PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Generalized solutions of a nonlinear parabolic equation with generalized functions as initial data

In [H. Brezis, A. Friedman, Nonlinear parabolic equations involving measures as initial conditions, J. Math. Pure Appl. (9) (1983) 73-97.] Brezis and Friedman prove that certain nonlinear parabolic equations, with the delta-measure as initial data, have no solution. However in [J.F. Colombeau, M. Langlais, Generalized solutions of nonlinear parabolic equations with distributions as initial conditions, J. Math. Anal. Appl (1990) 186-196.] Colombeau and Langlais prove that these equations have a unique solution even if the delta-measure is substituted by any Colombeau generalized function of compact support. Here we generalize Colombeau and Langlais` result proving that we may take any generalized function as the initial data. Our approach relies on recent algebraic and topological developments of the theory of Colombeau generalized functions and results from [J. Aragona, Colombeau generalized functions on quasi-regular sets, Publ. Math. Debrecen (2006) 371-399.]. (C) 2009 Elsevier Ltd. All rights reserved.

Bismuth Modified Gold Microelectrode for Pb(II) Determination in Wine Using Alkaline Medium

Electrodeposition of bismuth on gold microelectrodes for determination of Pb(II) by square wave anodic stripping voltammetry (SWASV) was accomplished by an in situ procedure in alkaline solution. A linear calibration plot for Pb(II) in the concentration range 40 to 6700 nmol L(-1) (r=0.998) was obtained, the detection limit was found to be 12.5 nmol L(-1) (S/N = 3) and the relative standard deviation in Solutions containing 1 mu mol L(-1) Pb(II) was 4% (n = 12). The analytical performance of the proposed sensor wits tested by measuring the Pb(II) concentration in a wine sample. The result Was in good agreement with the one obtained by GFAAS.

The role of oxygen in the interaction of emeraldine base polyaniline with Cu(II) or Fe(III) ions in NMP solution

The influence of molecular oxygen in the interactions of emeraldine base form of polyaniline (EB-PANI) with Fe(III) or Cu(II) ions in 1-methyl-2-pyrrolidinone (NMP) solutions has been investigated by UV-vis-NIR, resonance Raman and electron paramagnetic resonance (EPR) spectroscopies. Through the set of spectroscopic results it was possible to rationalize the role Of O(2) and to construct a scheme of preferential routes occurring in the interaction of EB-PANI with Fe(III) or Cu(II). Solutions of 4.0 mmol L(-1) EB-PANI with 0.8, 2.0 and 20 mmol L(-1) Fe(III) or Cu(II) ions in NMP were investigated and the main observed reactions were EB-PANI oxidation to pernigraniline (PB-PANI) and EB-PANI doping process by pseudo-protonation, or by a two-step redox process. In the presence Of O(2), PB-PANI is observed in all Fe(III)/EB solutions and EB-PANI doping only occurs in solutions with high Fe(III) concentrations through pseudo-protonation. On the other hand, emeraldine salt (ES-PANI) is formed in all Fe(III)/EB solutions under N(2) atmosphere and, in this case, doping occurs both by the pseudo-protonation and two-step redox mechanisms. In all Cu(II)/EB solutions PB-PANI is formed both in the presence and absence of O(2), and only for solutions with high Cu(II) concentrations doping process occurs in a very low degree. The most important result from EPR spectra was providing evidence for redox steps. The determined Cu(II) signal areas under oxygen are higher than under N(2) and, further. the initial metal proportions (1:2:20) are maintained in these spectra, indicating that Cu(I) formed are re-oxidized by O(2) and. so, Cu(II) ions are being recycled. Consistently, for the solutions prepared under nitrogen, the corresponding areas and proportions in the spectra are much lower, confirming that a partial reduction of Cu(II) ions actually occurs. (C) 2009 Elsevier B.V. All rights reserved.

Electrodeposition and characterization of thin selenium films modified with lead ad-atoms

The deposition and characterization of Se films doped with Pb underpotentially deposited (UPD) ad-atoms was studied in this work. The employed experimental techniques were cyclic voltammetry, chronoamperometry, electrochemical impedance spectroscopy, UV-vis spectroscopy and atomic force microscopy. The initial deposition of Se film by chronoamperometry yielded a thin film composed of approximately 700 layers. The Pb UPD on Se was achieved by chronoamperometry in a potential value previously determined in voltammetric experiments. This deposition yielded a deposition charge of approximately 7.5% of the total one. The film resistance altered from 320 Omega cm(2) for Se to 65 Omega cm(2) for the Se/Pb one. Flat band potential values and number of acceptors and donors were also calculated for both films and the values obtained were + 0.95 and -0.51 V for Se and Se/Pb, respectively. The Se coating presented 1.2 x 10(17) cm(3) acceptors while the Se/Pb one presented 3.2 x 10(17) cm(3) donors. The band gap values for both films were 2.4 eV and 1.9 eV, correspondingly. (C) 2008 Elsevier B.V. All rights reserved.

