Modeling ocean primary production: sensitivity to spectral resolution of attenuation and absorption of light

Modeling the vertical penetration of photosynthetically active radiation (PAR) through the ocean, and its utilization by phytoplankton, is fundamental to simulating marine primary production. The variation of attenuation and absorption of light with wavelength suggests that photosynthesis should be modeled at high spectral resolution, but this is computationally expensive. To model primary production in global 3d models, a balance between computer time and accuracy is necessary. We investigate the effects of varying the spectral resolution of the underwater light field and the photosynthetic efficiency of phytoplankton (α∗), on primary production using a 1d coupled ecosystem ocean turbulence model. The model is applied at three sites in the Atlantic Ocean (CIS (∼60°N), PAP (∼50°N) and ESTOC (∼30°N)) to include the effect of different meteorological forcing and parameter sets. We also investigate three different methods for modeling α∗ – as a fixed constant, varying with both wavelength and chlorophyll concentration [Bricaud, A., Morel, A., Babin, M., Allali, K., Claustre, H., 1998. Variations of light absorption by suspended particles with chlorophyll a concentration in oceanic (case 1) waters. Analysis and implications for bio-optical models. J. Geophys. Res. 103, 31033–31044], and using a non-spectral parameterization [Anderson, T.R., 1993. A spectrally averaged model of light penetration and photosynthesis. Limnol. Oceanogr. 38, 1403–1419]. After selecting the appropriate ecosystem parameters for each of the three sites we vary the spectral resolution of light and α∗ from 1 to 61 wavebands and study the results in conjunction with the three different α∗ estimation methods. The results show modeled estimates of ocean primary productivity are highly sensitive to the degree of spectral resolution and α∗. For accurate simulations of primary production and chlorophyll distribution we recommend a spectral resolution of at least six wavebands if α∗ is a function of wavelength and chlorophyll, and three wavebands if α∗ is a fixed value.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Quantitative structure-activity relationships for a series of inhibitors of cruzain from Trypanosoma cruzi: Molecular modeling, CoMFA and CoMSIA studies

Human parasitic diseases are the foremost threat to human health and welfare around the world. Trypanosomiasis is a very serious infectious disease against which the currently available drugs are limited and not effective. Therefore, there is an urgent need for new chemotherapeutic agents. One attractive drug target is the major cysteine protease from Trypanosoma cruzi, cruzain. In the present work, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) studies were conducted on a series of thiosemicarbazone and semicarbazone derivatives as inhibitors of cruzain. Molecular modeling studies were performed in order to identify the preferred binding mode of the inhibitors into the enzyme active site, and to generate structural alignments for the three-dimensional quantitative structure-activity relationship (3D QSAR) investigations. Statistically significant models were obtained (CoMFA. r(2) = 0.96 and q(2) = 0.78; CoMSIA, r(2) = 0.91 and q(2) = 0.73), indicating their predictive ability for untested compounds. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the information gathered from the 3D CoMFA and CoMSIA contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of cruzain inhibitors, and should be useful for the design of new structurally related analogs with improved potency. (C) 2009 Elsevier Inc. All rights reserved.

Structural basis for selective inhibition of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase: Molecular docking and 3D QSAR studies

The glycolytic enzyme glyceraldehyde-3 -phosphate dehydrogenase (GAPDH) is as an attractive target for the development of novel antitrypanosomatid agents. In the present work, comparative molecular field analysis and comparative molecular similarity index analysis were conducted on a large series of selective inhibitors of trypanosomatid GAPDH. Four statistically significant models were obtained (r(2) > 0.90 and q(2) > 0.70), indicating their predictive ability for untested compounds. The models were then used to predict the potency of an external test set, and the predicted values were in good agreement with the experimental results. Molecular modeling studies provided further insight into the structural basis for selective inhibition of trypanosomatid GAPDH.

Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4

Cytochrome P450 (CYP450) is a class of enzymes where the substrate identification is particularly important to know. It would help medicinal chemists to design drugs with lower side effects due to drug-drug interactions and to extensive genetic polymorphism. Herein, we discuss the application of the 2D and 3D-similarity searches in identifying reference Structures with higher capacity to retrieve Substrates of three important CYP enzymes (CYP2C9, CYP2D6, and CYP3A4). On the basis of the complementarities of multiple reference structures selected by different similarity search methods, we proposed the fusion of their individual Tanimoto scores into a consensus Tanimoto score (T(consensus)). Using this new score, true positive rates of 63% (CYP2C9) and 81% (CYP2D6) were achieved with false positive rates of 4% for the CYP2C9-CYP2D6 data Set. Extended similarity searches were carried out oil a validation data set, and the results showed that by using the T(consensus) score, not only the area of a ROC graph increased, but also more substrates were recovered at the beginning of a ranked list.

