How are close residues of protein structures distributed in primary sequence?

Structurally neighboring residues are categorized according to their separation in the primary sequence as proximal (1-4 positions apart) and otherwise distal, which in turn is divided into near (5-20 positions), far (21-50 positions), very far ( > 50 positions), and interchain (from different chains of the same structure). These categories describe the linear distance histogram (LDH) for three-dimensional neighboring residue types. Among the main results are the following: (i) nearest-neighbor hydrophobic residues tend to be increasingly distally separated in the linear sequence, thus most often connecting distinct secondary structure units. (ii) The LDHs of oppositely charged nearest-neighbors emphasize proximal positions with a subsidiary maximum for very far positions. (iii) Cysteine-cysteine structural interactions rarely involve proximal positions. (iv) The greatest numbers of interchain specific nearest-neighbors in protein structures are composed of oppositely charged residues. (v) The largest fraction of side-chain neighboring residues from beta-strands involves near positions, emphasizing associations between consecutive strands. (vi) Exposed residue pairs are predominantly located in proximal linear positions, while buried residue pairs principally correspond to far or very far distal positions. The results are principally invariant to protein sizes, amino acid usages, linear distance normalizations, and over- and underrepresentations among nearest-neighbor types. Interpretations and hypotheses concerning the LDHs, particularly those of hydrophobic and charged pairings, are discussed with respect to protein stability and functionality. The pronounced occurrence of oppositely charged interchain contacts is consistent with many observations on protein complexes where multichain stabilization is facilitated by electrostatic interactions.

Trapping of branched DNA in microfabricated structures.

We have observed electrostatic trapping of tribranched DNA molecules undergoing electrophoresis in a microfabricated pseudo-two-dimensional array of posts. Trapping occurs in a unique transport regimen in which the electrophoretic mobility is extremely sensitive to polymer topology. The arrest of branched polymers is explained by considering their center-of-mass motion; in certain conformations, owing to the constraints imposed by the obstacles a molecule cannot advance without the center of mass first moving a short distance backwards. The depth of the resulting local potential well can be much greater than the thermal energy so that escape of an immobilized molecule can be extremely slow. We summarize the expected behavior of the mobility as a function of field strength and topology and point out that the microfabricated arrays are highly suitable for detecting an extremely small number of branched molecules in a very large population of linear molecules.

Aplicações híbridas entre sistemas multiagentes e técnicas de inteligência artificial para redes inteligentes de distribuição de energia elétrica

Os smart grids representam a nova geração dos sistemas elétricos de potência, combinando avanços em computação, sistemas de comunicação, processos distribuídos e inteligência artificial para prover novas funcionalidades quanto ao acompanhamento em tempo real da demanda e do consumo de energia elétrica, gerenciamento em larga escala de geradores distribuídos, entre outras, a partir de um sistema de controle distribuído sobre a rede elétrica. Esta estrutura modifica profundamente a maneira como se realiza o planejamento e a operação de sistemas elétricos nos dias de hoje, em especial os de distribuição, e há interessantes possibilidades de pesquisa e desenvolvimento possibilitada pela busca da implementação destas funcionalidades. Com esse cenário em vista, o presente trabalho utiliza uma abordagem baseada no uso de sistemas multiagentes para simular esse tipo de sistema de distribuição de energia elétrica, considerando opções de controle distintas. A utilização da tecnologia de sistemas multiagentes para a simulação é baseada na conceituação de smart grids como um sistema distribuído, algo também realizado nesse trabalho. Para validar a proposta, foram simuladas três funcionalidades esperadas dessas redes elétricas: classificação de cargas não-lineares; gerenciamento de perfil de tensão; e reconfiguração topológica com a finalidade de reduzir as perdas elétricas. Todas as modelagens e desenvolvimentos destes estudos estão aqui relatados. Por fim, o trabalho se propõe a identificar os sistemas multiagentes como uma tecnologia a ser empregada tanto para a pesquisa, quanto para implementação dessas redes elétricas.

