The transcription initiation is the first step in gene expression and an important regulation step in all living organisms. In bacteria, it has been proposed that DNA bending and its wrapping on the surface of E. coli RNAP might facilitate the opening of the transcription bubble, which is necessary for the initiation of gene transcription. In this work, it is shown the first structural study to evaluate a DNA wrapping model, including its length and the relative position in the bacterial transcription initiation complex (RP complex), assembled between RNA polymerase-σ70 holoenzyme (RNAP) and a λPR promoter (-100 to +30 wild type). RP complex was prepared and negatively stained with 2% uranyl acetate on a thin-carbon coated grid and the data acquisition of 500 images was performed in a JEM-2100 (JEOL, Japan) microscope equipped with an F-416 CMOS camera (TVIPS, Germany). Single particle analysis of 16,015 particles, grouped in 666 class-averages, was conducted using IMAGIC 4D software (Image Science, Germany) to obtain a three-dimensional model of the RP complex at 20Å resolution. After the rigid-body fitting of the RNAP crystallographic structure (PDB 4YG2) and the modeled DNA promoter, it was observed that the regions 1.2 and 4.2 of the σ70 subunit interacts with the consensus zones, -10 and -35 hexamers of the promoter. Furthermore, it was possible to observe that αCTDs (C-terminal domain) in both alpha subunits would be oriented to facilitate the interaction with the first and second UP-elements regions, respectively (centered around –50 and -75 positions in the promoter). These was enabled by the presence of the characteristics motifs helix-hairpin-helix in these domains. In addition, the downstream DNA, from the transcription bubble, appears to be inside the protein main channel, oriented in a way to enable interactions with the RNAP clamp and jaws. Finally, it was observed that the DNA wrapping has ~32 nm of total length and involves a promoter bent of ~255° around the RNAP surface. The 3D-model obtained in this study is the very first direct structural confirmation of the DNA promoter wrapping in a bacterial transcription initiation complex. / A iniciação da transcrição é o primeiro passo na expressão gênica e importante ponto de regulação em todos os organismos vivos. Em bactérias, foi proposto que o enovelamento do DNA na superfície da RNAP de E. coli pode facilitar a abertura da bolha de transcrição, necessária para o início da transcrição gênica. Neste trabalho, é apresentado o primeiro estudo estrutural direto para avaliar o comprimento do enovelamento do DNA e sua posição no complexo de iniciação da transcrição bacteriana (complexo RP), montado entre a holoenzima RNA polimerase-σ70 (RNAP) e um promotor λPR (-100 para +30, tipo selvagem). Amostras do complexo RP foram preparadas e contrastadas negativamente com 2% de acetato de uranila em uma grade com filme fino de carbono e a aquisição de 500 imagens foi realizada em um microscópio JEM-2100 (Jeol, Japão) equipado com uma câmera CMOS F-416 (TVIPS, Alemanha). A análise de partículas isoladas de 16.015 partículas, agrupadas em 666 médias de classe, foi conduzida usando o software IMAGIC 4D (Image Science, Alemanha) para obter um modelo tridimensional do complexo RP, a 20Å de resolução, estimado pelo critério de ½ bit. Após o ajuste de corpo rígido da estrutura cristalográfica da RNAP (PDB 4YG2) e do promotor de DNA modelado, observou-se que as regiões 1.2 e 4.2 da subunidade σ70 interagem com as zonas de consenso, hexâmeros -10 e -35, do promotor. Além disso, foi possível observar que os αCTDs (domínio C-terminal) em ambas as subunidades alfa estariam orientados para facilitar uma possível interação com a primeira e segundas regiões dos elementos UP, respectivamente (centradas em torno das posições –50 e -75 do promotor). Estas seriam possíveis devido à presença de alguns motivos de características hélice-grampo-hélice nesses domínios. Além disso, a região do promotor, downstream da bolha de transcrição, parece estar dentro do canal principal da proteína, orientado de forma a possibilitar interações com o clamp e jaw da RNAP. Finalmente, foi observado que o comprimento total do enovelamento de DNA envolve cerca de 32 nm e 255° de rotação do DNA ao redor da superfície da RNAP. Portanto, este modelo 3D é a primeira confirmação estrutural direta do enovelamento de DNA em um complexo bacteriano de iniciação da transcrição.

