Broadband coaxial cavity resonator for complex permittivity measurements of liquids

A novel cavity perturbation technique using coaxial cavity resonators for the measurement of complex permittivity of liquids is presented. The method employs two types of resonators (Resonator I and Resonator II). Resonator I operates in the frequency range 600 MHz-7 GHz and resonator II operates in the frequency range 4 GHz-14 GHz. The introduction of the capillary tube filled with the sample liquid into the coaxial resonator causes shifts in the resonance frequency and loaded Q-factor of the resonator. The shifts in the resonance frequency and loaded Q-factor are used to determine the real and imaginary parts of the complex permittivity of the sample liquid, respectively. Using this technique, the dielectric parameters of water and nitrobenzene are measured. The results are compared with those obtained using other standard methods. The sources of errors are analyzed.

A Multi-Objective Antenna Placement Genetic Algorithm for Matched Array Synthesis on Complex Platforms

A Multi-Objective Antenna Placement Genetic Algorithm (MO-APGA) has been proposed for the synthesis of matched antenna arrays on complex platforms. The total number of antennas required, their position on the platform, location of loads, loading circuit parameters, decoupling and matching network topology, matching network parameters and feed network parameters are optimized simultaneously. The optimization goal was to provide a given minimum gain, specific gain discrimination between the main and back lobes and broadband performance. This algorithm is developed based on the non-dominated sorting genetic algorithm (NSGA-II) and Minimum Spanning Tree (MST) technique for producing diverse solutions when the number of objectives is increased beyond two. The proposed method is validated through the design of a wideband airborne SAR

Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

Optical Characterization of Organic Gain Materials for UV-emitting Hybrid Complex Coupled VCSELs

In this thesis, optical gain measurement setup based on variable stripe length method is designed, implemented and improved. The setup is characterized using inorganic and organic samples. The optical gain of spiro-quaterphenyl is calculated and compared with measurements from the setup. Films with various thicknesses of spiro-quaterphenyl, methoxy-spiro-quaterphenyl and phenoxy-spiro-quaterphenyl are deposited by a vacuum vapor deposition technique forming asymmetric slab waveguides. The optical properties, laser emission threshold, optical gain and loss coefficient for these films are measured. Additionally, the photodegradation during pumping process is investigated.

Plasma polymerization of C[subscript 4]F[subscript 8] thin film on high aspect ratio silicon molds

High aspect ratio polymeric micro-patterns are ubiquitous in many fields ranging from sensors, actuators, optics, fluidics and medical. Second generation PDMS molds are replicated against first generation silicon molds created by deep reactive ion etching. In order to ensure successful demolding, the silicon molds are coated with a thin layer of C[subscript 4]F[subscript 8] plasma polymer to reduce the adhesion force. Peel force and demolding status are used to determine if delamination is successful. Response surface method is employed to provide insights on how changes in coil power, passivating time and gas flow conditions affect plasma polymerization of C[subscript 4]F[subscript 8].

A Monte Carlo method for accelerating the computation of animated radiosity sequences

Realistic rendering animation is known to be an expensive processing task when physically-based global illumination methods are used in order to improve illumination details. This paper presents an acceleration technique to compute animations in radiosity environments. The technique is based on an interpolated approach that exploits temporal coherence in radiosity. A fast global Monte Carlo pre-processing step is introduced to the whole computation of the animated sequence to select important frames. These are fully computed and used as a base for the interpolation of all the sequence. The approach is completely view-independent. Once the illumination is computed, it can be visualized by any animated camera. Results present significant high speed-ups showing that the technique could be an interesting alternative to deterministic methods for computing non-interactive radiosity animations for moderately complex scenarios

A functional proteomic method for the enrichment of peripheral membrane proteins reveals the collagen binding protein Hsp47 is exposed on the surface of activated human platelets

