Structural requirement for PPAR gamma binding revealed by a meta analysis of holo-crystal structures

PPAR gamma is a ligand regulated transcriptional factor that modulates the transcription of several genes involved in fat and sugar metabolism. Due to its easy bacterial expression and crystallization, several crystal structures of holo-PPAR gamma have been reported and deposited in the Protein Data Bank. Here, we investigated the three-dimensional electrostatic properties of 55 PPAR gamma ligands and used this information for clustering them through principal component analysis. We found out that, according to their electrostatic potential, these ligands can be separated in three groups, with different binding features. We also observed that non-selective and selective ligands show different 3D electrostatic properties and are separated in different clusters. The relevance of this analysis for the development of new binders is discussed. (C) 2010 Elsevier Masson SAS. All rights reserved.

Eficiência econômica da produção de cana-de-açúcar de produtores independentes do Estado do Paraná

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

A study of neolignan compounds with biological activity against Paracoccidioides brasiliensis by using quantum chemical and chemometric methods

Métodos quimiométricos (estatísticos) são empregados para classificar um conjunto de compostos derivados de neolignanas com atividade biológica contra a Paracoccidioides brasiliensis. O método AM1 (Austin Model 1) foi utilizado para calcular um conjunto de descritores moleculares (propriedades) para os compostos em estudo. A seguir, os descritores foram analisados utilizando os seguintes métodos de reconhecimento de padrões: Análise de Componentes Principais (PCA), Análise Hierárquica de Agrupamentos (HCA) e o método de K-vizinhos mais próximos (KNN). Os métodos PCA e HCA mostraram-se bastante eficientes para classificação dos compostos estudados em dois grupos (ativos e inativos). Três descritores moleculares foram responsáveis pela separação entre os compostos ativos e inativos: energia do orbital molecular mais alto ocupado (EHOMO), ordem de ligação entre os átomos C1'-R7 (L14) e ordem de ligação entre os átomos C5'-R6 (L22). Como as variáveis responsáveis pela separação entre compostos ativos e inativos são descritores eletrônicos, conclui-se que efeitos eletrônicos podem desempenhar um importante papel na interação entre receptor biológico e compostos derivados de neolignanas com atividade contra a Paracoccidioides brasiliensis.

Investigação das características I x V e C x V de NCPS puro, com nitrogênio substitucional carregado (-1 e +1) e com grupos doador (NO2)-aceitador (NH2) através de métodos derivados de hartree-fock

Neste trabalho, fizemos uma investigação sobre o estudo teórico das características I x V e C x V de Nanotubo Carbono de Parede Simples (NCPS) puro, com Nitrogênio substitucional carregado com cargas -1 (caracterizando um indicativo de dopagem tipo n) e +1 (caracterizando um indicativo de dopagem tipo p) e na presença de grupos doador (NO₂)-aceitador (NH₂), através da simulação computacional do estado fundamental de NCPS, bem como de sua estrutura eletrônica e propriedades ópticas, utilizando parametrizações semi-empíricas AM1 (Austin Mudel 1) e ZINDO/S-ClS (Zerner´s lntermediate Neglect of Differential Orbital/Spectroscopic - Cunfiguration lnteraction Single) derivadas da Teoria de Hartree-Fock baseada em técnicas de química quântica. Por meio deste modelo teórico analisamos as propriedades ópticas e eletrônicas, de maior interesse para esses materiais, a fim de se entender a melhor forma de interação desses materiais na fabricação de dispositivos eletrônicos, tais como TECs (Transistores de Efeito de Campo) ou em aplicações em optoeletrônica tais como DEL (Dispositivo Emissor de Luz). Observamos que NCPS com Nitrogênio substitucional apresentam defeitos conformacionais do tipo polarônico. Fizemos as curvas dos espectros UV-visível de Absorção para NCPS armchair e zigzag puro, com Nitrogênio substitucional carregado com cargas (-1 e +1) e na presença de grupos doador (NO₂)-aceitador (NH₂), quando perturbados por intensidades diferentes de campo elétrico. Verificamos que em NCPS zigzag ao aumentarmos a intensidade do campo elétrico, suas curvas sofrem grandes perturbações. Obtivemos as curvas p x E, I x V e C x V para esses NCPS, concluímos que NCPS armchair possui comportamento resistor, pois suas curvas são lineares e zigzag possui comportamento semelhante ao dos dispositivos eletrônicos importantes para o avanço tecnológico. Assim, nossos resultados estão de bom acordo com os resultados experimentais e teóricos de NCPS puro e com Nitrogênio encontrados na literatura.