Particle-laden turbulent flow through a straight square duct at Reτ = 300 is studied using direct numerical simulation (DNS) and Lagrangian particle tracking. A parallelized 3-D particle tracking direct numerical simulation code has been developed to perform the large-scale turbulent particle transport computations reported in this thesis. The DNS code is validated after demonstrating good agreement with the published DNS results for the same flow and Reynolds number. Lagrangian particle transport computations are carried out using a large ensemble of passive tracers and finite-inertia particles and the assumption of one-way fluid-particle coupling. Using four different types of initial particle distributions, Lagrangian particle dispersion, concentration and deposition are studied in the turbulent straight square duct. Particles are released in a uniform distribution on a cross-sectional plane at the duct inlet, released as particle pairs in the core region of the duct, distributed randomly in the domain or distributed uniformly in planes at certain heights above the walls. One- and two-particle dispersion statistics are computed and discussed for the low Reynolds number inhomogeneous turbulence present in a straight square duct. New detailed statistics on particle number concentration and deposition are also obtained and discussed.

An Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) was used to obtain mass spectra of individual aerosol particles in the 0.5 – 2 µm size range in downtown Toronto, Canada for one to two month periods during each season of 2007. A modified version of the Adaptive Resonance Theory (ART-2a) clustering algorithm, which clusters particles based on the similarity of their mass spectra, was shown to be more accurate than the existing algorithm and was used to cluster the ambient data. A total of 21 unique particle types were identified and were characterized based on their chemical composition, their size, and their temporal trends and seasonal variations. Potential sources are also discussed. Particles containing trimethylamine (TMA) were also observed and a more detailed investigation of ambient trends in conjunction with a laboratory experiment was performed in order to elucidate conditions for which TMA will be observed in the particle phase in Southern Ontario.

An Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) was used to obtain mass spectra of individual aerosol particles in the 0.5 – 2 µm size range in downtown Toronto, Canada for one to two month periods during each season of 2007. A modified version of the Adaptive Resonance Theory (ART-2a) clustering algorithm, which clusters particles based on the similarity of their mass spectra, was shown to be more accurate than the existing algorithm and was used to cluster the ambient data. A total of 21 unique particle types were identified and were characterized based on their chemical composition, their size, and their temporal trends and seasonal variations. Potential sources are also discussed. Particles containing trimethylamine (TMA) were also observed and a more detailed investigation of ambient trends in conjunction with a laboratory experiment was performed in order to elucidate conditions for which TMA will be observed in the particle phase in Southern Ontario.

