Previous studies suggest a degree of homology between eukaryotic replication, transcription and translation proteins and archaeal ones. Hence, Archaea are considered a simplified model for understanding the complex molecular machinery involved in eukaryotic DNA metabolism. DNA replication in eukaryotic cells is widely studied. In recent years, DNA replication studies expanded on the archaeal DNA replication machinery. P. abyssi was the first archaeon whose genome was fully sequenced. Genome sequencing and comparative genomics have highlighted an MCM-like protein in P. abyssi. In this study, I report the biochemical and structural characterisation of PabMCM. PabMCM is explored as model for understanding more complex eukaryotic MCM proteins and unravelling the biochemical mechanism by which MCM proteins release their helicase activity. The crenarchaeon Sulfolobus solfataricus possesses a simplified toolset for DNA replication compared to Eukaryotes. In particular, S. solfataricus has a subset of the eukaryotic Okazaki fragment maturation factors, among which there are a heterotrimeric DNA sliding clamp, (the proliferating cell nuclear antigen, PCNA), the DNA polymerase B1 (PolB1), the flap endonuclease (Fen1) and the ATP-dependent DNA ligase I (LigI). PCNA functions as a scaffold with each subunit having a specific binding affinity for each of the factors involved in Okazaki fragment maturation. Here, the 3D reconstruction of PCNA in complex with the Okazaki fragment maturation proteins PolB1, LigI and Fen1 is reported.

Le contrôle fin de la structure et de la chimie de surface en milieu confiné a été développé dans des silices poreuses mésostucturées de type MCM-41 pour synthétiser des catalyseurs hétérogènes combinant confinement moléculaire, hydrophobicité et spécificité de sites à l'instar des métalloprotéines. La surface considérée comme lisse a en fait une rugosité de type alvéolaire due à l'empreinte de la tête ammonium du tensioactif de synthèse. Pour des températures croissantes du traitement hydrothermal, la taille des mésopores augmente par érosion de cette rugosité puis diminue par épaississement des parois. On a aussi trouvé des conditions de synthèse de zéolihes mésoporeuses avec une micro- et mésoporosité hiérarchisée. Ces surfaces sont polyfonctionnalisées grâce à la technique de pochoir moléculaire pour isoler des fonctions bidentatés aminoéthylaminopropyles par des groupements hydrophobes triméthylsimyles. Les ions cuivriques sont alors retenus dans le matériau par complexation à ces fonctions diamino.

Confining walls induce qualitative changes in adsorbed fluids. Among the most intriguing phenomena is hysteresis, where a pore fills with fluid at a greater pressure than it empties. The causes and mechanisms by which this occurs are intensely investigated yet still poorly understood. Ordered mesoporous silicas, recently discovered materials with well-defined pore size distributions, provide an opportunity to deepen our understanding of the fundamental physics of the interaction of fluids with complex solids.In part of this computational investigation we examine idealized pores. In agreement with other recent studies, we find that in 'inkbottle'-shaped pores, where a large cavity is accessible to the bulk fluid only by constrictions, there is no evidence of the long-hypothesized phenomenon of `pore blocking', where the constrictions inhibit fluid desorption from the cavity. We find that even in these simple systems the mechanism of hysteresis depends on pore characteristics, fluid properties and external conditions.For silicas containing cylindrical holes of nearly uniform diameter, such as MCM-41, the state-of-the-art is to consider only a single pore, but the poor qualitative agreement of theoretical with experimental results has improved little as wall representations of increasing sophistication have been developed. Using only a one-dimensional potential, we reproduce features of isotherms, including in the hysteresis region, by averaging over a narrow distribution of pore sizes. The qualitative behavior is shown to be a collective phenomenon not representative of any individual pore. Adding surface roughness and a constriction to the pores yields results quantitatively nearly indistinguishable from experiments.For materials larger than MCM-41, a continuum simulation proves too computationally taxing. Thus, a lattice model with adjustable fineness of site spacing is developed. It is found that a surprisingly low level of fineness is needed for confined systems to closely approximate continuum results. This model is applied to cubically symmetric materials, such as MCM-48 and SBA-16, finding that simulations are able to reproduce much of the qualitative behavior seen experimentally, but the lack of existing knowledge of the nature of silica walls proves to be a limiting factor.