Effect of temperature on dislocation emission from crack tip for BCC metal Mo

The effect of thermally activated energy on the dislocation emission from a crack tip in BCC metal Mo is simulated in this paper. Based on the correlative reference model on which the flexible displacement boundary scheme is introduced naturally, the simulation shows that as temperature increases the critical stress intensity factor for the first dislocation emission will decrease and the total number of emitted dislocations increase for the same external load. The dislocation velocity and extensive distance among partial dislocations are not sensitive to temperature. After a dislocation emission, two different deformation slates are observed, the stable and unstable deformation states. In the stable deformation slate, the nucleated dislocation will emit from the crack tip and piles up at a distance far away from the crack tip, after that the new dislocation can not be nucleated unless the external loading increases. In the unstable deformation state, a number of dislocations can be emitted from the crack lip continuously under the same external load.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.

Phonon dispersion curves and atomic mean square displacement for several fcc and bcc materials

The atomic mean square displacement (MSD) and the phonon dispersion curves (PDC's) of a number of face-centred cubic (fcc) and body-centred cubic (bcc) materials have been calclllated from the quasiharmonic (QH) theory, the lowest order (A2 ) perturbation theory (PT) and a recently proposed Green's function (GF) method by Shukla and Hiibschle. The latter method includes certain anharmonic effects to all orders of anharmonicity. In order to determine the effect of the range of the interatomic interaction upon the anharmonic contributions to the MSD we have carried out our calculations for a Lennard-Jones (L-J) solid in the nearest-neighbour (NN) and next-nearest neighbour (NNN) approximations. These results can be presented in dimensionless units but if the NN and NNN results are to be compared with each other they must be converted to that of a real solid. When this is done for Xe, the QH MSD for the NN and NNN approximations are found to differ from each other by about 2%. For the A2 and GF results this difference amounts to 8% and 7% respectively. For the NN case we have also compared our PT results, which have been calculated exactly, with PT results calculated using a frequency-shift approximation. We conclude that this frequency-shift approximation is a poor approximation. We have calculated the MSD of five alkali metals, five bcc transition metals and seven fcc transition metals. The model potentials we have used include the Morse, modified Morse, and Rydberg potentials. In general the results obtained from the Green's function method are in the best agreement with experiment. However, this improvement is mostly qualitative and the values of MSD calculated from the Green's function method are not in much better agreement with the experimental data than those calculated from the QH theory. We have calculated the phonon dispersion curves (PDC's) of Na and Cu, using the 4 parameter modified Morse potential. In the case of Na, our results for the PDC's are in poor agreement with experiment. In the case of eu, the agreement between the tlleory and experiment is much better and in addition the results for the PDC's calclliated from the GF method are in better agreement with experiment that those obtained from the QH theory.

Vibrational behaviour of bcc Cu-based shape memory alloys close to the martensitic transition

Experimental data from ultrasonic and inelastic neutron scattering measurements are analyzed for different families of Cu-based shape-memory alloys. It is shown that the transition occurs at a value, independent of composition and alloy family, of the ratio between the elastic constants associated with the two shears necessary to accomplish the lattice distortion from the bcc to the close-packed structure. The zone boundary frequency of the TA2[110] branch evaluated at the transition point (TM), weakly depends, for each family, on composition. A linear relationship between this frequency and the inverse of the elastic constant C', both quantities evaluated at TM, has been found, in agreement with the prediction of a Landau model proposed for martensitic transformations.

An AM1 semiempirical study of the mechanism of sintering for ZnO in the presence of water and carbon dioxide

AM1 calculations were performed for the absorption of H2O and CO2 molecules on the surface of model ZnO crystals. The absorption of isolated molecules of each species and the co-absorption of both compounds simultaneously were considered. It was found that the absorption of H2O near a site where CO; is already absorbed favors the process of sintering, in agreement with the experimental findings. This is explained by the formation of Zn(OH)CO3H bound to the surface, a more mobile species than the ZnO unit itself. The roundening of the grains observed in atmospheres containing dry CO2 but suppressed when H2O is present, is also explained by these calculations. After absorption of CO2, the rupture of one bond - so that diffusion of the ZnCO3 species on the surface is allowed - requires much less energy than the breaking of two bonds, necessary for ZnO migration. These facts explain why the speed of surface transport does not decrease in CO2 atmospheres while sintering is indeed slowed down. © 1994.

