On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (DeltaCp), enthalpy (DeltaH) and entropy (DeltaS) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (DeltaCp) and enthalpy (DeltaH) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

Absolute/Convective Instability Transition in a Backward Facing Step Combustor: Fundamental Mechanism and Influence of Density Gradient

Hydrodynamic instabilities of the flow field in lean premixed gas turbine combustors can generate velocity perturbations that wrinkle and distort the flame sheet over length scales that are smaller than the flame length. The resultant heat release oscillations can then potentially result in combustion instability. Thus, it is essential to understand the hydrodynamic instability characteristics of the combustor flow field in order to understand its overall influence on combustion instability characteristics. To this end, this paper elucidates the role of fluctuating vorticity production from a linear hydrodynamic stability analysis as the key mechanism promoting absolute/convective instability transitions in shear layers occurring in the flow behind a backward facing step. These results are obtained within the framework of an inviscid, incompressible, local temporal and spatio-temporal stability analysis. Vorticity fluctuations in this limit result from interaction between two competing mechanisms-(1) production from interaction between velocity perturbations and the base flow vorticity gradient and (2) baroclinic torque in the presence of base flow density gradients. This interaction has a significant effect on hydrodynamic instability characteristics when the base flow density and velocity gradients are colocated. Regions in the space of parameters characterizing the base flow velocity profile, i.e., shear layer thickness and ratio of forward to reverse flow velocity, corresponding to convective and absolute instability are identified. The implications of the present results on understanding prior experimental studies of combustion instability in backward facing step combustors and hydrodynamic instability in other flows such as heated jets and bluff body stabilized flames is discussed.

ABSOLUTE/CONVECTIVE INSTABILITY TRANSITION IN A BACKWARD FACING STEP COMBUSTOR: FUNDAMENTAL MECHANISM AND INFLUENCE OF DENSITY GRADIENT

Hydrodynamic instabilities of the flow field in lean premixed gas turbine combustors can generate velocity perturbations that wrinkle and distort the flame sheet over length scales that are smaller than the flame length. The resultant heat release oscillations can then potentially result in combustion instability. Thus, it is essential to understand the hydrodynamic instability characteristics of the combustor flow field in order to understand its overall influence on combustion instability characteristics. To this end, this paper elucidates the role of fluctuating vorticity production from a linear hydrodynamic stability analysis as the key mechanism promoting absolute/convective instability transitions in shear layers occurring in the flow behind a backward facing step. These results are obtained within the framework of an inviscid, incompressible, local temporal and spatio-temporal stability analysis. Vorticity fluctuations in this limit result from interaction between two competing mechanisms - (1) production from interaction between velocity perturbations and the base flow vorticity gradient and (2) baroclinic torque in the presence of base flow density gradients. This interaction has a significant effect on hydrodynamic instability characteristics when the base flow density and velocity gradients are co-located. Regions in the space of parameters characterizing the base flow velocity profile, i.e. shear layer thickness and ratio of forward to reverse flow velocity, corresponding to convective and absolute instability are identified. The implications of the present results on prior observations of flow instability in other flows such as heated jets and bluff-body stabilized flames is discussed.

Saturated duration for dynamic structural plastic response and fundamental periods of elastic vibration

The relationship is determined between saturated duration of rectangular pressure pulses applied to rigid, perfectly plastic structures and their fundamental periods of elastic vibration. It is shown that the ratio between the saturated duration and the fundamental period of elastic vibration of a structure is dependent upon two factors: the first one is the slenderness or thinness ratio of the structure; and the second one is the square root of ratio between the Young's elastic modulus and the yield stress of the structural material. Dimensional analysis shows that the aforementioned ratio is one of the basic similarity parameters for elastic-plastic modeling under dynamic loading.

Fundamental Studies of Carbon Oxygen Bond Activation in Nickel Diphosphine Ether Complexes. And, Metallomacrocycles as Ligands: Synthesis and Characterization of Aluminum-Bridged Bisglyoximato Complexes of Iron and Cobalt

In order to develop better catalysts for the cleavage of aryl-X bonds fundamental studies of the mechanism and individual steps of the mechanism have been investigated in detail. As the described studies are difficult at best in catalytic systems, model systems are frequently used. To study aryl-oxygen bond activation, a terphenyl diphosphine scaffold containing an ether moiety in the central arene was designed. The first three chapters of this dissertation focus on the studies of the nickel complexes supported by this diphosphine backbone and the research efforts in regards to aryl-oxygen bond activation.