Leakage current, ferroelectric and structural properties in Pb(1-x)Ba(x)TiO(3) thin films prepared by chemical route

Single-phase perovskite structure Pb(1-x)Ba(x)TiO(3) thin films (x = 0.30, 0.50 and 0.70) were deposited on Pt/Ti/SiO(2)/Si substrates by the spin-coating technique. The dielectric study reveals that the thin films undergo a diffuse type ferroelectric phase transition, which shows a broad peak. An increase of the diffusivity degree with the increasing Barium contents was observed, and it was associated to a grain decrease in the studied composition range. The temperature dependence of the phonon frequencies was used to characterize the phase transition temperatures. Raman modes persist above tetragonal to cubic phase transition temperature, although all optical modes should be Raman inactive. The origin of these modes was interpreted in terms of breakdown of the local cubic symmetry by chemical disorder. The absence of a well-defined transition temperature and the presence of broad bands in some interval temperature above FE-PE phase transition temperature Suggested a diffuse type phase transition. This result corroborates the dielectric constant versus temperature data, which showed a broad ferroelectric phase transition in these thin films. The leakage Current density of the PBT thin films was studied at different temperatures and the data follow the Schottky emission model. Through this analysis the Schottky barrier height values 0.75, 0.53 and 0.34 eV were obtained to the PBT70, PBT50 and PBT30 thin films, respectively. (C) 2008 Elsevier Ltd. All rights reserved.

How initial vocational education and training (IVET) teachers in Sweden perceive their prospects of being able to prepare upper secondary school pupils for a future occupation

Vocational teachers in Swedish upper secondary schools are a heterogeneous category of teachers, connected to different types of trade. These teachers represent a broad set of trade skills varying in content and character. In their teacher role, they continue to wear the clothes, speak the language, share the culture and remain mentally in their former professions. Still, it is central that they keep up this contact to be able to school the pupils into the environment of the trade in question, but also to help them to understand what skills a profession demands. However, the individual teacher also has to distance himself from the negative elements in the culture of the profession: patterns and habits that, for various reasons, have to be broken or changed. This paper draws attention to the ways in which a group of vocational teachers, who were participants in a project that aimed to train unauthorized vocational teachers, expressed their ambitions to prepare the pupils for a future professional career. When collecting information, we used the degree dissertations they produced and discussed in seminars, and informal dialogues. The result shows that it is important that the instruction location resembles a real working site as far as possible. These places are more or less realistic copies of a garage, a restaurant kitchen, a hairdressing salon, and so on, in order to give the pupils a realistic setting for instruction. However, the fact that these simulated workplaces lack the necessary support functions that exist in a company creates problems, problems which make a lot of extra work for the teachers. Vocational teachers also have to instruct the pupil in the experienced practitioner’s professional skills and working situation, but the pupil herself/himself must learn the job by doing it in practice. Some vocational upper secondary programs lack relevant course literature and the businesses give little support. This also makes extra work for the teachers. Moreover, the distance between the vocational programs and the trainee jobs was experienced as being difficult to overcome. One reason seems to be differences between businesses and differing preconditions between small and big companies’ abilities to take care of these pupils. The upper secondary school vocational programs also play a role in cementing existing gender roles, as well as perpetuating class-related patterns on the labour market.

How initial vocational education and training (IVET) teachers in Sweden perceive their prospects of being able to prepare upper secondary school pupils for a future occupation

Vocational teachers in Swedish upper secondary schools are a heterogeneous category of teachers, connected to different types of trade. These teachers represent a broad set of trade skills varying in content and character. In their teacher role, they continue to wear the clothes, speak the language, share the culture and remain mentally in their former professions. Still, it is central that they keep up this contact to be able to school the pupils into the environment of the trade in question, but also to help them to understand what skills a profession demands. However, the individual teacher also has to distance himself from the negative elements in the culture of the profession: patterns and habits that, for various reasons, have to be broken or changed. This paper draws attention to the ways in which a group of vocational teachers, who were participants in a project that aimed to train unauthorized vocational teachers, expressed their ambitions to prepare the pupils for a future professional career. When collecting information, we used the degree dissertations they produced and discussed in seminars, and informal dialogues. The result shows that it is important that the instruction location resembles a real working site as far as possible. These places are more or less realistic copies of a garage, a restaurant kitchen, a hairdressing salon, and so on, in order to give the pupils a realistic setting for instruction. However, the fact that these simulated workplaces lack the necessary support functions that exist in a company creates problems, problems which make a lot of extra work for the teachers. Vocational teachers also have to instruct the pupil in the experienced practitioner’s professional skills and working situation, but the pupil herself/himself must learn the job by doing it in practice. Some vocational upper secondary programs lack relevant course literature and the businesses give little support. This also makes extra work for the teachers. Moreover, the distance between the vocational programs and the trainee jobs was experienced as being difficult to overcome. One reason seems to be differences between businesses and differing preconditions between small and big companies’ abilities to take care of these pupils. The upper secondary school vocational programs also play a role in cementing existing gender roles, as well as perpetuating class-related patterns on the labour market.

