NMR Spectroscopic Properties of Nucleotides, and a New Method of Numeric Calculation of Raman Intensities for Organic Molecules

General and accurate computational methodologies are currently lacking for large chemical systems. This is primarily due to the computational expense required to perform calculations on systems with one hundred or more atoms. Calculated spectroscopic properties could aid in the process of elucidating structural features of large biologically relevant molecules if accurate and inexpensive methods are developed. Towards this end the first steps were taken to design a general methodology for predicting NMR chemical shifts of large nucleic acid systems. It was found that HF and semi-empirical methods were not sufficient for optimization of nucleobases, and therefore larger nucleotide or nucleic acid systems. It was also found that there is little difference in performance between DFT methods for prediction of NMR shifts of nucleobases as long as hydrogen bonding requirements are satisfied. To potentially reduce the computational expense of calculating Raman activities, a new and potentially inexpensive numerical method was developed. This method utilizes volume changes as a basis for approximating polarizability changes over the course of molecular vibrations. Raman intensities calculated using this methodology were compared to experimentally obtained Raman intensities by linear regression. While a positive correlation was found further refinement is needed

Fault propagation, detection and analysis in process systems

Process systems are often complicated and liable to experience faults and their effects. Faults can adversely affect the safety of the plant, its environmental impact and economic operation. As such, fault diagnosis in process systems is an active area of research and development in both academia and industry. The work reported in this thesis contributes to fault diagnosis by exploring the modelling and analysis of fault propagation and detection in process systems. This is done by posing and answering three research questions. What are the necessary ingredients of a fault diagnosis model? What information should a fault diagnosis model yield? Finally, what types of model are appropriate to fault diagnosis? To answer these questions , the assumption of the research is that the behaviour of a process system arises from the causal structure of the process system. On this basis, the research presented in this thesis develops a two-level approach to fault diagnosis based on detailed process information, and modelling and analysis techniques for representing causality. In the first instance, a qualitative approach is developed called a level 1 fusion. The level 1 fusion models the detailed causality of the system using digraphs. The level 1 fusion is a causal map of the process. Such causal maps can be searched to discover and analyse fault propagation paths through the process. By directly building on the level 1 fusion, a quantitative level 2 fusion is developed which uses a type of digraph called a Bayesian network. By associating process variables with fault variables, and using conditional probability theory, it is shown how measured effects can be used to calculate and rank the probability of candidate causes. The novel contributions are the development of a systematic approach to fault diagnosis based on modelling the chemistry, physics, and architecture of the process. It is also shown how the control and instrumentation system constrains the casualty of the process. By demonstrating how digraph models can be reversed, it is shown how both cause-to-effect and effect-to-cause analysis can be carried out. In answering the three research questions, this research shows that it is feasible to gain detailed insights into fault propagation by qualitatively modelling the physical causality of the process system. It is also shown that a qualitative fault diagnosis model can be used as the basis for a quantitative fault diagnosis modelOpen Acces

Comment on ``Neutrino oscillations in the early universe: how can large lepton asymmetry be generated?"

We comment on the recent paper by A. D. Dolgov, S. H. Hansen, S. Pastor and D. V. Semikoz (DHPS) [Astropart. Phys. {\bf 14}, 79 (2000)] on the generation of neutrino asymmetries from active-sterile neutrino oscillations. We demonstrate that the approximate asymmetry evolution equation obtained therein is an expansion, up to a minor discrepancy, of the well-established static approximation equation, valid only when the supposedly new higher order correction term is small. In the regime where this so-called ``back-reaction'' term is large and artificially terminates the asymmetry growth, their evolution equation ceases to be a faithful approximation to the Quantum Kinetic Equations (QKEs) simply because pure Mikheyev-Smirnov-Wolfenstein (MSW) transitions have been neglected. At low temperatures the MSW effect is the dominant asymmetry amplifier. Neither the static nor the DHPS approach contains this important physics. Therefore we conclude that the DHPS results have sufficient veracity at the onset of explosive asymmetry generation, but are invalid in the ensuing low temperature epoch where MSW conversions are able to enhance the asymmetry to values of order $0.2 - 0.37$. DHPS do claim to find a significant final asymmetry for very large $\delta m^2$ values. However, for this regime the effective potential they employed is not valid.Comment: RevTeX, 32 pages, including 4 embedded figures; this version to appear in Astropart.Phy

Thermal behavior and decomposition kinetics of rifampicin polymorphs under isothermal and non-isothermal conditions