Chapter 2 outlines the synthesis of a variety of diphosphine terphenyl ether ligand scaffolds. The metallation of these scaffolds with nickel is described. The reactivity of these nickel(0) systems is also outlined. The systems were found to typically undergo a reductive cleavage of the aryl oxygen bond. The mechanism was found to be a subsequent oxidative addition, β-H elimination, reductive elimination and (or) decarbonylation.

Chapter 3 presents kinetic studies of the aryl oxygen bond in the systems outlined in Chapter 2. Using a series of nickel(0) diphosphine terphenyl ether complexes the kinetics of aryl oxygen bond activation was studied. The activation parameters of oxidative addition for the model systems were determined. Little variation was observed in the rate and activation parameters of oxidative addition with varying electronics in the model system. The cause of the lack of variation is due to the ground state and oxidative addition transition state being affected similarly. Attempts were made to extend this study to catalytic systems.

Chapter 4 investigates aryl oxygen bond activation in the presence of additives. It was found that the addition of certain metal alkyls to the nickel(0) model system lead to an increase in the rate of aryl oxygen bond activation. The addition of excess Grignard reagent led to an order of magnitude increase in the rate of aryl oxygen bond activation. Similarly the addition of AlMe3 led to a three order of magnitude rate increase. Addition of AlMe₃ at -80 °C led to the formation of an intermediate which was identified by NOESY correlations as a system in which the AlMe3 is coordinated to the ether moiety of the backbone. The rates and activation parameters of aryl oxygen bond activation in the presence of AlMe3 were investigated.

The last two chapters involve the study of metalla-macrocycles as ligands. Chapter 5 details the synthesis of a variety of glyoxime backbones and diphenol precursors and their metallation with aluminum. The coordination chemistry of iron on the aluminum scaffolds was investigated. Varying the electronics of the aluminum macrocycle was found to affect the observed electrochemistry of the iron center.

Chapter 6 extends the studies of chapter 5 to cobalt complexes. The synthesis of cobalt dialuminum glyoxime metal complexes is described. The electrochemistry of the cobalt complexes was investigated. The electrochemistry was compared to the observed electrochemistry of a zinc analog to identify the redox activity of the ligand. In the presence of acid the cobalt complexes were found to electrochemically reduce protons to dihydrogen. The electronics of the ancillary aluminum ligands were found to affect the potential of proton reduction in the cobalt complexes. These potentials were compared to other diglyoximate complexes.

Investigation of Fundamental Processes Governing Secondary Organic Aerosol Formation in Laboratory Chambers

Our understanding of the processes and mechanisms by which secondary organic aerosol (SOA) is formed is derived from laboratory chamber studies. In the atmosphere, SOA formation is primarily driven by progressive photooxidation of SOA precursors, coupled with their gas-particle partitioning. In the chamber environment, SOA-forming vapors undergo multiple chemical and physical processes that involve production and removal via gas-phase reactions; partitioning onto suspended particles vs. particles deposited on the chamber wall; and direct deposition on the chamber wall. The main focus of this dissertation is to characterize the interactions of organic vapors with suspended particles and the chamber wall and explore how these intertwined processes in laboratory chambers govern SOA formation and evolution.

A Functional Group Oxidation Model (FGOM) that represents SOA formation and evolution in terms of the competition between functionalization and fragmentation, the extent of oxygen atom addition, and the change of volatility, is developed. The FGOM contains a set of parameters that are to be determined by fitting of the model to laboratory chamber data. The sensitivity of the model prediction to variation of the adjustable parameters allows one to assess the relative importance of various pathways involved in SOA formation.

