Crystal structure, DNA binding studies, nucleolytic property and topoisomerase I inhibition of zinc complex with 1,10-phenanthroline and 3-methyl-picolinic acid

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

System identification and active vibration control of a flexible structure

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

An algorithm for arranging response surface designs in small blocks

We consider the problem of blocking response surface designs when the block sizes are prespecified to control variation efficiently and the treatment set is chosen independently of the block structure. We show how the loss of information due to blocking is related to scores defined by Mead and present an interchange algorithm based on scores to improve a given blocked design. Examples illustrating the performance of the algorithm are given and some comparisons with other designs are made. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Intermolecular interactions and characterization of the novel factor Xa exosite involved in macromolecular recognition and inhibition: Crystal structure of human Gla-domainless factor Xa complexed with the anticoagulant protein NAPc2 from the hematophagous nematode Ancylostoma caninum

NAPc2, an anticoagulant protein from the hematophagous nematode Ancylostoma caninum evaluated in phase-II/IIa clinical trials, inhibits the extrinsic blood coagulation pathway by a two step mechanism, initially interacting with the hitherto uncharacterized factor Xa exosite involved in macromolecular recognition and subsequently inhibiting factor VIIa (K-i = 8.4 pM) of the factor VIIa/tissue factor complex. NAPc2 is highly flexible, becoming partially ordered and undergoing significant structural changes in the C terminus upon binding to the factor Xa exosite. In the crystal structure of the ternary factor Xa/NAPc2/selectide complex, the binding interface consists of an intermolecular antiparallel beta-sheet formed by the segment of the polypeptide chain consisting of residues 74-80 of NAPc2 with the residues 86-93 of factor Xa that is additional maintained by contacts between the short helical segment (residues 67-73) and a turn (residues 26-29) of NAPc2 with the short C-terminal helix of factor Xa (residues 233-243). This exosite is physiologically highly relevant for the recognition and inhibition of factor X/Xa by macromolecular substrates and provides a structural motif for the development of a new class of inhibitors for the treatment of deep vein thrombosis and angioplasty. (c) 2006 Elsevier Ltd. All rights reserved.

Use of genetic algorithms and solvation potential to study peptides structure

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains and implicit solvation potential are used to optimize the tertiary structure of peptides. We starting from the known PDB structure of its backbone which is kept fixed while the side chains allowed adopting the conformations present in the rotamer library. It was used rotamer library independent of backbone and a implicit solvation potential. The structure of Mastoporan-X was predicted using several force fields with a growing complexity; we started it with a field where the only present interaction was Lennard-Jones. We added the Coulombian term and we considered the solvation effects through a term proportional to the solvent accessible area. This paper present good and interesting results obtained using the potential with solvation term and rotamer library. Hence, the algorithm (called YODA) presented here can be a good tool to the prediction problem. (c) 2007 Elsevier B.V. All rights reserved.

Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Combining genetic algorithm and simulated annealing: A molecular geometry optimization study

We introduce a new hybrid approach to determine the ground state geometry of molecular systems. Firstly, we compared the ability of genetic algorithm (GA) and simulated annealing (SA) to find the lowest energy geometry of silicon clusters with six and 10 atoms. This comparison showed that GA exhibits fast initial convergence, but its performance deteriorates as it approaches the desired global extreme. Interestingly, SA showed a complementary convergence pattern, in addition to high accuracy. Our new procedure combines selected features from GA and SA to achieve weak dependence on initial parameters, parallel search strategy, fast convergence and high accuracy. This hybrid algorithm outperforms GA and SA by one order of magnitude for small silicon clusters (Si6 and Si10). Next, we applied the hybrid method to study the geometry of a 20-atom silicon cluster. It was able to find an original geometry, apparently lower in energy than those previously described in literature. In principle, our procedure can be applied successfully to any molecular system. © 1998 Elsevier Science B.V.

The substitution of cations by magnesium in the structure K3Ho(VO4)2

The cation substitutions in the crystal lattice of binary potassium-holmium vanadate (V) K3Ho(VO4)2 by magnesium have been studied using various types of chemical solid state reactions. It was shown that in the presence of the quasi-ternary system K3VO4-Mg3(VO4)2-HoVO 4 at 700°C there a compound defined as K3Ho(VO4)2 with a narrow homogeneity range where K and Ho are partially substituted by Mg in accordance with various schemes. © 1998 Published by Elsevier Science S.A.