Phonons in binary BCC lithium-sodium alloys

The dispersion relations along the principal symmetry directions in BCC lithium-sodium alloys are calculated using second-order perturbation theory. The local modified Hoshino-Youngmodel potential was used for the lithium and the local Harrison model potential for sodium. The phonon density of states, the root mean square displacements and (Θ-T) curves are also calculated. In the absence of experimental data, just the theoretical predictions are presented here.

Edge-to-edge matching and its applications - Part I. Application to the simple HCP/BCC system

The edge-to-edge matching crystallographic model has been used to predict all the orientation relationships (OR) between crystals that have simple hexagonal close packed (HCP) and body-centered cubic (BCC) structures. Using the critical values for the interatomic spacing misfit along the matching directions and the cl-value mismatch between matching planes, the model predicted all the four common ORs, namely the Burgers OR, the Potter OR, the Pitsch-Schrader OR and the Rong Dunlop OR, together with the corresponding habit planes. Taking the c(H)/a(H) and a(H)/a(B) ratios as variables, where H and B denote the HCP and BCC structures respectively, the model also predicted the relationship between these variables and the four ORs. These predictions are perfectly consistent with the published experimental results. As was the case in the FCC/BCC system, the edge-to-edge matching model has been shown to be a powerful tool for predicting the crystallographic features of diffusion-controlled phase transformations. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A bi-objective weighted model for improving the discrimination power in MCDEA

Lack of discrimination power and poor weight dispersion remain major issues in Data Envelopment Analysis (DEA). Since the initial multiple criteria DEA (MCDEA) model developed in the late 1990s, only goal programming approaches; that is, the GPDEA-CCR and GPDEA-BCC were introduced for solving the said problems in a multi-objective framework. We found GPDEA models to be invalid and demonstrate that our proposed bi-objective multiple criteria DEA (BiO-MCDEA) outperforms the GPDEA models in the aspects of discrimination power and weight dispersion, as well as requiring less computational codes. An application of energy dependency among 25 European Union member countries is further used to describe the efficacy of our approach. © 2013 Elsevier B.V. All rights reserved.

The effect of participation in a ``Greening the BCC Curriculum'' workshop series on the environmental literacy of a community college faculty

The purpose of this study was to develop a series of workshops designed to raise the environmental literacy of a community college faculty and facilitate infusion of an environmental perspective into the courses they teach. Data was gathered on the effect of the workshops on the level of environmental literacy of the participants as well as the persistence of any observed effect. How faculty infused an environmental perspective into their courses was also explored.^ The workshop model was developed by reviewing adult learning and change theories, case studies of workshops at other colleges, environmental education research, and results of a pilot study. Content, organization, and delivery methods from these sources were selected and integrated to create the 14 components of the model employed by the workshops in this study.^ Forty-two faculty from the North Campus of Broward Community College participated in the study. The 20 workshop participants from seven academic departments attended seven two hour workshops during the fall term of 1996, and implemented projects to infuse environmental topics into their courses the following term. A quasi-experimental pretest-posttest-delayed posttest nonequivalent control group design was employed in which the 22 members of the control group who did not attend the workshops were administered the Wisconsin Environmental Survey at the same time as the workshop participants (immediately before the first workshop, immediately following the last workshop, and four months following the completion of the workshop series). This instrument, an adaption of the Wisconsin High School Student Environmental Survey, yielded three measures of environmental literacy: Affective, Behavior, and Cognitive Subscale scores.^ The repeated measures MANOVA performed using the scores of the two groups on the three administrations of WES revealed a significant interaction for group by time, so repeated measures ANOVA were performed for each of the three subscales to investigate the interaction. Tukey-HSD post hoc comparisons indicated that for all three subscale scores, the two groups were not significantly different on the pretest, but on the posttest and the delayed posttest, the workshop participants demonstrated significantly higher levels of environmental literacy. All statistical tests were performed at $\alpha$ =.05. ^