QC 20101018

The main issue in this thesis is to minimize the number of operations and the energy consumption per operation for the computation (arithmetic operation) part of DSP circuits, such as Finite Impulse Response Filters (FIR), Discrete Cosine Transform (DCT), and Discrete Fourier Transform (DFT) etc. More specific, the focus is on the elimination of most frequent common sub-expression (CSE) in binary, Canonic Sign Digit (CSD), Twos Complement or Sign Digit representation of the coefficients of non-recursive multiple input multiple output (MIMO)  FIR system , which can be realized using shift-and-add based operations only. The possibilities to reduce the complexity i.e. the chip area, and the energy consumption have been investigated. We have proposed an algorithm which finds the most common sub expression in the binary/CSD/Twos Complement/Sign Digit representation of coefficients of non-recursive MIMO multiplier less FIR systems. We have implemented the algorithm in MATLAB. Also we have proposed different tie-breakers for the selection of most frequent common sub-expression, which will affect the complexity (Area and Power consumption) of the overall system. One choice (tie breaker) is to select the pattern (if there is a tie for the most frequent pattern) which will result in minimum number of delay elements and hence the area of the overall system will be reduced. Another tie-breaker is to choose the pattern which will result in minimum adder depth (the number of cascaded adders). Minimum adder depth will result in least number of glitches which is the main factor for the power consumption in MIMO multiplier less FIR systems. Switching activity will be increased when glitches are propagated to subsequent adders (which occur if adder depth is high). As the power consumption is proportional to the switching activity (glitches) hence we will use the sub-expression which will result in lowest adder depth for the overall system.

A photochemical mechanism is a very important component of an air quality model, which simulates the change of pollutant concentrations due to chemical reactions in the air. The accuracy of model prediction is directly impacted by the photochemical mechanism. In this study, two state-of-the-science photochemical mechanisms, SAPRC07 and Master Chemical Mechanism (MCM) v3.1, were implemented in the Community Multi-scale Air Quality Model (CMAQ) version 4.6 developed by the US EPA to study a high ozone (O3) episode during the 2000 Texas Air Quality Study (TexAQS) from August 16, 2000 to September 7, 2000. Predicted O3 concentrations by S07C are lower than those of S99 with a maximum difference as high as 20 percent. The two mechanisms also show significant differences in the predicted OH, PAN, HCHO and HNO3 concentrations. Although the two mechanisms predict different ozone concentrations, the relative response factors (RRFs) of O3 at rural, urban and industrial sites under emission controls of anthropogenic NOx and VOC by factors 0.6 – 1.4 predicted by the two mechanisms are very similar. Predicted O3 concentrations by MCM are similar to those of SAPRC07. The MCM predicted total VOC OH reactivity is similar to the SAPRC07 predictions at a suburban site where biogenic emissions dominate the OH reactivity and is slightly lower than the SAPRC07 predictions at an industrial site where anthropogenic emissions dominate. Besides, the predicted 1-hr and 24-hr average concentrations of major O3 precursor VOCs by MCM show under predictions of alkanes and alkenes by a factor of 2-5, 6 for ethane and 8.5 for propane. Major aromatic compounds generally agree better with observations, although benzene is under-predicted by 80 percent. Species specific emission adjustment factors can be derived from these direct comparisons to improve emission inventories in future studies. At the Clinton Drive site, most of the under-predictions occur in the afternoon when industrial facilities are in the immediate upwind direction and the missing industrial emissions are likely evaporative sources whose emission rates are temperature dependent.