A critical aspect of the environmental chamber is the presence of the wall, which can induce deposition of SOA-forming vapors and promote heterogeneous reactions. An experimental protocol and model framework are first developed to constrain the vapor-wall interactions. By optimal fitting the model predictions to the observed wall-induced decay profiles of 25 oxidized organic compounds, the dominant parameter governing the extent of wall deposition of a compound is identified, i.e., wall accommodation coefficient. By correlating this parameter with the molecular properties of a compound via its volatility, the wall-induced deposition rate of an organic compound can be predicted based on its carbon and oxygen numbers in the molecule.

Heterogeneous transformation of δ-hydroxycarbonyl, a major first-generation product from long-chain alkane photochemistry, is observed on the surface of particles and walls. The uniqueness of this reaction scheme is the production of substituted dihydrofuran, which is highly reactive towards ozone, OH, and NO3, thereby opening a reaction pathway that is not usually accessible to alkanes. A spectrum of highly-oxygenated products with carboxylic acid, ester, and ether functional groups is produced from the substituted dihydrofuran chemistry, thereby affecting the average oxidation state of the alkane-derived SOA.

The vapor wall loss correction is applied to several chamber-derived SOA systems generated from both anthropogenic and biogenic sources. Experimental and modeling approaches are employed to constrain the partitioning behavior of SOA-forming vapors onto suspended particles vs. chamber walls. It is demonstrated that deposition of SOA-forming vapors to the chamber wall during photooxidation experiments can lead to substantial and systematic underestimation of SOA. Therefore, it is likely that a lack of proper accounting for vapor wall losses that suppress chamber-derived SOA yields contribute substantially to the underprediction of ambient SOA concentrations in atmospheric models.

Approximate analytical description for fundamental-mode fields of graded-index fibers: Beyond the Gaussian approximation

An approximate analytical description for fundamental-mode fields of graded-index fibers is explicitly presented by use of the power-series expansion method, the maximum-value condition at the fiber axis, the decay properties of fundamental-mode fields at large distance from the fiber axis, and the approximate modal parameters U obtained from the Gaussian approximation. This analytical description is much more accurate than the Gaussian approximation and at the same time keep the simplicity of the latter. As two special examples, we present the approximate analytical formulas for the fundamental-mode fields of a step profile fiber and a Gaussian profile fiber, and we find that they are both highly accurate in the single-mode range by comparing them with the corresponding exact solutions.

Effect of bismuth oxide on the thermal stability and Judd-Ofelt parameters of Er 3(+)/Yb3(+) co-doped aluminophosphate glasses

The Er3+/Yb3+ co-doped glasses with compositions of xBi(2)O(3)-(65-x)P2O5-4Yb(2)O(3)-11Al(2)O(3)-5BaO-15Na(2)O (where x = 0, 2.5, 5, 7.5 and 10 mol%) were prepared using the normal melt quench technique. The optical absorption spectra of the glasses were recorded in the wavelength range 300-1700 nm. The effect of Bi2O3 content on the thermal stability and absorption spectra of glasses was investigated. In addition, the Judd-Ofelt parameters and oscillator strengths were calculated by employing Judd-Ofelt theory. It was observed that the positions of the fundamental absorption edge and cut-off wavelength shifted towards red as the content of Bi2O3 increased. However, there were no red shifts found both in the peak wavelength and in the center of mass wavelength of all absorption bands with Bi2O3 content increasing. The results of Judd-Ofelt theory analysis showed that Judd-Ofelt parameters Omega(t), (t = 2, 4, 6) changed sharply when Bi2O3 concentration exceeded 5 mol%. The variation trends of experimental oscillator strength were similar with those of Judd-Ofelt parameters as function of Bi2O3 concentrations. Moreover, differential scanning calorimetry experiments showed that the increases of Bi2O3 content weakened the network structure and then lowered the thermal stability of the glasses. The spontaneous emission probability A(rad), branching ratio beta and the radiative lifetime tau(rad) were also calculated and analyzed. The stimulated emission cross-section of Er3+ was calculated according to the McCumber theory. It was found that the stimulated emission cross-section of Er3+ was monotonically increases with Bi2O3 content increasing. (C) 2006 Elsevier B.V. All rights reserved.