The need for effective disposal of huge volumes of industrial waste is becoming more challenging due to expected imposition of stringent pollution control regulations in the near future. Thermochemical conversion, particularly gasification of organics in the waste is considered the best route from the perspective of volume reduction and prevalent eco-friendly concept of waste-to-energy transformation. It is considered imperative to have adequate understanding of basic combustion features as a part of the thermochemical conversion process, leading to gasification. The aim of this thesis is to understand the fundamental combustion processes associated with one of the top listed hazardous wastes from distilleries (Biochemical Oxygen Demand (BOD) ~ 40,000 - 50,000 mg/L), commonly known as vinasse, stillage or spent wash, through experiments and modeling efforts. Specially designed experiments on distillery effluent combustion and gasification are conducted in laboratory scale reactors. As an essential starting point of the studies on ignition and combustion of distillery effluent containing solids consisting of 62 ± 2 % organics and 38 ± 2 % inorganics (primarily sugarcane derivatives), the roles of solids concentration, drop size and ambient temperature were investigated through experiments on (1) liquid droplets of 65 % and 77 % solids (remaining water) and (2) spheres of dried effluent (100 % solids) of size 0.5 mm to 20 mm diameter combusted at ambient temperatures of 773 to 1273 K. The investigation reveals that the droplets burn with two distinct regimes of combustion, flaming and char glowing. The ignition delay ‘t1’ of the droplets increased with size as is in the case of non-volatile droplets, while that of bone-dry spheres was found to be independent of size. The ‘t1’ decreased with increase in solids concentration. The ignition delay has showed an Arrhenius dependence on temperature. The initial ignition of the droplets and the dry spheres led to either homogeneous (flaming) or heterogeneous (flameless) combustion, depending on the ambient temperature in the case of sphere and on solid concentration and the ambient temperature, in the case of liquid droplets. The weight loss during the flaming combustion was found to be 50 - 80 % while during the char glowing it was 10-20 % depending on the ambient temperature. The flaming time tc is observed as tc~ d2c , as in the case of liquid fuel droplets and wood spheres. The char glowing time tc' is observed as tc ~ d2c as in the case of wood char, though the inert content of effluent char is as large as 50 % compared to 2 - 3 % in wood char. In the case of initial flameless combustion, the char combustion rate is observed to be lower. The heterogeneous char combustion in quiescent air in controlled temperature conditions has been studied and modeled using one-dimensional, spherico-symmetric conservation equations and the model predicts most of the features of char combustion satisfactorily. The measured surface and core temperatures during char glowing typically are in the range of 200 to 400 K and are higher than the controlled temperature of the furnace. Based on the results of single droplet combustion studies, combustion experiments were conducted in a laboratory scale vertical reactor (throughput ranging from 4 to 10 g/s) with the primary aim of obtaining sustained combustion. Spray of effluents with 50 % and 60 % solids (calorific value 6.8 - 8.2 MJ/kg), achieved by an air blast atomizer, was injected into a hot oxidizing environment to determine the parameters (ambient temperature and air-fuel ratio) at which auto-ignition could occur and subsequently studies were continued to investigate pre-ignition, ignition and combustion processes. Effluent with lower solids concentration was considered first from the point of view of the less expensive evaporator required in the field conditions for concentration and a spin-off in terms of better atomization consequently. Three classes of experiments were conducted: 1) Effluent injection from the wall with no auxiliary heat input, 2) Effluent injection with auxiliary heat input and 3) effluent injection within kerosene enveloping flame. Though individual particles in the spray periphery were found to combust, sustained spray combustion was not achieved in any of the three sets of experiments even with fine atomization. While conducting the third class of experiments in an inclined metallic reactor, sustained combustion of the pool resulting of accumulated spray seemed to result in large conversion of carbon. This led to the adoption of a new concept for effluent combustion in which the residence time is controlled by varying reactor inclination and the regenerative heat transfer from the product gases supplies heat for endothermic pre-ignition process occurring on the bed. Combustion and gasification experiments were conducted in an inclined plate reactor with rectangular cross section (80 mm x 160 mm) and 3000 mm long. A support flame was found necessary in the injection zone in addition to the regenerative heat transfer. Effluent with 60% solids was injected as film on the reactor bed. This film disintegrated into fine particles due to induced aerodynamic stretching and shear stripping. Combustion of individual particles provided exothermic heat profile and resulted into high carbon conversion. However, effluent clogging in the cold injection zone hindered system from attaining steady state. Effluent injected directly on the hot zone caused it to remain mobile due to the spheroidal evaporation and thus assuaging this problem. Improved mass distribution was achieved by displacing nozzle laterally in a cycle, actuated by a mechanism. Consistent injection led to sustained effluent combustion with resulting carbon conversion in excess of 98 %. The typical gas fractions obtained during gasification condition (air ratio = 0.3) were CO2 = 14.0 %, CO = 7.0 %, H2 = 12.9 %, CH4 - 1 % H2S = 0.6 - 0.8 % and about 2 % of saturated moisture. This composition varied due to variation in temperature (± 30 K) and is attributed to combined effect of local flow variations, shifting zones of endothermic processes due to flowing of evaporating effluent over a large area. In order to minimize this problem, experiments were conducted by injecting effluent at higher solids (73 % solids is found injectable). The effluent was found to combust close to the injection location-due to the reduced ignition delay and lower endothermic evaporation load helped raising the local temperature. This caused the pyrolysis to occur in this hottest zone of the reactor with higher heating rates resulting in larger yield of devolatilized products and improved char conversion. Effluent combustion was found to sustain temperature in the reactor under sub-stoichiometric conditions without support of auxiliary heat input and achieved high carbon conversion. These results inspired the use of higher concentration effluent, which is also known in the case of wood to have improved gasification efficiency due to reduction in moisture fraction. In addition, the recent studies on the sulfur emission in the case of black liquor combustion in recovery boilers have revealed that with increase in solids concentration, release of sulfur in gas phase is reduces. The required concentration can be carried out using low-grade waste heat from the reactor itself. It was found through experiments that, even though spray ignition occurred at this concentration, the confined reactor space prevented the spray from attaining sustained combustion. This led to the conduct of experiments in a new vertical reactor with adequate thermal inertia, essential to prevent variations in local temperature to reach a steady state gasification and required space to accommodate the spray. The results of the experiments conducted in the vertical reactor in which effluents with 73 % solids, heated close to the boiling point and injected as fine spray in a top-down firing mode are consolidated and reported in the thesis in detail. Single particle combustion with enveloping faint flame was seen unlike stable flame found in coal water slurry spray combustion. Sustained gasification of gas-entrained particles occurred at reactor temperature in the range of 950 K - 1000 K and sub-stoichiometric air ratio 03 - 0.35 without the support of auxiliary fuel. The typical gas fractions obtained during gasification condition (air ratio = 0.3) were CO2 = 10.0 -11.5 %, CO - 10.0 - 12.0 %, H2 - 6.7 - 8.0 %, CH4 = 1.75 % H2S = 0.2 - 0.4 % and about 2 % of saturated moisture. The carbon conversion obtained was in the range of 95 - 96 %. These experiments have provided the conditions for gasification. The extraction of potassium salts (mostly sulfates, carbonate and chloride) from the ash, using a simple water leaching process, was found to recover these chemicals to as high an extent as 70 - 75 % of total ash. In summary it is concluded that increasing the solid concentrations to as high levels as acceptable to the system (~ 75 %) and introducing as a fine spray of heated material (~ 363 K) into furnace with air at sub-stoichiometric conditions in a counter current combustion reactor will provide the frame work for the design of a gasification system for vinasse and similar effluent material. The thesis consists of seven chapters. Chapter 1 introduces the problem and motivation of the work presented in the thesis. Literature review is presented in Chapter 2. The Chapter 3 deals with the single particle combustion studies. The results of effluent spray combustion experiments conducted in a laboratory scale vertical reactor are presented in Chapter 4. The results of combustion and gasification experiments conducted in another variant of a reactor, namely, inclined flat plate rectangular reactor is consolidated in Chapter 5. The results of gas-entrained spray gasification experiment of higher concentration effluent injected as spray in the vertical reactor are presented in Chapter 6. The general conclusions and scope for the future work are presented in the concluding chapter 7.

