solvency is quantified with the refractive indices of the oil and its solution with paraffinic precipitants. Interfacial tension and zeta potential of the oil/brine interface are measured to investigate the effect of surface-active compounds on interfacial properties. Two experimental methods to characterize surface wetting (contact angle and adhesion) are conducted. Wetting transition pH is calculated based on the DLVO theory and good agreement is observed in comparison with experimental results for two crude oils. Statistical analysis is preformed on the parameters affecting wettability. When the candidate parameter set is properly chosen, the two important factors (asphaltene content and base number/acid number) that most affect wetting emerge from the analysis. Atomic force microscopy (AFM is used to characterize mica surfaces that have first been equilibrated in 0.01 M NaCl pH 6 brine and then aged in crude oil at elevated temperature. The AFM images show the mixed-wet surface to be patches of bare mica and patches of asphaltene with a characteristic areal dimension of about 200 nm. A contact-angle model is developed based on the hypothesis that mineral surface is covered with circular, hydrophobic patches on a hydrophilic mineral surface in hexagonal pattern. A numerical simulation combined thin-film hydrodynamics (lubrication theory) with creeping flow model (local-wedge) to simulate advancing/receding motion of a gas/liquid interface over a solid. The equilibrium and apparent (advancing, receding) angles are examined. Equilibrium angle can be calculated exactly utilizing disjoining pressure. The apparent dynamic angles are observed to be a function of disjoining pressure (equilibrium angle) and line-speed of the interface (capillary number).