Desenvolvimento artificial autônomo de um grafo sensório-motor auto-organizável.

A teoria de Jean Piaget sobre o desenvolvimento da inteligência tem sido utilizada na área de inteligência computacional como inspiração para a proposição de modelos de agentes cognitivos. Embora os modelos propostos implementem aspectos básicos importantes da teoria de Piaget, como a estrutura do esquema cognitivo, não consideram o problema da fundamentação simbólica e, portanto, não se preocupam com os aspectos da teoria que levam à aquisição autônoma da semântica básica para a organização cognitiva do mundo externo, como é o caso da aquisição da noção de objeto. Neste trabalho apresentamos um modelo computacional de esquema cognitivo inspirado na teoria de Piaget sobre a inteligência sensório-motora que se desenvolve autonomamente construindo mecanismos por meio de princípios computacionais pautados pelo problema da fundamentação simbólica. O modelo de esquema proposto tem como base a classificação de situações sensório-motoras utilizadas para a percepção, captação e armazenamento das relações causais determiníscas de menor granularidade. Estas causalidades são então expandidas espaço-temporalmente por estruturas mais complexas que se utilizam das anteriores e que também são projetadas de forma a possibilitar que outras estruturas computacionais autônomas mais complexas se utilizem delas. O modelo proposto é implementado por uma rede neural artificial feed-forward cujos elementos da camada de saída se auto-organizam para gerar um grafo sensóriomotor objetivado. Alguns mecanismos computacionais já existentes na área de inteligência computacional foram modificados para se enquadrarem aos paradigmas de semântica nula e do desenvolvimento mental autônomo, tomados como base para lidar com o problema da fundamentação simbólica. O grafo sensório-motor auto-organizável que implementa um modelo de esquema inspirado na teoria de Piaget proposto neste trabalho, conjuntamente com os princípios computacionais utilizados para sua concepção caminha na direção da busca pelo desenvolvimento cognitivo artificial autônomo da noção de objeto.

Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae): adequação de uma dieta artificial e avaliação do seu controle biológico com Trichogramma pretiosum Riley em tomateiro

Tuta absoluta (Meyrick, 1917) é uma das pragas-chave da cultura do tomate e outras solanáceas na América do Sul e atualmente também na Eurásia e África. Devido aos grandes prejuízos que causa à cultura, são principalmente usados inseticidas para o seu controle. Entretanto, na busca de estratégias mais sustentáveis, cada dia adquire maior importância o uso do controle biológico, como uma das estratégias do manejo integrado de pragas. Para o desenvolvimento destas estratégias é fundamental desenvolver um método de criação de T. absoluta em laboratório, em dieta artificial, sem necessitar do hospedeiro natural, muitas vezes difícil de ser obtido e mantido em laboratório, e, de grande importância para produzir parasitoides específicos para esta praga. Dentre os parasitoides mais usados para ovos de lepidópteros está Trichogramma pretiosum Riley 1879 que é usado no controle biológico aplicado desta praga. Tendo como foco principal T. absoluta, neste trabalho foram pesquisados 1) a seleção de uma dieta artificial para este lepidóptero baseando-se em características físicas e químicas, avaliando o seu desempenho por várias gerações em laboratório, e 2) avaliação de aspectos biológicos e reprodutivos de T. pretiosum parasitando ovos de T. absoluta e aspectos físicos da planta (tricomas) para compreender o controle biológico desta praga no tomateiro. Foi encontrado que uma dieta à base de germe-de-trigo, caseína e celulose é apropriada para a criação deste lepidóptero, já que o inseto mostrou adaptação à mesma no transcorrer das gerações com base em características biológicas e de tabela de vida; adicionalmente, os ovos provenientes de T. absoluta alimentada com dieta artificial são comparáveis aos da dieta natural, no parasitismo de T. pretiosum. Com relação ao controle biológico foi demonstrado que este parasitoide desenvolvido em ovos de T. absoluta, diminui seu tamanho e desempenho com o transcorrer das gerações, apresentando menor capacidade de voo do que os insetos produzidos em A. kuenhiella, sendo necessária a liberação de altas densidades de parasitoides por ovo da praga. Foi observado que, embora o parasitismo de T. pretiosum de ovos de T. absoluta seja melhor em variedades com poucos tricomas, uma alta densidade destas estruturas não impede o controle da praga alvo dependendo da disposição destas estruturas. O controle biológico de T. absoluta com T. pretiosum tem uma ação momentânea, sendo necessárias liberações frequentes devido ao fato de os parasitoides desenvolvidos na praga serem menos competitivos com aqueles provenientes do hospedeiro alternativo que apresenta ovos maiores do que T. absoluta.