Fast depletion of oil reserves necessitates the development of novel alternative motor vehicle fuels. Global warming problems also initiated new research to develop new fuels creating less CO2 emission. Nowadays, dimethyl ether (DME) and diethyl ether (DEE) are considered as important alternative clean energy sources. These valuable ethers are produced by the dehydration reaction of methanol and ethanol, respectively, in the presence of acidic catalysts. Besides DEE, ethylene which is very important in petrochemical industry, can also be produced by ethanol dehydration reaction. In the first part of this study, the catalytic activity of tungstophosphoric acid (TPA), silicotungstic acid (STA) and molybdophosphoric acid (MPA), which are well-known heteropolyacids were tested in ethanol dehydration reaction. The activities of other solid acid catalysts, such as Nafion and mesoporous aluminosilicate, were also tested in the dehydration reaction of ethanol. In the case of DME production by dehydration of methanol, activities of STA, TPA and aluminosilicate catalysts were tested. Among the heteropolyacid catalysts, STA showed the highest activity in both ethanol and methanol dehydration reactions. With an increase of temperature from 180oC to 250oC, Ethylene selectivities increased while DEE selectivities decreased. Ethylene yield values over 0.70 were obtained at 250oC. The presence of water in the feed stream caused some reduction in the activity of TPA catalyst. Very high DME yields were obtained using mesoporous aluminosilicate catalyst at about 450oC. The surface area of heteropolyacids are very low and they are soluble in polar solvents such as water and alcohols. Considering these drawbacks of heteropolyacid catalysts, novel mesoporous STA based high surface area catalysts were synthesized following a hydrothermal synthesis route. These novel catalysts were highly stable and they did not dissolve in polar solvents. The catalysts containing W/Si ratios of 0.19 (STA62(550)) and 0.34 (STA82(550)) have BJH surface area values of 481 m2/g and 210 m2/g, respectively, with pore size distributions ranging in between 2-15 nm. These catalysts were characterized by XRD, EDS, SEM, TGA, DTA, DSC, FTIR and Nitrogen Adsorption techniques and their activities were tested in ethanol dehydration reaction. Calcination temperature of the catalysts was shown to be a very important parameter for the activities of these catalysts. Considering the partial decomposition and proton lost of the catalysts over 375oC, they are calcined at 350oC and 550oC before testing them in ethanol dehydration reaction. The catalysts calcined at 350oC showed much higher activity at temperature as low as 180oC. However, the catalysts calcined at 550oC showed activity over 280oC. Ethylene yield values approaching to 0.90 were obtained at about 350oC with catalysts calcined at 350oC. DEE yield past through a maximum with an increase in temperature indicating its decomposition to Ethylene at higher temperatures. However, at lower temperatures (&lt / 300oC) Ethylene and DEE were concluded to be formed through parallel routes. Formation of some acetaldehyde at lower temperatures indicated a possible reaction path through acetaldehyde in the formation of DEE. DRIFTS results also proved the presence of ethoxy, acetate and ethyl like species in addition to adsorbed ethanol molecules on the catalyst surface and gave additional information related to the mechanism.

Plastic materials are widely used throughout the world due to their low prices and easy processing methods. A serious problem of environmental pollution is brought with the widespread use of these materials due to their non-biodegradabilty. For this reason, plastic materials are degraded into lower molecular weight liquid and gaseous products which are potential raw materials and fuels for petrochemical industry. The use of catalysts enhances the formation of more valuable hydrocarbons at lower reaction temperatures and residence times. In this study, aluminum containing MCM-41 and tungstophosphoric acid (TPA) loaded SBA-15 materials were synthesized by impregnation of Al and TPA into hydrothermally synthesized MCM-41 and SBA-15, respectively to be used in catalytic degradation of polyethylene. Al was incorporated into MCM-41 framework with different Al/Si ratios using aluminum triisopropylate as the aluminum source and TPA was incorporated to the porous framework of SBA-15 with different W/Si ratios, using tungstophosphoric acid hydrate as the acid source. From XRD analysis, it was observed that introducing acidic compounds did not cause deformations in the regularity and by EDS analysis, it was found out that at lower loadings, acidic compounds were introduced more effectively for MCM-41 materials. Nitrogen adsorption-desorption isotherms showed that the synthesized materials exhibited type IV isotherms. SEM and TEM pictures showed the hexagonal regularly ordered structure of SBA-15 and MCM-41 materials. FTIR analysis of the pyridine adsorbed synthesized materials revealed the existence of Lewis and Br&oslash / nsted acid sites in the synthesized materials. From TGA analysis it was observed that aluminum impregnated MCM-41 samples reduced the temperature of the degradation reaction significantly and TPA loaded SBA-15 samples reduced activation energy of the reaction effectively. In the degradation reaction system, non-catalytic and catalytic degradation experiments of polyethylene were performed. In non-catalytic degradation and catalytic degradation reactions carried out using aluminum containing MCM-41 materials, selectivity of C3 and C4 hydrocarbon gases was high and in catalytic degradation reactions carried out using TPA impregnated SBA-15 materials, selectivity of ethylene was high. In the liquid analysis of non-catalytic degradation reactions, it was observed that the product distribution was mainly composed of hydrocarbons greater than C18. The use of aluminum loaded MCM-41 and TPA loaded SBA-15 materials resulted in a liquid product distribution in the range of C5-C14, which is the hydrocarbon range of gasoline fuel.

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