Transformação genética em cevada por bombardeamento de partículas

A presente Tese de Doutorado objetivou: (1) definir um método eficiente de transformação genética, por bombardeamento de partículas, para a obtenção de plantas transgênicas de cultivares brasileiras de cevada e (2) identificar gene(s) codificante(s) de quitinase(s) potencialmente capaz(es) de conferir resistência ao fungo patogênico de cevada Bipolaris sorokiniana. Culturas de calos obtidos a partir de escutelos imaturos das cultivares Brasileiras de cevada MN-599 e MN-698 (Cia. de Bebidas das Américas, AMBEV) foram bombardeadas com partículas de tungstênio e avaliadas quanto à expressão do gene repórter gusA através de ensaios histoquímicos de GUS e quanto ao efeito dos bombardeamentos na indução estruturas embriogênicas e regeneração de plantas. As condições de biobalística analisadas incluíram a região promotora regulando a expressão de gusA, tipo e pressão de gás hélio de dois aparelhos de bombardeamento, distância de migração das partículas, número de tiros e a realização de pré e pós-tratamento osmótico dos tecidos-alvo. No presente trabalho foram obtidos um número bastante alto de pontos azuis por calo, a indução de calos embriogênicos e embriões somáticos em uma freqüência de até 58,3% e a regeneração de 60 plantas, sendo 43 de calos bombardeados. As melhores condições observadas foram o promotor e primeiro íntron do gene Adh de milho (plasmídeo pNGI), o aparelho de bombardeamento “ Particle Inflow Gun” (PIG) utilizando-se a distância de migração de partículas de 14,8 cm, dois tiros disparados por placa e a realização de tratamento osmótico dos explantes com 0,2 M de manitol e 0,2 M de sorbitol 4-5 horas antes e 17-19 horas depois dos bombardeamentos. Das 43 plantas obtidas de calos bombardeadas, 3 apresentaram atividade de GUS na base das suas folhas. A utilização de primers sintéticos definidos a partir de genes de quitinases descritos na literatura em PCRs resultou na amplificação de dois fragmentos de aproximadamente 700 e 500 pb a partir de DNA total das cvs. MN-599 e MN-698 de cevada e um fragmento, com aproximadamente 500 pb, a partir do DNA total do isolado A4c de Trichoderma sp. Estes fragmentos foram purificados dos géis de agarose e diretamente seqüenciados de forma manual e automática. Os fragmentos de 700 e 500 pb amplificados do genoma da cultivar MN-599 foram identificados como genes de quitinases de cevada e o fragmento de 500 pb do isolado A4c de Trichoderma sp. não apresentou homologia com seqüências conhecidas de quitinases depositadas no EMBL/GenBank. A utilização de novos pares de primers, representando seqüências conservadas de quitinases do fungo Metarhizium anisopliae, resultou na amplificação de 3 fragmentos a partir do DNA total do isolado A4b de Trichoderma sp., que estão sendo purificados para realização de seqüenciamento.

Fonologia lexical e controvérsia neogramática : análise das regras de monotongação de /ow/ e vocalização de /l/ no PB

