RF-sputter fabrication of magnetic garnet thin films and simulation modeling for 1-D magnetic photonic crystal waveguide devices

One dimensional magnetic photonic crystals (1D-MPC) are promising structures for integrated optical isolator applications. Rare earth substituted garnet thin films with proper Faraday rotation are required to fabricate planar 1D-MPCs. In this thesis, flat-top response 1D-MPC was proposed and spectral responses and Faraday rotation were modeled. Bismuth substituted iron garnet films were fabricated by RF magnetron sputtering and structures, compositions, birefringence and magnetooptical properties were studied. Double layer structures for single mode propagation were also fabricated by sputtering for the first time. Multilayer stacks with multiple defects (phase shift) composed of Ce-YIG and GGG quarter-wave plates were simulated by the transfer matrix method. The transmission and Faraday rotation characteristics were theoretically studied. It is found that flat-top response, with 100% transmission and near 45o rotation is achievable by adjusting the inter-defect spacing, for film structures as thin as 30 to 35 μm. This is better than 3-fold reduction in length compared to the best Ce-YIG films for comparable rotations, thus allows a considerable reduction in size in manufactured optical isolators. Transmission bands as wide as 7nm were predicted, which is considerable improvement over 2 defects structure. Effect of repetition number and ratio factor on transmission and Faraday rotation ripple factors for the case of 3 and 4 defects structure has been discussed. Diffraction across the structure corresponds to a longer optical path length. Thus the use of guided optics is required to minimize the insertion losses in integrated devices. This part is discussed in chapter 2 in this thesis. Bismuth substituted iron garnet thin films were prepared by RF magnetron sputtering. We investigated or measured the deposition parameters optimization, crystallinity, surface morphologies, composition, magnetic and magnetooptical properties. A very high crystalline quality garnet film with smooth surface has been heteroepitaxially grown on (111) GGG substrate for films less than 1μm. Dual layer structures with two distinct XRD peaks (within a single sputtered film) start to develop when films exceed this thickness. The development of dual layer structure was explained by compositional gradient across film thickness, rather than strain gradient proposed by other authors. Lower DC self bias or higher substrate temperature is found to help to delay the appearance of the 2nd layer. The deposited films show in-plane magnetization, which is advantageous for waveguide devices application. Propagation losses of fabricated waveguides can be decreased by annealing in an oxygen atmosphere from 25dB/cm to 10dB/cm. The Faraday rotation at λ=1.55μm were also measured for the waveguides. FR is small (10° for a 3mm long waveguide), due to the presence of linear birefringence. This part is covered in chapter 4. We also investigated the elimination of linear birefringence by thickness tuning method for our sputtered films. We examined the compressively and tensilely strained films and analyze the photoelastic response of the sputter deposited garnet films. It has been found that the net birefringence can be eliminated under planar compressive strain conditions by sputtering. Bi-layer GGG on garnet thin film yields a reduced birefringence. Temperature control during the sputter deposition of GGG cover layer is critical and strongly influences the magnetization and birefringence level in the waveguide. High temperature deposition lowers the magnetization and increases the linear birefringence in the garnet films. Double layer single mode structures fabricated by sputtering were also studied. The double layer, which shows an in-plane magnetization, has an increased RMS roughness upon upper layer deposition. The single mode characteristic was confirmed by prism coupler measurement. This part is discussed in chapter 5.

SURFACTANT-OIL INTERACTIONS: FOAMING & TOXICITY

Surfactants find large applications in detergents, paints, coatings, food and pharmaceutical industries. Other than that, much focused work has been carried out in oil recovery in petroleum industries and raw material extraction in mining industries. This is because of their unique structure and ability to simultaneously adhere to materials which are both structurally and physically different. The current thesis focuses on interactions of oil with different commercially available and laboratory synthesized surfactants in terms of characteristics such as foaming, ultrasound exposure and toxicity. Foaming is one important characteristic of surfactants that is widely utilized for oil recovery purposes. Researchers utilize surfactants' special ability to provide foam stability to for more efficient oil herding capability. The foam stability and foam volumes are calculated using static foam height tests. Further dispersion or oil in water emulsion formation is observed using ultrasound sources. As described earlier surfactants are not only used as foams for oil displacement, but they are also used for dispersion purposes where they are key components of dispersant formulations. During such operations, especially in sea conditions where adverse effects on aquatic life are a concern, toxicity of chemicals used becomes an important factor. Our toxicity testing experiments involves different surfactants, solvents and crude oil combinations through exposure to special light luminescent bacteria. The decrease in light intensity of the exposed bacteria is related to toxic effects of the samples.