Software Tools For Large Scale Interactive Hydrodynamic Modeling

Running hydrodynamic models interactively allows both visual exploration and change of model state during simulation. One of the main characteristics of an interactive model is that it should provide immediate feedback to the user, for example respond to changes in model state or view settings. For this reason, such features are usually only available for models with a relatively small number of computational cells, which are used mainly for demonstration and educational purposes. It would be useful if interactive modeling would also work for models typically used in consultancy projects involving large scale simulations. This results in a number of technical challenges related to the combination of the model itself and the visualisation tools (scalability, implementation of an appropriate API for control and access to the internal state). While model parallelisation is increasingly addressed by the environmental modeling community, little effort has been spent on developing a high-performance interactive environment. What can we learn from other high-end visualisation domains such as 3D animation, gaming, virtual globes (Autodesk 3ds Max, Second Life, Google Earth) that also focus on efficient interaction with 3D environments? In these domains high efficiency is usually achieved by the use of computer graphics algorithms such as surface simplification depending on current view, distance to objects, and efficient caching of the aggregated representation of object meshes. We investigate how these algorithms can be re-used in the context of interactive hydrodynamic modeling without significant changes to the model code and allowing model operation on both multi-core CPU personal computers and high-performance computer clusters.

Structural deformation monitored by vibrational properties and orbital modeling in (Pb,Sm)TiO3 systems

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies

Tensor3D is a geometric modeling program with the capacity to simulate and visualize in real-time the deformation, specified through a tensor matrix and applied to triangulated models representing geological bodies. 3D visualization allows the study of deformational processes that are traditionally conducted in 2D, such as simple and pure shears. Besides geometric objects that are immediately available in the program window, the program can read other models from disk, thus being able to import objects created with different open-source or proprietary programs. A strain ellipsoid and a bounding box are simultaneously shown and instantly deformed with the main object. The principal axes of strain are visualized as well to provide graphical information about the orientation of the tensor's normal components. The deformed models can also be saved, retrieved later and deformed again, in order to study different steps of progressive strain, or to make this data available to other programs. The shape of stress ellipsoids and the corresponding Mohr circles defined by any stress tensor can also be represented. The application was written using the Visualization ToolKit, a powerful scientific visualization library in the public domain. This development choice, allied to the use of the Tcl/Tk programming language, which is independent on the host computational platform, makes the program a useful tool for the study of geometric deformations directly in three dimensions in teaching as well as research activities. (C) 2007 Elsevier Ltd. All rights reserved.

Turbulence modeling in engineering applications

A brief review is given of turbulence models in use today for engineering applications. The main categories covered are simple eddy-viscosity models, the k-ε two-equation model and Reynolds-stress-equation models as well as their algebraic stress derivatives. Calculation examples are presented for a variety of 2D and 3D flows.

Hyaluronidase from the venom of the social wasp Polybia paulista (Hymenoptera, Vespidae): Cloning, structural modeling, purification, and immunological analysis

In this study, we describe the cDNA cloning, sequencing, and 3-D structure of the allergen hyaluronidase from Polybia paulista venom (Pp-Hyal). Using a proteomic approach, the native form of Pp-Hyal was purified to homogeneity and used to produce a Pp-specific polyclonal antibody. The results revealed that Pp-Hyal can be classified as a glycosyl hydrolase and that the full-length Pp-Hyal cDNA (1315 bp; GI: 302201582) is similar (80-90%) to hyaluronidase from the venoms of endemic Northern wasp species. The isolated mature protein is comprised of 338 amino acids, with a theoretical pI of 8.77 and a molecular mass of 39,648.8 Da versus a pI of 8.13 and 43,277.0 Da indicated by MS. The Pp-Hyal 3D-structural model revealed a central core (α/β)7 barrel, two sulfide bonds (Cys 19-308 and Cys 185-197), and three putative glycosylation sites (Asn79, Asn187, and Asn325), two of which are also found in the rVes v 2 protein. Based on the model, residues Ser299, Asp107, and Glu109 interact with the substrate and potential epitopes (five conformational and seven linear) located at surface-exposed regions of the structure. Purified native Pp-Hyal showed high similarity (97%) with hyaluronidase from Polistes annularis venom (Q9U6V9). Immunoblotting analysis confirmed the specificity of the Pp-Hyal-specific antibody as it recognized the Pp-Hyal protein in both the purified fraction and P. paulista crude venom. No reaction was observed with the venoms of Apis mellifera, Solenopsis invicta, Agelaia pallipes pallipes, and Polistes lanio lanio, with the exception of immune cross-reactivity with venoms of the genus Polybia (sericea and ignobilis). Our results demonstrate cross-reactivity only between wasp venoms from the genus Polybia. The absence of cross-reactivity between the venoms of wasps and bees observed here is important because it allows identification of the insect responsible for sensitization, or at least of the phylogenetically closest insect, in order to facilitate effective immunotherapy in allergic patients. © 2013 Elsevier Ltd.