The thermal behavior of two polymorphic forms of rifampicin was studied by DSC and TG/DTG. The thermoanalytical results clearly showed the differences between the two crystalline forms. Polymorph I was the most thermally stable form, the DSC curve showed no fusion for this species and the thermal decomposition process occurred around 245 ºC. The DSC curve of polymorph II showed two consecutive events, an endothermic event (Tpeak = 193.9 ºC) and one exothermic event (Tpeak = 209.4 ºC), due to a melting process followed by recrystallization, which was attributed to the conversion of form II to form I. Isothermal and non-isothermal thermogravimetric methods were used to determine the kinetic parameters of the thermal decomposition process. For non-isothermal experiments, the activation energy (Ea) was derived from the plot of Log β vs 1/T, yielding values for polymorph form I and II of 154 and 123 kJ mol-1, respectively. In the isothermal experiments, the Ea was obtained from the plot of lnt vs 1/T at a constant conversion level. The mean values found for form I and form II were 137 and 144 kJ mol-1, respectively.O comportamento térmico de duas formas polimórficas da rifampicina foi estudado por DSC e TG/DTG. Os resultados termoanalíticos mostraram claramente as diferenças entre as duas formas cristalinas. O polimorfo I é a forma mais estável termicamente, a curva DSC não mostrou a fusão dessa espécie e o processo de decomposição térmica ocorreu próximo a 245 ºC. A curva DSC do Polimorfo II apresentou dois eventos consecutivos, um endotérmico (Tpico = 193,9 ºC) e outro exotérmico (Tpico = 209,4 ºC), devido à fusão seguida de recristalização, a qual foi atribuída à conversão da forma II à forma I. Métodos termogravimétricos isotérmicos e não-isotérmicos foram empregados para determinar os parâmetros cinéticos do processo de decomposição térmica. Para experimentos não-isotérmicos, a energia de ativação (Ea) foi obtida a partir do gráfico de Log β vs 1/T, e os valores 154 e 123 kJ mol-1 foram encontrados, respectivamente, para os polimorfos I e II. Para os experimentos isotérmicos, a Ea foi obtida a partir do gráfico de lnt vs. 1/T a um nível de conversão constante. O valor médio encontrado foi 137 e 144 kJ mol-1, respectivamente, para a forma I e forma II.CNPqCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)FAPES

Surfactant-induced relative permeability modifications for oil recovery enhancement

Surfactants have been considered for enhanced oil recovery by reduced oil-water interfacial tension. However, these surfactants may enhance oil recovery via wettability alteration as well. This study experimentally determines the influence of surfactant type and concentration on oil recovery, oil-water relative permeabilities and wettability in reservoir rocks. Several coreflood experiments were conducted using Yates reservoir fluids in Berea rocks and two types of surfactants (nonionic and anionic) in varying concentrations. A coreflood simulator was used to calculate oil-water relative permeabilities by history matching recovery and pressure drop measured during the corefloods. These relative permeability variations were interpreted using Craig\u27s rules-of-thumb to characterize wettability alterations induced by the surfactants. The two main mechanisms behind the use of surfactants to enhance oil recovery are (1) reduction in interfacial tension and (2) alteration of wettability. To discern the relative contributions from these two mechanisms on enhanced oil recovery, two series of coreflood experiments have been conducted using a nonionic surfactant in varying concentrations. The first series used decane as the oil phase to quantify the effect of reduction in interfacial tension on oil recovery, while considering wettability effects in the decane-brine-Berea system to be negligible. The second series used Yates crude oil in place of decane to quantify the effects of reduction in interfacial tension as well as wettability alteration on enhanced oil recovery. The same two sets of experiments are then repeated with the anionic surfactant. The comparison of results of these four sets of experiments showed significantly higher oil recoveries for second series of experiments, indicating that the surfactants have altered wettability. The optimum surfactant concentration was found to be 3500 ppm. In three of the four cases studied, oil/water emulsions caused high pressure drops during the flooding experiments, strongly affecting the relative permeability curves. Craig\u27s rules-of-thumb may not be applicable in systems containing emulsions. This study suggests that the development of a mixed-wettability state yields significantly higher oil recoveries observed in Yates crude oil systems. The significant contributions of this study are the quantification of the wettability altering capability of surfactants and the consequent enhancement of oil recovery

The Role of Inversion in the Genesis, Development and the Structure of Scientific Knowledge

The main thrust of the argument of this thesis is to show the possibility of articulating a method of construction or of synthesis--as against the most common method of analysis or division--which has always been (so we shall argue) a necessary component of scientific theorization. This method will be shown to be based on a fundamental synthetic logical relation of thought, that we shall call inversion--to be understood as a species of logical opposition, and as one of the basic monadic logical operators. Thus the major objective of this thesis is to This thesis can be viewed as a response to Larry Laudan's challenge, which is based on the claim that ``the case has yet to be made that the rules governing the techniques whereby theories are invented (if any such rules there be) are the sorts of things that philosophers should claim any interest in or competence at.'' The challenge itself would be to show that the logic of discovery (if at all formulatable) performs the epistemological role of the justification of scientific theories. We propose to meet this challenge head on: a) by suggesting precisely how such a logic would be formulated; b) by demonstrating its epistemological relevance (in the context of justification) and c) by showing that a) and b) can be carried out without sacrificing the fallibilist view of scientific knowledge. OBJECTIVES: We have set three successive objectives: one general, one specific, and one sub-specific, each one related to the other in that very order. (A) The general objective is to indicate the clear possibility of renovating the traditional analytico-synthetic epistemology. By realizing this objective, we attempt to widen the scope of scientific reason or rationality, which for some time now has perniciously been dominated by pure analytic reason alone. In order to achieve this end we need to show specifically that there exists the possibility of articulating a synthetic (constructive) logic/reason, which has been considered by most mainstream thinkers either as not articulatable, or simply non-existent. (B) The second (specific) task is to respond to the challenge of Larry Laudan by demonstrating the possibility of an epistemologically significant generativism. In this context we will argue that this generativism, which is our suggested alternative, and the simplified structuralist and semantic view of scientific theories, mutually reinforce each other to form a single coherent foundation for the renovated analytico-synthetic methodological framework. (C) The third (sub-specific) objective, accordingly, is to show the possibility of articulating a synthetic logic that could guide us in understanding the process of theorization. This is realized by proposing the foundations for developing a logic of inversion, which represents the pattern of synthetic reason in the process of constructing scientific definitions