DEVELOPMENT OF AN OPTIMIZATION MODEL FOR BIOFUEL FACILITY SIZE AND LOCATION AND A SIMULATION MODEL FOR DESIGN OF A BIOFUEL SUPPLY CHAIN

A range of societal issues have been caused by fossil fuel consumption in the transportation sector in the United States (U.S.), including health related air pollution, climate change, the dependence on imported oil, and other oil related national security concerns. Biofuels production from various lignocellulosic biomass types such as wood, forest residues, and agriculture residues have the potential to replace a substantial portion of the total fossil fuel consumption. This research focuses on locating biofuel facilities and designing the biofuel supply chain to minimize the overall cost. For this purpose an integrated methodology was proposed by combining the GIS technology with simulation and optimization modeling methods. The GIS based methodology was used as a precursor for selecting biofuel facility locations by employing a series of decision factors. The resulted candidate sites for biofuel production served as inputs for simulation and optimization modeling. As a precursor to simulation or optimization modeling, the GIS-based methodology was used to preselect potential biofuel facility locations for biofuel production from forest biomass. Candidate locations were selected based on a set of evaluation criteria, including: county boundaries, a railroad transportation network, a state/federal road transportation network, water body (rivers, lakes, etc.) dispersion, city and village dispersion, a population census, biomass production, and no co-location with co-fired power plants. The simulation and optimization models were built around key supply activities including biomass harvesting/forwarding, transportation and storage. The built onsite storage served for spring breakup period where road restrictions were in place and truck transportation on certain roads was limited. Both models were evaluated using multiple performance indicators, including cost (consisting of the delivered feedstock cost, and inventory holding cost), energy consumption, and GHG emissions. The impact of energy consumption and GHG emissions were expressed in monetary terms to keep consistent with cost. Compared with the optimization model, the simulation model represents a more dynamic look at a 20-year operation by considering the impacts associated with building inventory at the biorefinery to address the limited availability of biomass feedstock during the spring breakup period. The number of trucks required per day was estimated and the inventory level all year around was tracked. Through the exchange of information across different procedures (harvesting, transportation, and biomass feedstock processing procedures), a smooth flow of biomass from harvesting areas to a biofuel facility was implemented. The optimization model was developed to address issues related to locating multiple biofuel facilities simultaneously. The size of the potential biofuel facility is set up with an upper bound of 50 MGY and a lower bound of 30 MGY. The optimization model is a static, Mathematical Programming Language (MPL)-based application which allows for sensitivity analysis by changing inputs to evaluate different scenarios. It was found that annual biofuel demand and biomass availability impacts the optimal results of biofuel facility locations and sizes.

TIME LAPSE SEISMIC OBSERVATIONS AND EFFECTS OF RESERVOIR COMPRESSIBILITY AT TEAL SOUTH OIL FIELD

One of the original ocean-bottom time-lapse seismic studies was performed at the Teal South oil field in the Gulf of Mexico during the late 1990’s. This work reexamines some aspects of previous work using modern analysis techniques to provide improved quantitative interpretations. Using three-dimensional volume visualization of legacy data and the two phases of post-production time-lapse data, I provide additional insight into the fluid migration pathways and the pressure communication between different reservoirs, separated by faults. This work supports a conclusion from previous studies that production from one reservoir caused regional pressure decline that in turn resulted in liberation of gas from multiple surrounding unproduced reservoirs. I also provide an explanation for unusual time-lapse changes in amplitude-versus-offset (AVO) data related to the compaction of the producing reservoir which, in turn, changed an isotropic medium to an anisotropic medium. In the first part of this work, I examine regional changes in seismic response due to the production of oil and gas from one reservoir. The previous studies primarily used two post-production ocean-bottom surveys (Phase I and Phase II), and not the legacy streamer data, due to the unavailability of legacy prestack data and very different acquisition parameters. In order to incorporate the legacy data in the present study, all three poststack data sets were cross-equalized and examined using instantaneous amplitude and energy volumes. This approach appears quite effective and helps to suppress changes unrelated to production while emphasizing those large-amplitude changes that are related to production in this noisy (by current standards) suite of data. I examine the multiple data sets first by using the instantaneous amplitude and energy attributes, and then also examine specific apparent time-lapse changes through direct comparisons of seismic traces. In so doing, I identify time-delays that, when corrected for, indicate water encroachment at the base of the producing reservoir. I also identify specific sites of leakage from various unproduced reservoirs, the result of regional pressure blowdown as explained in previous studies; those earlier studies, however, were unable to identify direct evidence of fluid movement. Of particular interest is the identification of one site where oil apparently leaked from one reservoir into a “new” reservoir that did not originally contain oil, but was ideally suited as a trap for fluids leaking from the neighboring spill-point. With continued pressure drop, oil in the new reservoir increased as more oil entered into the reservoir and expanded, liberating gas from solution. Because of the limited volume available for oil and gas in that temporary trap, oil and gas also escaped from it into the surrounding formation. I also note that some of the reservoirs demonstrate time-lapse changes only in the “gas cap” and not in the oil zone, even though gas must be coming out of solution everywhere in the reservoir. This is explained by interplay between pore-fluid modulus reduction by gas saturation decrease and dry-frame modulus increase by frame stiffening. In the second part of this work, I examine various rock-physics models in an attempt to quantitatively account for frame-stiffening that results from reduced pore-fluid pressure in the producing reservoir, searching for a model that would predict the unusual AVO features observed in the time-lapse prestack and stacked data at Teal South. While several rock-physics models are successful at predicting the time-lapse response for initial production, most fail to match the observations for continued production between Phase I and Phase II. Because the reservoir was initially overpressured and unconsolidated, reservoir compaction was likely significant, and is probably accomplished largely by uniaxial strain in the vertical direction; this implies that an anisotropic model may be required. Using Walton’s model for anisotropic unconsolidated sand, I successfully model the time-lapse changes for all phases of production. This observation may be of interest for application to other unconsolidated overpressured reservoirs under production.