Nanometer-scale particles of the noble metals have been used for decades as contrast enhancement agents in electron microscopy. Over the past several years it has been demonstrated that these particles also function as excellent contrast agents for optical imaging techniques. The resonant optical scattering they exhibit enables scattering cross sections that may be many orders of magnitude greater than the analogous efficiency factor for fluorescent dye molecules. Biologically relevant labeling with nanoparticles generally results in aggregates containing a few to several tens of particles. The electrodynamic coupling between particles in these aggregates produces observable shifts in the resonance-scattering spectrum. This dissertation provides a theoretical analysis of the scattering from nanoparticle aggregates. The key objectives are to describe this scattering behavior qualitatively and to provide numerical codes usable for modeling its application to biomedical engineering. Considerations of the lowest-order dipole-dipole coupling lead to simple qualitative predictions of the behavior of the spectral properties of the optical cross sections as they depend on number of particles, inter-particle spacing, and aggregate aspect ratio. More comprehensive analysis using the multiple-particle T-matrix formalism allows the elaboration of more subtle cross-section spectral features depending on the interactions of the electrodynamic collective-modes of the aggregate, of individual-particle modes, and of modes associated with groups of particles within the aggregate sub-structure. In combination these analyses and the supporting numerical code-base provide a unified electrodynamic approach which facilitates interpretation of experimental cross section spectra, guides the design of new biophysical experiments using nanoparticle aggregates, and enables optimal fabrication of nanoparticle structures for biophysical applications. / text