Photocatalytic Degradation of Hazardous Safranin (O) Dye by Using Self Synthesized TIO2 Nanoparticles

The textile industries generates extremely high amount of colour waste water, which are mainly poisons. A traditional biological treatment process is not helpful in treating the dye effluent because of low biodegradability of dyes. The presence of safranin (O) dye causes distinct acute impact on health therefore the removal of this dye from aqueous solution is highly desirable. The aim of this study was to assess the efficiency of photo-degradation of safanin (O) dye with application of nanoparticles of TiO2 as a photocatalyst. For this purpose nanoparticles of TiO2 were synthesized by a very simple sol-gel method with absence of additives and hydrolysing agents. The synthesized nanoparticles of TiO2 were characterized by FTIR, XRD, SEM, BET and UV-vis spectroscopy. It was found that change in polymorphic phase occurs as temperature changes from 600 to 800 0C and also the crystallinity of TiO2 increases with annealing temperature. The application of prepared TiO2 nanoparticles for photocatalytic degradation of safranin (O) dye from aqueous solution was explored. It was determined that anatase phase TiO2 shown highest photo-degradability of safranin (O) dye. The blank tests investigated for light irradiated to safranin (O) dye solution without TiO2 catalyst and for the suspension carrying TiO2 and safranin (O) dye in the dark that revealed both the photocatalyst and light energy were required for the photo-degradation of safranin (O) dye. The effect of several factors such as catalyst dose, initial concentration, pH of solution and temperature, was studied on the photocatalytic degradation of safranin (O) dye and optimized it. Results indicated that photo-degradation of safranin (O) dye increases at higher alkaline pH. The photo-degradation rate was strongly influenced by activation of TiO2 photocatalyst with photon and production of hydroxyl radicals’ hence suggested optimum catalyst dose and initial concentration of dye for photo-degradation process

Structure Determination of Derivatized Disaccharides by Tandem Mass Spectrometry and Molecular Modeling.

This research entails the synthesis of derivatized disaccharides, mass spectrometry studies for structural elucidation of the synthetic disaccharides and molecular modeling of the native and derivatized disaccharides. Peralkylated (methyl to pentyl), peresterifed and tert-butyl-dimethyl silylated linkage isomeric glucose-glucose disaccharides were synthesized to eventually be used in mass spectrometry studies. In this dissertation, mass spectrometry was used to examine anomeric pair discrimination of two sets of peralkylated (methyl to pentyl) disaccharides (maltose/cellobiose and isomaltose/gentiobiose). This was carried out by electrospray ionization and collision experiments on a triple quadrupole mass spectrometer. In addition, effects of alkyl substitution on cleavage of the glycosidic bond were observed. Collision energy offset voltages were plotted versus Product/Parent (D/P) ion ratios generating a trend observed for both the 1→4 and 1→6 alpha and beta isomers. The methyl derivative had the lowest D/P ion ratio followed by ethyl, propyl, butyl, and pentyl. Collision energy is converted to rotational-vibrational modes in competition with bond cleavage represented by the slope of offset energy versus D/P ion ratio. Rotational freedom at the glycosidic linkage is hypothesized to play a major role in this phenomenon. Molecular modeling was carried out using MM3 to validate differences observed in the rates of cleavage in the mass spectrometer. A flexible residue calculation was used involving rotation of the monomeric residues around the glycosidic bond having torsion angles &phis; and psi. Three dimensional energy plots of &phis;,psi and energy were plotted with the volumes of the wells taken as an indication of the conformational freedom of motion around the glycosidic bond. Two dimensional &phis;-psi energy surfaces of both the 1→1, 1→2, 1→3, and 1→4 native and permethylated disaccharides were also plotted to study their characteristics. The calculated freedom of motion volumes for the beta-(1→4) were smaller than for the alpha-(1→4) bonded glucoses, which may account for the higher rate of bond cleavage for the beta-(1→4) linkage. Additionally an interesting outcome was noted from the difference maps between the permethylated and native disaccharides, which were plotted to study the effect of the methyl groups on the energy surfaces