Nesta dissertação, assumimos os pressupostos formais do modelo não-linear da Fonologia Lexical (FL). Adotamos, como hipótese de trabalho - nos termos de Labov (1981), Labov (1994) e Kiparsky (1988)- a resolução da controvérsia neogramática a partir deste modelo. Para tanto, apresentamos a análise de dois fenômenos do Português Brasileiro (PB), com base em dados empíricos extraídos da cidade de Porto Alegre, os quais confrontamos com as predições que emanam do modelo teórico. Num primeiro momento, discutimos o status lexical e pós-lexical das regras de vocalização de /l/ e monotongação de /ow/. Num segundo momento, apresentamos a caracterização desses dois tipos de mudança. Essas discussões fundamentam-se em resultados estatísticos, obtidos a partir da utilização do pacote VARBRUL. Partindo dessas discussões, propomos o ordenamento dessas regras nos componentes do modelo da Fonologia Lexical (FL), rastreando esses processos nos módulos do léxico e do pós-léxico. A escolha destes dois fenômenos não é aleatória: da análise destas regras nos termos da FL emergem questões não devidamente tratadas no PB, como a opacidade e a presença de regras variáveis no léxico. Também destacamos a controvérsia sobre a representação dos segmentos envolvidos nestes processos: dedicamos um capítulo para a discussão sobre a representação da lateral e do processo de vocalização; e outro para a discussão sobre a representação subjacente do ditongo /ow/. Conforme a análise dos resultados, concluímos que a regra de monotongação de /ow/ comporta-se como regra lexical e implementa um tipo de mudança que se difunde lexicalmente. Já a regra de vocalização de /l/ caracteriza-se como regra pós-lexical e encaixa-se no molde de mudança neogramática.

Análise da vazão máxima outorgável e da introdução simplificada da qualidade da água no processo de outorga da bacia do rio Gramame (PB)

O estado dos recursos hídricos da bacia do rio Gramame, localizada no litoral sul do Estado da Paraíba, tem se revelado insustentável, principalmente nesses últimos anos. Tanto a escassez quantitativa quanto a qualitativa inserem-se no contexto da bacia, tornando frreqüentes os conflitos entre os principais usuários de água (abastecimento urbano, indústrias e irrigantes). Em virtude disso, surge a necessidade de implementação de um sistema de outorga na bacia, para uma alocação eficiente das disponibidades hídricas. Neste trabalho, foram abordados os principais problemas para essa implementação: (a) a definição da vazão m[axima outorgável; e (iii) a intrtodução dos aspectos qualitativos da água. Par ao primeiro problema, foram estabelecidos e avaliados como passíveis de emprego na bacia os seguintes critérios de outorga: (a) vazão excedente; (b) garantia de suprimento; (c) vazão de referência com probabilidade de superação de 90% (Q90); (d) 2 vazões de referência Q90 para as estações seca e chuviosa e (e) 12 vazões de referência Q90 referentes a cada mês do ano. No tocante à qualidade da água no processo de outorga, foi verificada a sensibilidade do sistema hídrico e suas demandas à consideração dos poluentes lançados nos cursos dágua da bacia como demanda para diluição da concentração de Demanda Bioquímica de Oxigênio (DBO). ALém disso, foi abordado, de forma simplificada, o processo de autodepuração da DBO, através de coeficientes de depuração, visando avaliar a relevância das vazões liberadas para novoo usos nas seções à jusante dos deesejos de efluentes. Através da comparação dos parâmetros de desempenho (garantia volumétrica, garantia temporal, garantia crítica temporal, garantia volumétrica mensal mínima, resiliência e vulnerabilidade) obtidos da simulação de cada cenário da bacia, de ocorrência em curto prazo, foram avaliados os critérios de outorga e a introdução da qualidade da água. Priorizando o atendimento das demandas para abastecimento urbano, em ordem crescente de redução do suprimento das demandas existentes na bacia, os critérios de determinação da vazão máxima outorgável puderam ser ordenados como: vazão excendente, vazões de referência mensais, vazões de referência das estações seca e chuvosa, vazão de referência única e garantia de suprimento. Quanto à consideração das demandas para diluição de despejos, verificou-se que, de modo geral, estas poucos reduziram o suprimento das demandas já instaladas na bacia e também não foram significativas as vazões liberadas pela autodepuração a ponto de melhorar o atendimento das seções por ela afetadas. Entretanto, excetuando a demanda para diluição dos efluentes domésticos do município do Conde, foi verificada a inviabilidade de suprimento dos atuais lançamentos de efluentes na bacia, cujo percentual de atendimento não atingiu 50% do volume requerido.

Planejamento balanceado - PB elaboração e implementação de um sistema de gestão estratégica que integra as técnicas do planejamento estratégico com o Balanced Scorecard

Este trabalho propõe um critério estruturado de elaboração, implementação e operacionalização de um Sistema de Gestão Estratégica definido como Planejamento Balanceado, o qual é resultado do uso de conceitos do Planejamento Estratégico, adaptados a partir das obras de autores como Pagnoncelli e Vasconcellos (1992), Lobato (1997), entre outros e, aliando na seqüência deste, o uso do Balanced Scorecard de Kaplan e Norton (1997) para estabelecer as “Relações de Causa-e-efeito” entre as Estratégias e definir um processo sistemático para implementar e obter feedback sobre as mesmas, contribuindo assim para que a organização fique alinhada e focalizada na implementação e operacionalização das estratégias elaboradas.