An hybrid parallel algorithm for solving tridiagonal linear systems versus the Wang’s method in a Cray T3D BSP computer

In this paper we describe an hybrid algorithm for an even number of processors based on an algorithm for two processors and the Overlapping Partition Method for tridiagonal systems. Moreover, we compare this hybrid method with the Partition Wang’s method in a BSP computer. Finally, we compare the theoretical computation cost of both methods for a Cray T3D computer, using the cost model that BSP model provides.

Control of Redundant Joint Structures Using Image Information During the Tracking of Non-Smooth Trajectories

Visual information is increasingly being used in a great number of applications in order to perform the guidance of joint structures. This paper proposes an image-based controller which allows the joint structure guidance when its number of degrees of freedom is greater than the required for the developed task. In this case, the controller solves the redundancy combining two different tasks: the primary task allows the correct guidance using image information, and the secondary task determines the most adequate joint structure posture solving the possible joint redundancy regarding the performed task in the image space. The method proposed to guide the joint structure also employs a smoothing Kalman filter not only to determine the moment when abrupt changes occur in the tracked trajectory, but also to estimate and compensate these changes using the proposed filter. Furthermore, a direct visual control approach is proposed which integrates the visual information provided by this smoothing Kalman filter. This last aspect permits the correct tracking when noisy measurements are obtained. All the contributions are integrated in an application which requires the tracking of the faces of Asperger children.

Direct Visual Servoing Framework based on Optimal Control for Redundant Joint Structures

This paper presents a new framework based on optimal control to define new dynamic visual controllers to carry out the guidance of any serial link structure. The proposed general method employs optimal control to obtain the desired behaviour in the joint space based on an indicated cost function which determines how the control effort is distributed over the joints. The proposed approach allows the development of new direct visual controllers for any mechanical joint system with redundancy. Finally, authors show experimental results and verifications on a real robotic system for some derived controllers obtained from the control framework.

Ecological effects of an artificial island, Rincon Island, Punta Gorda, California /

This study documents marine ecological conditions at Rincon Island, located approximately 0.8 kilometer offshore between Ventura and Santa Barbara, California, in a depth of 14 meters. The island, which was constructed between 1957 and 1958 to serve as a permanent platform for oil and gas production, is particularly suitable for ecological study. Habitat features associated with the armor rock and concrete tetrapods surrounding the island support a 'microecosystem' which differs in biotic composition from surrounding natural bottom areas. A major part of the study was devoted to analysis of seasonal dynamics in biotic composition. Permanent transects extending from the high intertidal to natural bottom were established normal to each of the four cardinal sides of the island. All macrobiota were censused in duplicate 1-square meter quadrats along each transect during each of the four seasons. Data analysis indicated that many species exhibit significant variability in abundance from one season to the next. In general, the findings indicate a rich and varied fauna and flora associated with the high-relief solid substrate of Rincon Island which differs substantially from the more depauperate natural bottom habitats in the area.