A pertinência da produção dos gêneros orais nas aulas do 6 ao 9 ano do ensino fundamental

Esta dissertação se propõe a analisar e a dimensionar a relevância que as propostas de produção de texto oral recebem nos livros didáticos do 6 ao 9 ano do Ensino Fundamental selecionados e indicados pelo Ministério da Educação, em seu Guia do Programa Nacional do Livro Didático (PNLD), em contraste com as de produção escrita. Também analisa a adequação dos gêneros textuais trabalhados em tais propostas, tendo em vista a preparação do aluno para o exercício da cidadania e a participação no mercado de trabalho por meio do domínio da linguagem oral, conforme orientação dos Parâmetros Curriculares Nacionais (PCN). Na impossibilidade de se analisarem todas as coleções indicadas no referido documento, optou-se por selecionar as duas mais frequentemente adotadas nas escolas públicas em todo o território nacional. Cumpre ressaltar que os PCN, documento oficial que apresenta um conjunto de orientações teóricas e metodológicas para o ensino de Língua Portuguesa, colocam em evidência o estudo dos gêneros textuais como um dos eixos do trabalho com a língua materna e têm abrangência nacional naquilo que recomendam. O PNLD, por seu turno, garante a quase trinta milhões de alunos brasileiros do 6 ao 9 anos do Ensino Fundamental o acesso a livros didáticos de seis componentes curriculares, incluindo a Língua Portuguesa, daí a relevância da pesquisa. Os resultados da investigação apontam para uma menor relevância atribuída à oralidade nas coleções analisadas, apesar da consonância das obras com as orientações dos PCN, as quais recomendam que sejam priorizados os gêneros textuais da comunicação pública. O presente trabalho ainda sugere linhas de ação no ensino da língua materna, de modo a reforçar, no aluno, o uso de variedades linguísticas orais publicamente adequadas, visando à participação social mais ampla e legítima, às exigências do mercado de trabalho e à realização plena do indivíduo que pensa e tem necessidade prática de exprimir seus anseios

Concepções de texto e a correção de produção escrita no ensino fundamental.

O objetivo desta dissertação é verificar, de forma teórico-conceitual, como as escolhas do professor sobre o objeto da produção textual estão pautadas em documentos oficiais, tendo como base os estudos linguísticos ou a gramática normativa. Busca-se refletir sobre a abordagem que atualmente é encontrada no ensino da Língua Portuguesa, uma visão preponderantemente voltada para a interação discursiva, tendo como objetivo o estudo da textualidade e dos diferentes gêneros textuais. Como tal abordagem trabalha com o texto de forma reduzida, pois não considera o que é dito, mas atribui maior importância a estrutura do texto, o ensino acaba por não considerar o sujeito do discurso. Para entender a linha teórica escolhida pelos documentos oficiais e que acabam por refletir na prática do professor, realiza-se uma análise dos principais documentos oficiais que servem como base ao processo de ensino-aprendizagem (Parâmetros Curriculares Nacionais, Diretrizes Curriculares e Matrizes de Referência do Sistema de Avaliação da Educação Básica) e uma comparação com dados da histórica do ensino de Língua Portuguesa e da teoria do currículo, buscando relacionar o paradigma de educação Moderno e o Pós-moderno com as práticas em sala de aula.

Can fundamental shock-wave/boundary-layer interaction research be relevant to inlet aerodynamics?

The important influence of shock waves on supersonic inlet performance has led to much time and effort being expended in the area of shock wave/boundary layer interaction research (SWBLI) and SWBLI control. In this short review, the impact of SWBLIs on supersonic inlet aerodynamic research is discussed and is contrasted with fundamental SWBLI research. Inlet research focussed on internal flow performance is reviewed, based on the salient results, conclusions, and the limitations of such work. The role of fundamental SWBLI research in relation to supersonic inlet research is considered, and the possible positive impact of improving the link between fundamental SWBLI research and inlet design is considered. A simple flow-field is discussed which is thought to be able to simulate at least some more of the flow physics found in a typical inlet. A brief review of real inlet parameters is then given to help determine appropriate fundamental experimental parameters such as incoming Mach number, incoming boundary-layer thickness and subsonic difiuser angle. Copyright © 2012 by N. Titchener, H. Babinsky, and E. Loth.

