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.

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.

Simulation of computational grids scheduling politics

Computational grids allow users to share resources of distributed machines, even if those machines belong to different corporations. The scheduling of applications must be performed aiming at performance goals, and focusing on choose which processes can have access to specif resources, and which resources. In this article we discuss aspects of scheduling of application in grid computing environment. We also present a tool for scheduling simulation along with test scenarios and results.

Integrated X-ray crystallography, optical and computational methods in studies of structure and luminescence of new synthesized complexes of lanthanides with ligands derived from 2,6-diformylpyridine

The reaction of 2,6-diformylpyridine-bis(benzoylhydrazone) [dfpbbh] and 2,6-diformylpyridine-bis(4-phenylsemicarbazone) [dfpbpsc] with lanthanides salts yielded the new chelates complexes [Eu(dfpbpsc-H +) 2]NO 3 (1), [Dy(fbhmp) 2][Dy(dfpbbh-2H +) 2]·2EtOH·2H 2O (fbhmp = 2-formylbenzoylhydrazone-6-methoxide-pyridine; Ph = phenyl; Py = pyridine; Et = ethyl) and [Er 2(dfpbbh-2H +) 2(μ-NO 3)(H 2O) 2(OH)]·H 2O. X-ray diffraction analysis was employed for the structural characterization of the three chelate complexes. In the case of complex 1, optical, synthetic and computational methods were also exploited for ground state structure determinations and triplet energy level of the ligand and HOMO-LUMO calculations, as well as for a detailed study of its luminescence properties. © 2010 Elsevier Ltd. All rights reserved.

Methodology analysis of a computational tool used in electronic circuit design

This paper considers the importance of using a top-down methodology and suitable CAD tools in the development of electronic circuits. The paper presents an evaluation of the methodology used in a computational tool created to support the synthesis of digital to analog converter models by translating between different tools used in a wide variety of applications. This tool is named MS 2SV and works directly with the following two commercial tools: MATLAB/Simulink and SystemVision. Model translation of an electronic circuit is achieved by translating a mixed-signal block diagram developed in Simulink into a lower level of abstraction in VHDL-AMS and the simulation project support structure in SystemVision. The method validation was performed by analyzing the power spectral of the signal obtained by the discrete Fourier transform of a digital to analog converter simulation model. © 2011 IEEE.

Computational tool to support design of DAC Converter model AD7528 with the object code in XML

Based on literature review, electronic systems design employ largely top-down methodology. The top-down methodology is vital for success in the synthesis and implementation of electronic systems. In this context, this paper presents a new computational tool, named BD2XML, to support electronic systems design. From a block diagram system of mixed-signal is generated object code in XML markup language. XML language is interesting because it has great flexibility and readability. The BD2XML was developed with object-oriented paradigm. It was used the AD7528 converter modeled in MATLAB / Simulink as a case study. The MATLAB / Simulink was chosen as a target due to its wide dissemination in academia and industry. From this case study it is possible to demonstrate the functionality of the BD2XML and make it a reflection on the design challenges. Therefore, an automatic tool for electronic systems design reduces the time and costs of the design.

Computational support for the process of software requirement specification

The software industry has become more and more concerned with the appropriate application of activities that composes requirement engineering as a way to improve the quality of its products. In order to support these activities, several computational tools have been available in the market, although it is still possible to find a lack of resources related to some activities. In this context, this paper proposes the inclusion of a module to aid in the requirements specification to a tool called Requirements Elicitation Support Tool. This module allows to specify requirements in accordance with IEEE 830 standard, thus contributing to the documentation of the requirements established for a software system, besides supporting the learning of concepts related to the requirements specification, which improves the skills of users of the tool. © 2012 IEEE.

Exploring the multifactorial nature of autism through computational systems biology: Calcium and the Rho GTPase RAC1 under the spotlight

Autism is a neurodevelopmental disorder characterized by impaired social interaction and communication accompanied with repetitive behavioral patterns and unusual stereotyped interests. Autism is considered a highly heterogeneous disorder with diverse putative causes and associated factors giving rise to variable ranges of symptomatology. Incidence seems to be increasing with time, while the underlying pathophysiological mechanisms remain virtually uncharacterized (or unknown). By systematic review of the literature and a systems biology approach, our aims were to examine the multifactorial nature of autism with its broad range of severity, to ascertain the predominant biological processes, cellular components, and molecular functions integral to the disorder, and finally, to elucidate the most central contributions (genetic and/or environmental) in silico. With this goal, we developed an integrative network model for gene-environment interactions (GENVI model) where calcium (Ca2+) was shown to be its most relevant node. Moreover, considering the present data from our systems biology approach together with the results from the differential gene expression analysis of cerebellar samples from autistic patients, we believe that RAC1, in particular, and the RHO family of GTPases, in general, could play a critical role in the neuropathological events associated with autism. © 2013 Springer Science+Business Media New York.

Simplified computational routine to correct the modal decoupling in transmission lines and power systems modelling

Modal analysis is widely approached in the classic theory of power systems modelling. This technique is also applied to model multiconductor transmission lines and their self and mutual electrical parameters. However, this methodology has some particularities and inaccuracies for specific applications, which are not clearly described in the technical literature. This study provides a brief review on modal decoupling applied in transmission line digital models and thereafter a novel and simplified computational routine is proposed to overcome the possible errors embedded by the modal decoupling in the simulation/ modelling computational algorithm. © The Institution of Engineering and Technology 2013.

On computational aspects of discrete Sobolev inner products on the unit circle

In this paper, we show how to compute in O(n2) steps the Fourier coefficients associated with the Gelfand-Levitan approach for discrete Sobolev orthogonal polynomials on the unit circle when the support of the discrete component involving derivatives is located outside the closed unit disk. As a consequence, we deduce the outer relative asymptotics of these polynomials in terms of those associated with the original orthogonality measure. Moreover, we show how to recover the discrete part of our Sobolev inner product. © 2013 Elsevier Inc. All rights reserved.

Development of computational 3D MoM algorithm for nanoplasmonics

In this paper, we present an algorithm for full-wave electromagnetic analysis of nanoplasmonic structures. We use the three-dimensional Method of Moments to solve the electric field integral equation. The computational algorithm is developed in the language C. As examples of application of the code, the problems of scattering from a nanosphere and a rectangular nanorod are analyzed. The calculated characteristics are the near field distribution and the spectral response of these nanoparticles. The convergence of the method for different discretization sizes is also discussed.