Modelagem numérica de dados MCSEM 3D usando computação paralela

Desenvolvemos a modelagem numérica de dados sintéticos Marine Controlled Source Electromagnetic (MCSEM) usada na exploração de hidrocarbonetos para simples modelos tridimensionais usando computação paralela. Os modelos são constituidos de duas camadas estrati cadas: o mar e o sedimentos encaixantes de um delgado reservatório tridimensional, sobrepostas pelo semi-espaço correspondente ao ar. Neste Trabalho apresentamos uma abordagem tridimensional da técnica dos elementos nitos aplicada ao método MCSEM, usando a formulação da decomposição primária e secundária dos potenciais acoplados magnético e elétrico. Num pós-processamento, os campos eletromagnéticos são calculados a partir dos potenciais espalhados via diferenciação numérica. Exploramos o paralelismo dos dados MCSEM 3D em um levantamento multitransmissor, em que para cada posição do transmissor temos o mesmo processo de cálculos com dados diferentes. Para isso, usamos a biblioteca Message Passing Interface (MPI) e o modelo servidor cliente, onde o processador administrador envia os dados de entradas para os processadores clientes computar a modelagem. Os dados de entrada são formados pelos parâmetros da malha de elementos nitos, dos transmissores e do modelo geoelétrico do reservatório. Esse possui geometria prismática que representa lentes de reservatórios de hidrocarbonetos em águas profundas. Observamos que quando a largura e o comprimento horizontais desses reservatório têm a mesma ordem de grandeza, as resposta in-line são muito semelhantes e conseqüentemente o efeito tridimensional não é detectado. Por sua vez, quando a diferença nos tamanhos da largura e do comprimento do reservatório é signi cativa o efeito 3D é facilmente detectado em medidas in-line na maior dimensão horizontal do reservatório. Para medidas na menor dimensão esse efeito não é detectável, pois, nesse caso o modelo 3D se aproxima de um modelo bidimensional. O paralelismo dos dados é de rápida implementação e processamento. O tempo de execução para a modelagem multitransmissor em ambiente paralelo é equivalente ao tempo de processamento da modelagem para um único transmissor em uma máquina seqüêncial, com o acréscimo do tempo de latência na transmissão de dados entre os nós do cluster, o que justi ca o uso desta metodologia na modelagem e interpretação de dados MCSEM. Devido a reduzida memória (2 Gbytes) em cada processador do cluster do departamento de geofísica da UFPA, apenas modelos muito simples foram executados.

Modelagens direta e inversa de dados mCSEM 3D

Marine Controlled Source Electromagnetic - mCSEM é um método geofísico eletromagnético que nos últimos dez anos vem sendo usado na prospecção de hidrocarbonetos com bastante êxito. Este método consiste em um dipolo elétrico horizontal (DEH) localizado um pouco acima do assoalho marinho, operando em baixa frequência (0,1-1,0 Hz) e receptores regularmente distribuídos no fundo do mar que captam os campos eletromagnéticos provenientes da difusão de energia gerada pelo dipolo transmissor. Neste trabalho vamos apresentar o problema direto do método mCSEM 3D, propondo soluções numéricas, através do método dos elementos finitos tridimensionais, para modelos geoelétricos mCSEM 3D. Para fins de análise de coerência, os resultados obtidos são comparados com soluções disponíveis na literatura. Em seguida, apresentaremos a inversão de um de seus modelos segundo uma proposta de metodologia de inversão juntamente com a proposta de solução direta para o mCSEM 3D, acima mencionada, realizando assim a inversão de um modelo geoelétrico do mCSEM 3D para duas frequências.

Representação e armazenamento de dados cadastrais 3D em banco de dados geográficos

Pós-graduação em Ciências Cartográficas - FCT

Evolução geomórfica e modelagem termocinemática 3D da região do planalto de Poços de Caldas (SP/MG)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelagem em 3D de uma patela humana e análise de esforços utilizando o método dos elementos finitos

Throughout the history of medicine surgeons realized the importance of the patella to the functioning of the knee. The main function of the patella is to increase the mechanical efficiency of the quadriceps tendon and knee extensor mechanism. It was found that 50% to 80% of the fractures without deviation of the patella have the transversal pattern, possibly due to excessive tensile forces applied to the extensor mechanism. The purpose of this study is to analyze the loads to which a patella is submitted during a normal extension movement of knee. This analysis will be done by modeling a 3D patella and subsequent load simulation as, described in medical literature, using the finite element method