The energy required to produce materials: constraints on energy-intensity improvements, parameters of demand.

In this paper, we review the energy requirements to make materials on a global scale by focusing on the five construction materials that dominate energy used in material production: steel, cement, paper, plastics and aluminium. We then estimate the possibility of reducing absolute material production energy by half, while doubling production from the present to 2050. The goal therefore is a 75 per cent reduction in energy intensity. Four technology-based strategies are investigated, regardless of cost: (i) widespread application of best available technology (BAT), (ii) BAT to cutting-edge technologies, (iii) aggressive recycling and finally, and (iv) significant improvements in recycling technologies. Taken together, these aggressive strategies could produce impressive gains, of the order of a 50-56 per cent reduction in energy intensity, but this is still short of our goal of a 75 per cent reduction. Ultimately, we face fundamental thermodynamic as well as practical constraints on our ability to improve the energy intensity of material production. A strategy to reduce demand by providing material services with less material (called 'material efficiency') is outlined as an approach to solving this dilemma.

Fundamental studies on the application of enzymes when brewing with unmalted oats and sorghum

The use of unmalted oats or sorghum in brewing has great potential for creating new beer types/flavors and saving costs. However, the substitution of barley malt with oat or sorghum adjunct is not only innovative but also challenging due to their specific grain characteristics. The overall objectives of this Ph.D. project were: 1) to investigate the impact of various types and levels of oats or sorghum on the quality/processability of mashes, worts, and beers; 2) to provide solutions as regards the application of industrial enzymes to overcome potential brewing problems. For these purposes, a highly precise rheological method using a controlled stress rheometer was developed and successfully applied as a tool for optimizing enzyme additions and process parameters. Further, eight different oat cultivars were compared in terms of their suitability as brewing adjuncts and two very promising types identified. In another study, the limitations of barley malt enzymes and the benefits of the application of industrial enzymes in high-gravity brewing with oats were determined. It is recommended to add enzymes to high-gravity mashes when substituting 30% or more barley malt with oats in order to prevent filtration and fermentation problems. Pilot-scale brewing trials using 10–40% unmalted oats revealed that the sensory quality of oat beers improved with increasing adjunct level. In addition, commercially available oat and sorghum flours were implemented into brewing. The use of up to 70% oat flour and 50% sorghum flour, respectively, is not only technically feasible but also economically beneficial. In a further study on sorghum was demonstrated that the optimization of industrial mashing enzymes has great potential for reducing beer production costs. A comparison of the brewing performance of red Italian and white Nigerian sorghum clearly showed that European grown sorghum is suitable for brewing purposes; 40% red sorghum beers were even found to be very low in gluten.

Fundamental Amplitude Noise Limitations to Supercontinuum Spectra Generated in a Microstructured Fiber

Broadband supercontinuum spectra are generated in a microstructured fiber using femtosecond laser pulses. Noise properties of these spectra are studied through experiments and numerical simulations based on a generalized stochastic nonlinear Schrödinger equation. In particular, the relative intensity noise as a function of wavelength across the supercontinuum is measured over a wide range of input pulse parameters, and experimental results and simulations are shown to be in good quantitative agreement. For certain input pulse parameters, amplitude fluctuations as large as 50% are observed. The simulations clarify that the intensity noise on the supercontinuum arises from the amplification of two noise inputs during propagation - quantum-limited shot noise on the input pulse, and spontaneous Raman scattering in the fiber. The amplification factor is a sensitive function of the input pulse parameters. Short input pulses are critical for the generation of very broad supercontinua with low noise.

Fundamental Noise Limitations to Supercontinuum Generation in Microstructure Fiber

Broadband noise on supercontinuum spectra generated in microstructure fiber is shown to lead to amplitude fluctuations as large as 50% for certain input laser pulse parameters. We study this noise using both experimental measurements and numerical simulations with a generalized stochastic nonlinear Schrödinger equation, finding good quantitative agreement over a range of input-pulse energies and chirp values. This noise is shown to arise from nonlinear amplification of two quantum noise inputs: the input-pulse shot noise and the spontaneous Raman scattering down the fiber.