Platelets are small blood cells vital for hemostasis. Following vascular damage, platelets adhere to collagens and activate, forming a thrombus that plugs the wound and prevents blood loss. Stimulation of the platelet collagen receptor glycoprotein VI (GPVI) allows recruitment of proteins to receptor-proximal signaling complexes on the inner-leaflet of the plasma membrane. These proteins are often present at low concentrations; therefore, signaling-complex characterization using mass spectrometry is limited due to high sample complexity. We describe a method that facilitates detection of signaling proteins concentrated on membranes. Peripheral membrane proteins (reversibly associated with membranes) were eluted from human platelets with alkaline sodium carbonate. Liquid-phase isoelectric focusing and gel electrophoresis were used to identify proteins that changed in levels on membranes from GPVI-stimulated platelets. Immunoblot analysis verified protein recruitment to platelet membranes and subsequent protein phosphorylation was preserved. Hsp47, a collagen binding protein, was among the proteins identified and found to be exposed on the surface of GPVI-activated platelets. Inhibition of Hsp47 abolished platelet aggregation in response to collagen, while only partially reducing aggregation in response to other platelet agonists. We propose that Hsp47 may therefore play a role in hemostasis and thrombosis.

Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments

Establishing the mechanisms by which microbes interact with their environment, including eukaryotic hosts, is a major challenge that is essential for the economic utilisation of microbes and their products. Techniques for determining global gene expression profiles of microbes, such as microarray analyses, are often hampered by methodological restraints, particularly the recovery of bacterial transcripts (RNA) from complex mixtures and rapid degradation of RNA. A pioneering technology that avoids this problem is In Vivo Expression Technology (IVET). IVET is a 'promoter-trapping' methodology that can be used to capture nearly all bacterial promoters (genes) upregulated during a microbe-environment interaction. IVET is especially useful because there is virtually no limit to the type of environment used (examples to date include soil, oomycete, a host plant or animal) to select for active microbial promoters. Furthermore, IVET provides a powerful method to identify genes that are often overlooked during genomic annotation, and has proven to be a flexible technology that can provide even more information than identification of gene expression profiles. A derivative of IVET, termed resolvase-IVET (RIVET), can be used to provide spatio-temporal information about environment-specific gene expression. More recently, niche-specific genes captured during an IVET screen have been exploited to identify the regulatory mechanisms controlling their expression. Overall, IVET and its various spin-offs have proven to be a valuable and robust set of tools for analysing microbial gene expression in complex environments and providing new targets for biotechnological development.

Nucleic acid recovery from complex environmental samples

Effective extraction of nucleic acid from environmental samples is an essential starting point in the molecular analysis of microbial communities in the environment. However, there are many different extraction methods in the literature and deciding which one is best suited to a particular sample is very difficult. This article details the important steps and choices in deciding how to extract nucleic acids from environmental samples and gives specific details of one method that has proven very successful at extracting DNA and RNA from a range of different samples.

Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm. to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker. demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.

A novel Bayesian approach to drug design with simple and complex enzymes: Use with lens aldehyde dehydrogenase and the glyoxalase pathway

Purpose: Acquiring details of kinetic parameters of enzymes is crucial to biochemical understanding, drug development, and clinical diagnosis in ocular diseases. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. Methods: We have developed Bayesian utility functions to minimise kinetic parameter variance involving differentiation of model expressions and matrix inversion. These have been applied to the simple kinetics of the enzymes in the glyoxalase pathway (of importance in posttranslational modification of proteins in cataract), and the complex kinetics of lens aldehyde dehydrogenase (also of relevance to cataract). Results: Our successful application of Bayesian statistics has allowed us to identify a set of rules for designing optimum kinetic experiments iteratively. Most importantly, the distribution of points in the range is critical; it is not simply a matter of even or multiple increases. At least 60 % must be below the KM (or plural if more than one dissociation constant) and 40% above. This choice halves the variance found using a simple even spread across the range.With both the glyoxalase system and lens aldehyde dehydrogenase we have significantly improved the variance of kinetic parameter estimation while reducing the number and costs of experiments. Conclusions: We have developed an optimal and iterative method for selecting features of design such as substrate range, number of measurements and choice of intermediate points. Our novel approach minimises parameter error and costs, and maximises experimental efficiency. It is applicable to many areas of ocular drug design, including receptor-ligand binding and immunoglobulin binding, and should be an important tool in ocular drug discovery.

