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.

Lessons of spin and torsion: Reply to Consistent coupling to Dirac fields in teleparallelism

In reply to the criticism made by Mielke in the preceding Comment on our recent paper, we once again explicitly demonstrate the inconsistency of the coupling of a Dirac field to gravitation in the teleparallel equivalent of general relativity. Moreover, we stress that the mentioned inconsistency is generic for all sources with spin and is by no means restricted to the Dirac field. In this sense the SL(4,R)-covariant generalization of the spinor fields in the teleparallel gravity theory is irrelevant to the inconsistency problem.

On an Optimal Linear Control Applied to a Non-Ideal Load Transportation System, Modeled with Periodic Coefficients

In this paper, a load transportation system in platforms or suspended by cables is considered. It is a monorail device and is modelled as an inverted pendulum built on a car driven by a DC motor. The governing equations of motion were derived via Lagrange's equations. In the mathematical model we consider the interaction between the DC motor and the dynamical system, that is, we have a so-called non-ideal periodic problem. The problem is analysed and we also developed an optimal linear control design to stabilize the problem.

Métodos de geração de colunas para problemas de atribuição

Este trabalho apresenta métodos de geração de colunas para dois importantes problemas de atribuição: o Problema Generalizado de Atribuição (PGA) e o Problema de Atribuição de Antenas a Comutadores (PAAC). O PGA é um dos mais representativos problemas de Otimização Combinatória e consiste em otimizar a atribuição de n tarefas a m agentes, de forma que cada tarefa seja atribuída a exatamente um agente e a capacidade de cada agente seja respeitada. O PAAC consiste em atribuir n antenas a m comutadores em uma rede de telefonia celular, de forma a minimizar os custos de cabeamento entre antenas e comutadores e os custos de transferência de chamadas entre comutadores. A abordagem tradicional de geração de colunas é comparada com as propostas neste trabalho, que utilizam a relaxação lagrangeana/surrogate. São apresentados testes computacionais que demonstram a efetividade dos algoritmos propostos.

Relax and fix heuristics to solve one-stage one-machine lot-scheduling models for small-scale soft drink plants

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

An evolutionary algorithm for the one-dimensional cutting stock problem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Optimal control problem for deflection plate with crack

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the resolution of the generalized nonlinear complementarity problem

Minimization of a differentiable function subject to box constraints is proposed as a strategy to solve the generalized nonlinear complementarity problem (GNCP) defined on a polyhedral cone. It is not necessary to calculate projections that complicate and sometimes even disable the implementation of algorithms for solving these kinds of problems. Theoretical results that relate stationary points of the function that is minimized to the solutions of the GNCP are presented. Perturbations of the GNCP are also considered, and results are obtained related to the resolution of GNCPs with very general assumptions on the data. These theoretical results show that local methods for box-constrained optimization applied to the associated problem are efficient tools for solving the GNCP. Numerical experiments are presented that encourage the use of this approach.

Alocação de zeros aplicada a sistemas de controle via LMI

A systematic procedure of zero placement to design control systems is proposed. A state feedback controller with vector gain K is used to perform the pole placement. An estimator with vector gain L is also designed for output feedback control. A new systematic method of zero assignment to reduce the effect of the undesirable poles of the plant and also to increase the velocity error constant is presented. The methodology places the zeros in a specific region and it is based on Linear Matrix Inequalities (LMIs) framework, which is a new approach to solve this problem. Three examples illustrate the effectiveness of the proposed method.

Meta-heuristic approaches for a soft drink industry problem

The present paper evaluates meta-heuristic approaches to solve a soft drink industry problem. This problem is motivated by a real situation found in soft drink companies, where the lot sizing and scheduling of raw materials in tanks and products in lines must be simultaneously determined. Tabu search, threshold accepting and genetic algorithms are used as procedures to solve the problem at hand. The methods are evaluated with a set of instance already available for this problem. This paper also proposes a new set of complex instances. The computational results comparing these approaches are reported. © 2008 IEEE.