Damage detection in a benchmark structure using AR-ARX models and statistical pattern recognition

Structural health monitoring (SHM) is related to the ability of monitoring the state and deciding the level of damage or deterioration within aerospace, civil and mechanical systems. In this sense, this paper deals with the application of a two-step auto-regressive and auto-regressive with exogenous inputs (AR-ARX) model for linear prediction of damage diagnosis in structural systems. This damage detection algorithm is based on the. monitoring of residual error as damage-sensitive indexes, obtained through vibration response measurements. In complex structures there are. many positions under observation and a large amount of data to be handed, making difficult the visualization of the signals. This paper also investigates data compression by using principal component analysis. In order to establish a threshold value, a fuzzy c-means clustering is taken to quantify the damage-sensitive index in an unsupervised learning mode. Tests are made in a benchmark problem, as proposed by IASC-ASCE with different damage patterns. The diagnosis that was obtained showed high correlation with the actual integrity state of the structure. Copyright © 2007 by ABCM.

Distribution network reconfiguration using an efficient evolutionary algorithm

Network reconfiguration is an important tool to optimize the operating conditions of a distribution system. This is accomplished modifying the network structure of distribution feeders by changing the open/close status of sectionalizing switches. This not only reduces the power losses, but also relieves the overloading of the network components. Network reconfiguration belongs to a complex family of problems because of their combinatorial nature and multiple constraints. This paper proposes a solution to this problem, using a specialized evolutionary algorithm, with a novel codification, and a brand new way of implement the genetic operators considering the problem characteristics. The algorithm is presented and tested in a real distribution system, showing excellent results and computational efficiency. © 2007 IEEE.

Variable structure control of switched systems based on Lyapunov-Metzler-SPR systems

This paper presents two Variable Structure Controllers (VSC) for continuous-time switched plants. It is assumed that the state vector is available for feedback. The proposed control system provides a switching rule and also the variable structure control input. The design is based on Lyapunov-Metzler (LM) inequalities and also on Strictly Positive Real (SPR) systems stability results. The definition of Lyapunov-Metzler-SPR (LMS) systems and its direct application in the design of VSC for switched systems are introduced in this paper. Two examples illustrate the design of the proposed VSC, considering a plant given by a switched system with a switched-state control law and two linear time-invariant systems, that are not controllable and also can not be stabilized with state feedback. ©2008 IEEE.

Evaluating genetic algorithms with different population structures on a lot sizing and scheduling problem

This paper studies the use of different population structures in a Genetic Algorithm (GA) applied to lot sizing and scheduling problems. The population approaches are divided into two types: single-population and multi-population. The first type has a non-structured single population. The multi-population type presents non-structured and structured populations organized in binary and ternary trees. Each population approach is tested on lot sizing and scheduling problems found in soft drink companies. These problems have two interdependent levels with decisions concerning raw material storage and soft drink bottling. The challenge is to simultaneously determine the lot sizing and scheduling of raw materials in tanks and products in lines. Computational results are reported allowing determining the better population structure for the set of problem instances evaluated. Copyright 2008 ACM.

Monitoramento da queima da peça no processo de retificação plana baseado no estudo espectral do sinal de emissão acústica com implementação por hardware

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Effects of environmental factors on community structure of Leptophlebiidae (Insecta, Ephemeroptera) in Cerrado streams, Brazil

O efeito de fatores ambientais sobre a abundância, riqueza de espécies e grupos funcionais alimentares de Leptophlebiidae foi analisado em 16 locais pertencentes a quatro córregos de Cerrado, a partir de coletas de substrato em três períodos de 2005. Foram amostradas 5.492 larvas distribuídas em 14 espécies, classificadas em três grupos funcionais alimentares: raspadores, coletores-filtradores e fragmentadores. A abundância e riqueza de espécies não foram afetadas por nenhum dos fatores ambientais investigados, mas a integridade dos hábitats exerceu efeito positivo sobre a abundância dos fragmentadores, consequência da intrínseca interação desses organismos com a mata ciliar. Dessa forma, acreditamos que este trabalho agrega informações bioecológicas sobre as espécies e grupos funcionais de insetos aquáticos e poderá contribuir no monitoramento e conservação de riachos do Cerrado.

Global optimization using a genetic algorithm with hierarchically structured population

This paper applies a genetic algorithm with hierarchically structured population to solve unconstrained optimization problems. The population has individuals distributed in several overlapping clusters, each one with a leader and a variable number of support individuals. The hierarchy establishes that leaders must be fitter than its supporters with the topological organization of the clusters following a tree. Computational tests evaluate different population structures, population sizes and crossover operators for better algorithm performance. A set of known benchmark test problems is solved and the results found are compared with those obtained from other methods described in the literature, namely, two genetic algorithms, a simulated annealing, a differential evolution and a particle swarm optimization. The results indicate that the method employed is capable of achieving better performance than the previous approaches in regard as the two criteria usually employed for comparisons: the number of function evaluations and rate of success. The method also has a superior performance if the number of problems solved is taken into account. (C) 2013 Elsevier B.V. All rights reserved.