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 traditional heuristic algorithms on an initial genetic algorithm population applied to the transmission expansion planning problem

This paper analyses the impact of choosing good initial populations for genetic algorithms regarding convergence speed and final solution quality. Test problems were taken from complex electricity distribution network expansion planning. Constructive heuristic algorithms were used to generate good initial populations, particularly those used in resolving transmission network expansion planning. The results were compared to those found by a genetic algorithm with random initial populations. The results showed that an efficiently generated initial population led to better solutions being found in less time when applied to low complexity electricity distribution networks and better quality solutions for highly complex networks when compared to a genetic algorithm using random initial populations.

Vectorized algorithms for quadtree construction and descent

This paper presents vectorized methods of construction and descent of quadtrees that can be easily adapted to message passing parallel computing. A time complexity analysis for the present approach is also discussed. The proposed method of tree construction requires a hash table to index nodes of a linear quadtree in the breadth-first order. The hash is performed in two steps: an internal hash to index child nodes and an external hash to index nodes in the same level (depth). The quadtree descent is performed by considering each level as a vector segment of a linear quadtree, so that nodes of the same level can be processed concurrently. © 2012 Springer-Verlag.

Using Threads to Overcome Synchronization Delays in Parallel Multiple Progressive Alignment Algorithms

Sao Paulo State Research Foundation-FAPESP

Search schemes for random optimization algorithms that preserve the asymptotic distribution

Markovian algorithms for estimating the global maximum or minimum of real valued functions defined on some domain Omega subset of R-d are presented. Conditions on the search schemes that preserve the asymptotic distribution are derived. Global and local search schemes satisfying these conditions are analysed and shown to yield sharper confidence intervals when compared to the i.i.d. case.

Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach

Background: The tectum is a structure localized in the roof of the midbrain in vertebrates, and is taken to be highly conserved in evolution. The present article assessed three hypotheses concerning the evolution of lamination and citoarchitecture of the tectum of nontetrapod animals: 1) There is a significant degree of phylogenetic inertia in both traits studied (number of cellular layers and number of cell classes in tectum); 2) Both traits are positively correlated accross evolution after correction for phylogeny; and 3) Different developmental pathways should generate different patterns of lamination and cytoarchitecture.Methodology/Principal Findings: The hypotheses were tested using analytical-computational tools for phylogenetic hypothesis testing. Both traits presented a considerably large phylogenetic signal and were positively associated. However, no difference was found between two clades classified as per the general developmental pathways of their brains.Conclusions/Significance: The evidence amassed points to more variation in the tectum than would be expected by phylogeny in three species from the taxa analysed; this variation is not better explained by differences in the main course of development, as would be predicted by the developmental clade hypothesis. Those findings shed new light on the evolution of an functionally important structure in nontetrapods, the most basal radiations of vertebrates.

Beam Search Algorithms for Minimizing Tool Switches on a Flexible Manufacturing System

In the minimization of tool switches problem we seek a sequence to process a set of jobs so that the number of tool switches required is minimized. In this work different variations of a heuristic based on partial ordered job sequences are implemented and evaluated. All variations adopt a depth first strategy of the enumeration tree. The computational test results indicate that good results can be obtained by a variation which keeps the best three branches at each node of the enumeration tree, and randomly choose, among all active nodes, the next node to branch when backtracking.

Allocation of protective devices in distribution circuits using nonlinear programming models and genetic algorithms

The optimized allocation of protective devices in strategic points of the circuit improves the quality of the energy supply and the system reliability index. This paper presents a nonlinear integer programming (NLIP) model with binary variables, to deal with the problem of protective device allocation in the main feeder and all branches of an overhead distribution circuit, to improve the reliability index and to provide customers with service of high quality and reliability. The constraints considered in the problem take into account technical and economical limitations, such as coordination problems of serial protective devices, available equipment, the importance of the feeder and the circuit topology. The use of genetic algorithms (GAs) is proposed to solve this problem, using a binary representation that does (1) or does not (0) show allocation of protective devices (reclosers, sectionalizers and fuses) in predefined points of the circuit. Results are presented for a real circuit (134 busses), with the possibility of protective device allocation in 29 points. Also the ability of the algorithm in finding good solutions while improving significantly the indicators of reliability is shown. (C) 2003 Elsevier B.V. All rights reserved.

Multistage and coordinated planning of the expansion of transmission systems

In this paper, an efficient genetic algorithm (GA) is presented to solve the problem of multistage and coordinated transmission expansion planning. This is a mixed integer nonlinear programming problem, difficult for systems of medium and large size and high complexity. The GA presented has a set of specialized genetic operators and an efficient form of generation of the initial population that finds high quality suboptimal topologies for large size and high complexity systems. In these systems, multistage and coordinated planning present a lower investment than static planning. Tests results are shown in one medium complexity system and one large size high complexity system.

Frequency synthesizer using a hybrid analog/digital loop filter: A low complexity approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sistemas distribuídos aplicados à compressão e recuperação de imagens

Digital image processing is a field that demands great processing capacity. As such it becomes relevant to implement software that is based on the distribution of the processing into several nodes divided by computers belonging to the same network. Specifically discussed in this work are distributed algorithms of compression and expansion of images using the discrete cosine transform. The results show that the savings in processing time obtained due to the parallel algorithms in comparison to its sequential equivalents is a function that depends on the resolution of the image and the complexity of the involved calculation; that is efficiency is greater the longer the processing period is in terms of the time involved for the communication between the network points.

Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families

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

Natural and artificially-induced habitat complexity and freshwater fish species composition

The effects of habitat complexity, induced by construction of artificial reefs, on the fish assemblages in the Barra Bonita reservoir, Brazil, and in the lotic zone immediately below the dam were studied. Four artificial reefs were constructed in each habitat at variable distances from the shore. Multiple correspondence analysis showed that the factors distance from the shore and type of habitat were determinants for the group formation, and artificial reefs had a lesser effect. Fish species composition was about the same at locations with and without reefs.

Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a poly-isolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. (C) 2007 Elsevier B.V. All rights reserved.