Modeling of human P450 oxidoreductase structure by in silico mutagenesis and MD simulation

P450 oxidoreductase (POR) is the obligate electron donor for microsomal cytochrome P450s and mutations in POR cause several metabolic disorders. We have modeled the structure of human P450 oxidoreductase by in silico amino acid replacements in the rat POR crystal structure. The rat POR has 94% homology with human POR and 38 amino acids were replaced to make its sequence identical to human POR. Several rounds of molecular dynamic simulations refined the model and removed structural clashes from side chain alterations of replaced amino acids. This approach has the advantage of keeping the cofactor contacts and structural features of the core enzyme intact which could not be achieved by homology based approaches. The final model from our approach was of high quality and compared well with experimentally determined structures of other PORs. This model will be used for analyzing the structural implications of mutations and polymorphisms in human POR.

Realistic Single Cell Modeling – from Experiment to Simulation

This tutorial gives a step by step explanation of how one uses experimental data to construct a biologically realistic multicompartmental model. Special emphasis is given on the many ways that this process can be imprecise. The tutorial is intended for both experimentalists who want to get into computer modeling and for computer scientists who use abstract neural network models but are curious about biological realistic modeling. The tutorial is not dependent on the use of a specific simulation engine, but rather covers the kind of data needed for constructing a model, how they are used, and potential pitfalls in the process.

Modeling the heterogeneous ice and gas coma of Comet 103P/Hartley 2

The spectacular images of Comet 103P/Hartley 2 recorded by the Medium Resolution Instrument (MRI) and High Resolution Instrument (HRI) on board of the Extrasolar Planet Observation and Deep Impact Extended Investigation (EPOXI) spacecraft, as the Deep Impact extended mission, revealed that its bi-lobed very active nucleus outgasses volatiles heterogeneously. Indeed, CO2 is the primary driver of activity by dragging out chunks of pure ice out of the nucleus from the sub-solar lobe that appear to be the main source of water in Hartley 2's coma by sublimating slowly as they go away from the nucleus. However, water vapor is released by direct sublimation of the nucleus at the waist without any significant amount of either CO2 or icy grains. The coma structure for a comet with such areas of diverse chemistry differs from the usual models where gases are produced in a homogeneous way from the surface. We use the fully kinetic Direct Simulation Monte Carlo model of Tenishev et al. (Tenishev, V.M., Combi, M.R., Davidsson, B. [2008]. Astrophys. J. 685, 659-677; Tenishev, V.M., Combi, M.R., Rubin, M. [2011]. Astrophys. J. 732, 104-120) applied to Comet 103P/Hartley 2 including sublimating icy grains to reproduce the observations made by EPOXI and ground-based measurements. A realistic bi-lobed nucleus with a succession of active areas with different chemistry was included in the model enabling us to study in details the coma of Hartley 2. The different gas production rates from each area were found by fitting the spectra computed using a line-by-line non-LTE radiative transfer model to the HRI observations. The presence of icy grains with long lifetimes, which are pushed anti-sunward by radiation pressure, explains the observed OH asymmetry with enhancement on the night side of the coma.

Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK.

A model of Drosophila circadian rhythm generation was developed to represent feedback loops based on transcriptional regulation of per, Clk (dclock), Pdp-1, and vri (vrille). The model postulates that histone acetylation kinetics make transcriptional activation a nonlinear function of [CLK]. Such a nonlinearity is essential to simulate robust circadian oscillations of transcription in our model and in previous models. Simulations suggest that two positive feedback loops involving Clk are not essential for oscillations, because oscillations of [PER] were preserved when Clk, vri, or Pdp-1 expression was fixed. However, eliminating positive feedback by fixing vri expression altered the oscillation period. Eliminating the negative feedback loop in which PER represses per expression abolished oscillations. Simulations of per or Clk null mutations, of per overexpression, and of vri, Clk, or Pdp-1 heterozygous null mutations altered model behavior in ways similar to experimental data. The model simulated a photic phase-response curve resembling experimental curves, and oscillations entrained to simulated light-dark cycles. Temperature compensation of oscillation period could be simulated if temperature elevation slowed PER nuclear entry or PER phosphorylation. The model makes experimental predictions, some of which could be tested in transgenic Drosophila.

Monte Carlo modeling of polarized light propagation: Stokes vs Jones - Part I

This bipartite comparative study aims at inspecting the similarities and differences between the Jones and Stokes–Mueller formalisms when modeling polarized light propagation with numerical simulations of the Monte Carlo type. In this first part, we review the theoretical concepts that concern light propagation and detection with both pure and partially/totally unpolarized states. The latter case involving fluctuations, or “depolarizing effects,” is of special interest here: Jones and Stokes–Mueller are equally apt to model such effects and are expected to yield identical results. In a second, ensuing paper, empirical evidence is provided by means of numerical experiments, using both formalisms.

CO2, light and temperature influence senescence and protein degradation in wheat leaf segments

Effects of environmental conditions influencing photosynthesis and photorespiration on senescence and net protein degradation were investigated in segments from the first leaf of young wheat (Triticum aestivum L. cv. Arina) plants. The segments were floated on H2O at 25, 30 or 35°C in continuous light (PAR: 50 or 150 µmol m−2 s−1) in ambient air and in CO2-depleted air. Stromal enzymes, including phosphoglycolate phosphatase, glutamine synthetase, ferredoxin-dependent glutamate synthase, phosphoribulokinase, and the peroxisomal enzyme, glycolate oxidase, were detected by SDS-PAGE followed by immunoblotting with specific antibodies. In general, the net degradation of proteins and chlorophylls was delayed in CO2-depleted air. However, little effect of CO2 on protein degradation was observed at 25°C under the lower level of irradiance. The senescence retardation by the removal of CO2 was most pronounced at 30°C and at the higher irradiance. The stromal enzymes declined in a coordinated manner. Immunoreactive fragments from the degraded polypeptides were in most cases not detectable. However, an insolubilized fragment of glycolate oxidase accumulated in vivo, especially at 25°C in the presence of CO2. Detection of this fragment was minimal after incubation at 30°C and completely absent on blots from segments kept at 35°C. In CO2-depleted air, the fragment was only weakly detectable after incubation at 25°C. The results from these investigations indicate that environmental conditions that influence photosynthesis may interfere with senescence and protein catabolism in wheat leaves.

Numerical modeling of marine radiocarbon reservoir ages during the last deglaciation

A critical problem in radiocarbon dating is the spatial and temporal variability of marine reservoir ages (MRAs). We assessed the MRA evolution during the last deglaciation by numerical modeling, applying a self-consistent iteration scheme in which an existing radiocarbon chronology (derived by Hughen et al., Quat. Sci. Rev., 25, pp. 3216-3227, 2006) was readjusted by transient, 3-D simulations of marine and atmospheric Delta14C. To estimate the uncertainties regarding the ocean ventilation during the last deglaciation, we considered various ocean overturning scenarios which are based on different climatic background states (PD: modern climate, GS: LGM climate conditions). Minimum and maximum MRAs are included in file 'MRAminmax_21-14kaBP.nc'. Three further files include MRAs according to equilibrium simulations of the preindustrial ocean (file 'C14age_preindustrial.nc'; this is an update of our results published in 2005) and of the glacial ocean (files 'C14age_spinupLGM_GS.nc' and 'C14age_spinupLGM_PD.nc').