Particle-laden turbulent flow through a straight square duct at Reτ = 300 is studied using direct numerical simulation (DNS) and Lagrangian particle tracking. A parallelized 3-D particle tracking direct numerical simulation code has been developed to perform the large-scale turbulent particle transport computations reported in this thesis. The DNS code is validated after demonstrating good agreement with the published DNS results for the same flow and Reynolds number. Lagrangian particle transport computations are carried out using a large ensemble of passive tracers and finite-inertia particles and the assumption of one-way fluid-particle coupling. Using four different types of initial particle distributions, Lagrangian particle dispersion, concentration and deposition are studied in the turbulent straight square duct. Particles are released in a uniform distribution on a cross-sectional plane at the duct inlet, released as particle pairs in the core region of the duct, distributed randomly in the domain or distributed uniformly in planes at certain heights above the walls. One- and two-particle dispersion statistics are computed and discussed for the low Reynolds number inhomogeneous turbulence present in a straight square duct. New detailed statistics on particle number concentration and deposition are also obtained and discussed.

No description available.

Single-particle tracking (SPT) is a method used to study the diffusion of various molecules within the cell. SPT involves tagging proteins with optical labels and observing their individual two-dimensional trajectories with a microscope. The analysis of this data provides important information about protein movement and mechanism, and is used to create multistate biological models. One of the challenges in SPT analysis is the variety of complex environments that contribute to heterogeneity within movement paths. In this thesis, we explore the limitations of current methods used to analyze molecular movement, and adapt analytical methods used in animal movement analysis, such as correlated random walks and first-passage time variance, to SPT data of leukocyte function-associated antigen-1 (LFA-1) integral membrane proteins. We discuss the consequences of these methods in understanding different types of heterogeneity in protein movement behaviour, and provide support to results from current experimental work. / Applied Mathematics

This thesis investigates novel algorithms for enabling the use of first-principle electrochemical models for battery monitoring and control in advanced battery management systems (BMSs). Specifically, the fast solution and state estimation of a high-fidelity spatially resolved thermal-electrochemical lithium-ion battery model commonly referred to as the pseudo two-dimensional (P2D) model are investigated. The partial-differential algebraic equations (PDAEs) constituting the model are spatially discretised using Chebyshev orthogonal collocation enabling fast and accurate simulations up to high C-rates. This implementation of the P2D model is then used in combination with an extended Kalman filter (EKF) algorithm modified for differential-algebraic equations (DAEs) to estimate the states of the model, e.g. lithium concentrations, overpotential. The state estimation algorithm is able to rapidly recover the model states from current, voltage and temperature measurements. Results show that the error on the state estimate falls below 1% in less than 200s despite a 30% error on battery initial state-of-charge (SoC) and additive measurement noise with 10mV and 0.5°C standard deviations. The parameter accuracy of such first-principle models is of utmost importance for the trustworthy estimation of internal battery electrochemical states. Therefore, the identifiability of the simpler single particle (SP) electrochemical model is investigated both in principle and in practice. Grouping parameters and partially non-dimensionalising the SP model equations in order to understand the maximum expected degrees of freedom in the problem reveals that there are only six unique parameters in the SP model. The structural identifiability is then examined by asking whether the transfer function of the linearised SP model is unique. It is found that the model is unique provided that the electrode open circuit voltage curves have a non-zero gradient, the parameters are ordered, and that the behaviour of the kinetics of each electrode is lumped together into a single parameter which is the charge transfer resistance. The practical estimation of the SP model parameters from frequency-domain experimental data obtained by electrochemical impedance spectroscopy (EIS) is then investigated and shows that estimation at a single SoC is insufficient to obtain satisfactory results and EIS data at multiple SoCs must be combined.