An application of a modified constructive heuristic algorithm to transmission expansion planning

Transmission expansion planning (TEP) is a non-convex optimization problem that can be solved via different heuristic algorithms. A variety of classical as well as heuristic algorithms in literature are addressed to solve TEP problem. In this paper a modified constructive heuristic algorithm (CHA) is proposed for solving such a crucial problem. Most of research papers handle TEP problem by linearization of the non-linear mathematical model while in this research TEP problem is solved via CHA using non-linear model. The proposed methodology is based upon Garver's algorithm capable of applying to a DC model. Simulation studies and tests results on the well known transmission network such as: Garver and IEEE 24-bus systems are carried out to show the significant performance as well as the effectiveness of the proposed algorithm. © 2011 IEEE.

Application of ontologies in peer-to-peer database with routing queries based on ant colony algorithm

A significant set of information stored in different databases around the world, can be shared through peer-topeer databases. With that, is obtained a large base of knowledge, without the need for large investments because they are used existing databases, as well as the infrastructure in place. However, the structural characteristics of peer-topeer, makes complex the process of finding such information. On the other side, these databases are often heterogeneous in their schemas, but semantically similar in their content. A good peer-to-peer databases systems should allow the user access information from databases scattered across the network and receive only the information really relate to your topic of interest. This paper proposes to use ontologies in peer-to-peer database queries to represent the semantics inherent to the data. The main contribution of this work is enable integration between heterogeneous databases, improve the performance of such queries and use the algorithm of optimization Ant Colony to solve the problem of locating information on peer-to-peer networks, which presents an improve of 18% in results. © 2011 IEEE.

Domain reduction using GRASP construction phase for transmission expansion planning problem

This paper proposes a new strategy to reduce the combinatorial search space of a mixed integer linear programming (MILP) problem. The construction phase of greedy randomized adaptive search procedure (GRASP-CP) is employed to reduce the domain of the integer variables of the transportation model of the transmission expansion planning (TM-TEP) problem. This problem is a MILP and very difficult to solve specially for large scale systems. The branch and bound (BB) algorithm is used to solve the problem in both full and the reduced search space. The proposed method might be useful to reduce the search space of those kinds of MILP problems that a fast heuristic algorithm is available for finding local optimal solutions. The obtained results using some real test systems show the efficiency of the proposed method. © 2012 Springer-Verlag.

A social network approach to trust management in VANETs

In the past few years, vehicular ad hoc networks(VANETs) was studied extensively by researchers. VANETs is a type of P2P network, though it has some distinct characters (fast moving, short lived connection etc.). In this paper, we present several limitations of current trust management schemes in VANETs and propose ways to counter them. We first review several trust management techniques in VANETs and argue that the ephemeral nature of VANETs render them useless in practical situations. We identify that the problem of information cascading and oversampling, which commonly arise in social networks, also adversely affects trust management schemes in VANETs. To the best of our knowledge, we are the first to introduce information cascading and oversampling to VANETs. We show that simple voting for decision making leads to oversampling and gives incorrect results in VANETs. To overcome this problem, we propose a novel voting scheme. In our scheme, each vehicle has different voting weight according to its distance from the event. The vehicle which is more closer to the event possesses higher weight. Simulations show that our proposed algorithm performs better than simple voting, increasing the correctness of voting. © 2012 Springer Science + Business Media, LLC.

Particle competition and cooperation to prevent error propagation from mislabeled data in semi-supervised learning

Semi-supervised learning is applied to classification problems where only a small portion of the data items is labeled. In these cases, the reliability of the labels is a crucial factor, because mislabeled items may propagate wrong labels to a large portion or even the entire data set. This paper aims to address this problem by presenting a graph-based (network-based) semi-supervised learning method, specifically designed to handle data sets with mislabeled samples. The method uses teams of walking particles, with competitive and cooperative behavior, for label propagation in the network constructed from the input data set. The proposed model is nature-inspired and it incorporates some features to make it robust to a considerable amount of mislabeled data items. Computer simulations show the performance of the method in the presence of different percentage of mislabeled data, in networks of different sizes and average node degree. Importantly, these simulations reveals the existence of the critical points of the mislabeled subset size, below which the network is free of wrong label contamination, but above which the mislabeled samples start to propagate their labels to the rest of the network. Moreover, numerical comparisons have been made among the proposed method and other representative graph-based semi-supervised learning methods using both artificial and real-world data sets. Interestingly, the proposed method has increasing better performance than the others as the percentage of mislabeled samples is getting larger. © 2012 IEEE.