Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Wavelet-Galerkin method for one-dimensional elastoplasticity and damage problems: Constitutive modeling and computational aspects

This work presents an analysis of the wavelet-Galerkin method for one-dimensional elastoplastic-damage problems. Time-stepping algorithm for non-linear dynamics is presented. Numerical treatment of the constitutive models is developed by the use of return-mapping algorithm. For spacial discretization we can use wavelet-Galerkin method instead of standard finite element method. This approach allows to locate singularities. The discrete formulation developed can be applied to the simulation of one-dimensional problems for elastic-plastic-damage models. (C) 2007 Elsevier B.V. All rights reserved.

Growth mechanism of octahedron-like BaMoO4 microcrystals processed in microwave-hydrothermal: Experimental observations and computational modeling

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Re-examination of the anion derivatives of isoflavones by radical fragmentation in negative electrospray ionization tandem mass spectrometry: experimental and computational studies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Coexisting spatio-temporal scales in neuroscience

In this study I propose an epistemological discussion of multiple spatio-temporal scales in neuroscience. Are such scales merely convenient levels of description of structure and function, or do they correspond to irreducible levels of brain organization? What criteria should we employ in order to reduce one level to another, or to identify levels that are not reducible to others? Should we think of these criteria as based on empirical and/or theoretical reasons? Beginning with an empirical criterion - the necessity of different experimental methodologies for the measurement of different phenomena in the same system - I summarize spatial and temporal scales currently used in neuroscience and discuss the possibility of a more general theoretical criterion. I conclude that multiscaling should be recognized as a central concept in the epistemology of neuroscience.

Criteria for mixed grids in computational fluid dynamics

The finite volume method is used as a numerical method for solving the fluid flow equations. This method is appropriate to employ under structured and unstructured meshes. Mixed grids, combining both types of grids, are investigated. The coupling of different grids is done by overlapping strategy. The computational effort for the mixed grid is evaluated by the CPU-time, with different percentage of covering area of the unstructured mesh. The present scheme is tested for the driven cavity problem, where the incompressible fluid is integrated by calculating the velocity fields and computing the pressure field in each time step. Several schemes for unstructured grid are examined, and the compatibility condition is applied to check their consistency. A scheme to verify the compatibility condition for the unstructured grids is presented. (c) 2006 IMACS. Published by Elsevier B.V. All rights reserved.

Computational studies of the reversible domain swapping of p13suc1

A minimalist representation of protein structures using a Go- like potential for interactions is implemented to investigate the mechanisms of the domain swapping of p13suc1, a protein that exists in two native conformations: a monomer and a domain- swapped dimer formed by the exchange of a beta- strand. Inspired by experimental studies which showed a similarity of the transition states for folding of the monomer and the dimer, in this study we justify this similarity in molecular descriptions. When intermediates are populated in the simulations, formation of a domain- swapped dimer initiates from the ensemble of unfolded monomers, given by the fact that the dimer formation occurs at the folding/ unfolding temperature of the monomer ( T-f). It is also shown that transitions, leading to a dimer, involve the presence of two intermediates, one of them has a dimeric form and the other is monomeric; the latter is much more populated than the former. However, at temperatures lower than T-f, the population of intermediates decreases. It is argued that the two folded forms may coexist in absence of intermediates at a temperature much lower than T-f. Computational simulations enable us to find a mechanism, `` lock- and- dock'', for domain swapping of p13suc1. To explore the route toward dimer formation, the folding of unstructured monomers must be retarded by first locking one of the free ends of each chain. Then, the other free termini could follow and dock at particular regions, where most intrachain contacts are formed, and thus de. ne the transition states of the dimer. The simulations also showed that a decrease in the maximum distance between monomers increased their stability, which is explained based on confinement arguments. Although the simulations are based on models extracted from the native structure of the monomer and the dimer of p13suc1, the mechanism of the domain- swapping process could be general, not only for p13suc1.

Representation in cognitive neuroscience

This article discusses the possible representational nature of two brain cognitive functions: perceptual and executive. Assuming the Newellian definition of representational processes as those that establish an isomorphic relation between two structures, I claim that perceptual processes generate only a partial correspondence (between stimuli properties and brain states) and therefore should not be properly conceived as representational. on the other hand, executive processes encompass the combination of copies (i.e., representations) of perceptual patterns, generating new patterns that subserve behavior. In summary, I criticize the notion of perceptual representations, and propose that brain representational processes are related to executive functions, having a pragmatic dimension.

Computational Aspects of the Calculation of Isometry Groups in General Relativity

We describe the ideas behind the package 'isometry', implemented in Maple to calculate isometry groups of dimensions 2, 3 and 4 in General Relativity. The package extends the functionality of previous programs written to perform invariant classification of space-times in General Relativity. Programming solutions used to surmount problems encountered with the calculation of eigenvectors and the determination of the signs of expressions are described. We also show how the package can be used to find the Killing vectors of a space-time.

A joint computational and experimental study of a novel dioxomolybdenum(VI) complex bearing chiral N,N-dimethyllactamide ligand

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Exploring the binding mechanism of Guaijaverin to human serum albumin: Fluorescence spectroscopy and computational approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sensitivity of AMPA receptor channel to calcium oscillations: A computational study

We used a computational model of biochemical pathways that are involved in the phosphorylation/dephosphorylation of AMPA receptor to study the receptor responses to calcium oscillations. In the model, the biochemical pathways are assumed to be located immediately under the postsynaptic membrane and we included three states of AMPA receptor: dephosphorylated, and phosphorylated in one or in two sites. To characterize the effects of calcium oscillations on the AMPA receptor, we exposed the model to stimuli with three varying parameters, namely frequency, number of pulses and calcium spike duration. Our model showed sensitivity to all of these three parameters. © 2002 Elsevier Science B.V. All rights reserved.

Computational linguistic systematization of a lexicon from the ibitinga embroidery industry conceptual domain

This work discusses a proposition for organizing the lexical items from the conceptual domain labeled THE EMBROIDERY INDUSTRY OF IBITINGA in terms of a natural ontology. It also aims to establish the alignment between this ontology and the bases WordNet.Pr and WordNet.Br. © 2009 IEEE.