Intermediate ion stability and regio selectivity polymerization using neutral salicyladiminato in propene nickel(II) and palladium(II) complexes as catalysts

The mechanism of the Heck reaction has been studied with regard to transition metal catalysis of the addition of propene and the formation of unsaturated polymers. The reactivity of nickel and palladium complexes with five different bidentate ligands with O,N donor atoms has been investigated by computational methods involving density functional theory. Hence, it is possible to understand the electronic and steric factors affecting the reaction and their relative importance in determining the products formed in regard of their control of the regiochemistry of the products. Our results show that whether the initial addition of propene is trans to O or to N of the bidentate ligand is of crucial importance to the subsequent reactions. Thus when the propene is trans to 0, 1,2-insertion is favoured, but when the propene is trans to N, then 2,1-insertion is favoured. This difference in the preferred insertion pathway can be related to the charge distribution engendered in the propene moiety when the complex is formed. Indeed charge effects are important for catalytic activity but also for regioselectivity. Steric effects are shown to be of lesser importance even when t-butyl is introduced into the bidentate ligand as a substituent. (C) 2007 Elsevier B.V. All rights reserved.

Design and theoretical study of nickel catalysts for syndiotactic polyolefins

A nickel catalyst was modeled with ligand L-2, [ NH = CH-CH = CH-O](-), which should have potential use as a syndiotactic polyolefin catalyst, and the reaction mechanism was studied by theoretical calculations using the density functional method at the B3LYP/ LANL2MB level. The mechanism involves the formation of the intermediate [(NiLMe)-Me-2](+), in which the metal occuples a T-shaped geometry. - This intermediate has two possible structures with the methyl group trans either to the oxygen or to the nitrogen atom of L-2. The results show that both structures can lead to the desired product via similar reaction paths, A and B. Thus, the polymerization could be considered as taking place either with the alkyl group occupying the position trans to the Ni-O or trans to the Ni-N bond in the catalyst. The polymerization process thus favors the catalysis of syndiotactic polyolefins. The syndiotactic synthesis effects could also be enhanced by variations in the ligand substituents. From energy considerations, we can conclude that it is more favorable for the methyl group to occupy the trans-O position to form a complex than to occupy the trans-N position. From bond length considerations, it is also more favoured for ethene to occupy the trans-O position than to occupy the trans-N position.

Rapid, uncatalyzed ring-opening polymerization of individual macrocyclic poly(arylene thioether ketone)s under dynamic heating conditions

Uncatalyzed, ring-opening polymerization of individual macrocyclic poly(arylene thioether ketone)s (1-4) and mixtures (5) under dynamic heating conditions has been demonstrated for the first time. High-molecular-weight, film-forming products were obtained after heating of the macrocycles up to 480 degreesC, with a heating rate of 10-20 degreesC /min. Depending on the macrocyclic structure and heat treatment conditions, the polymers obtained were amorphous or semicrystalline, soluble or slightly crosslinked. NMR analyses of the soluble polymers revealed their linear, highly regular structure. According to NMR, DSC, and TGA studies, the polymers obtained do not contain any residual macrocycles. The polymers with thio-p-arylene moieties in the main chain were thermally stabile. The catalyzed ring opening polymerization of 5 carried out in diphenyl sulfone solution is also reported for comparison. Using quantum mechanical calculations of the ring opening of macrocycles, a reaction mechanism is suggested. Preparation of nanosized poly(thioether ketone) fibrils by a replication method is described.

Mapping fibre orientation in complex-shaped biological systems with micrometre resolution by scanning X-ray microdiffraction

A fully automated procedure to extract and to image local fibre orientation in biological tissues from scanning X-ray diffraction is presented. The preferred chitin fibre orientation in the flow sensing system of crickets is determined with high spatial resolution by applying synchrotron radiation based X-ray microbeam diffraction in conjunction with advanced sample sectioning using a UV micro-laser. The data analysis is based on an automated detection of azimuthal diffraction maxima after 2D convolution filtering (smoothing) of the 2D diffraction patterns. Under the assumption of crystallographic fibre symmetry around the morphological fibre axis, the evaluation method allows mapping the three-dimensional orientation of the fibre axes in space. The resulting two-dimensional maps of the local fibre orientations - together with the complex shape of the flow sensing system - may be useful for a better understanding of the mechanical optimization of such tissues.