Beach changes at Long Beach Island, New Jersey, 1962-73 /

Beach profile line data collected from 32 profile sites along Long Beach Island, New Jersey. A total of 2,158 profile line surveys were examined, using empirical eigenfunction analysis and other measures of beach variability. Most profile lines have shown an accretionary trend since 1962 with rates between 2.3 and 0.24 meter per year in spite of erosion estimates due to sea level rise on the order of 0.68 meter per year. A great deal of variability in profile line change takes place along the beach, increasing from north to south, due to the location of profile lines relative to structures and offshore linear shoals. Detailed closely spaced profile lines taken over a year in a groin field near the north end of the island indicate littoral transport directions shift from north to south. Evidence of a littoral transport node near the north end of the groin field has been found. Net transport of the node is toward the south, but the rate could not be established due to lack of adequate wave data. Profile line variability within groin cells shows that single profile lines are not sufficient to determine the net change within a cell. The design of future beach monitoring studies should consider coastal structures, offshore bathymetry, the method of analysis, and the scales of processes under study. A coastal storm in November 1968 moved the MSL back as much as 22 meters; however, the beach recovered without artificial measures. The offshore bathymetry shows a series of shoreface-connected linear shoals at several locations along the island. Limited data show that these have remained stable and that most beach variability takes place in water shallower than 3 meters.

Engineering and ecological evaluation of artificial-island design, Rincon Island, Punta Gorda, California /

"March 1974."

RCS/linear discrete actuator study /

"AFAL-TR-88-039."

Hydraulic investigation for the construction of artificial islands in Peoria Lake : final report /

Prepared for Illinois Dept. of Energy and Natural Resources, Energy and Environmental Affairs Division.

In situ damage detection in frame structures through coupled response measurements

Due to the existence of global modes and local modes of the neighbouring members, damage detection on a structure is more challenging than damage on isolated beams. Detection of an artificial circumferential crack on a joint in a frame-like welded structure is studied in this paper using coupled response measurements. Similarity to real engineering structures is maintained in the fabrication of the test frame. Both the chords and the branch members have hollow sections and the branch members have smaller sizes. The crack is created by a hacksaw on a joint where a branch meets the chord. The methodology is first demonstrated on a single hollow section beam. The test results are then presented for the damaged and undamaged frame. The existence of the damage is clearly observable from the experimental results. It is suggested that this approach offers the-potential to detect damage in welded structures such as cranes, mining equipment, steel-frame bridges, naval and offshore structures. (C) 2003 Elsevier Ltd. All rights reserved.

Designing supramolecular structures from models of cyclic peptide scaffolds with heterocyclic constraints

Cyclic peptides containing oxazole and thiazole heterocycles have been examined for their capacity to be used as scaffolds in larger, more complex, protein-like structures. Both the macrocyclic scaffolds and the supramolecular structures derived therefrom have been visualised by molecular modelling techniques. These molecules are too symmetrical to examine structurally by NMR spectroscopy. The cyclic hexapeptide ([Aaa-Thz](3), [Aaa-Oxz](3)) and cyclic octapeptide ([Aaa-Thz](4), [Aaa-Oxz](4)) analogues are composed of dipeptide surrogates (Aaa: amino acid, Thz: thiazole, Oxz: oxazole) derived from intramolecular condensation of cysteine or serine/threonine side chains in dipeptides like Aaa-Cys, Aaa-Ser and Aaa-Thr. The five-membered heterocyclic rings, like thiazole, oxazole and reduced analogues like thiazoline, thiazolidine and oxazoline have profound influences on the structures and bioactivities of cyclic peptides derived therefrom. This work suggests that such constrained cyclic peptides can be used as scaffolds to create a range of novel protein-like supramolecular structures (e.g. cylinders, troughs, cones, multi-loop structures, helix bundles) that are comparable in size, shape and composition to bioactive surfaces of proteins. They may therefore represent interesting starting points for the design of novel artificial proteins and artificial enzymes. (C) 2002 Elsevier Science Inc. All rights reserved.