Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.

Electronic properties of graphene grain boundaries

Grain boundaries and defect lines in graphene are intensively studied for their novel electronic and magnetic properties. However, there is not a complete comprehension of the appearance of localized states along these defects. Graphene grain boundaries are herein seen as the outcome of matching two semi-infinite graphene sheets with different edges. We classify the energy spectra of grain boundaries into three different types, directly related to the combination of the four basic classes of spectra of graphene edges. From the specific geometry of the grains, we are able to obtain the band structure and the number of localized states close to the Fermi energy. This provides a new understanding of states localized at grain boundaries, showing that they are derived from the edge states of graphene. Such knowledge is crucial for the ultimate tailoring of electronic and optoelectronic applications.

On contractive cyclic fuzzy maps in metric spaces and some related results on fuzzy best proximity points and fuzzy fixed points

This paper investigates some properties of cyclic fuzzy maps in metric spaces. The convergence of distances as well as that of sequences being generated as iterates defined by a class of contractive cyclic fuzzy mapping to fuzzy best proximity points of (non-necessarily intersecting adjacent subsets) of the cyclic disposal is studied. An extension is given for the case when the images of the points of a class of contractive cyclic fuzzy mappings restricted to a particular subset of the cyclic disposal are allowed to lie either in the same subset or in its next adjacent one.

A Terapia de Exposição com Realidade Virtual para pacientes com TEPT controlada por um Sistema de Lógica Fuzzy

Nos últimos anos, a área da saúde vem explorando o potencial das novas tecnologias para diagnóstico e tratamentos de muitos distúrbios. Em especial, a tecnologia de Realidade Virtual se destaca por oferecer novas perspectivas de tratamento para diferentes distúrbios neuropsiquiátricos. Por outro lado, a ocorrência de problemas causados por situações traumáticas vem crescendo em todo o mundo. Nesse contexto, o Transtorno de Estresse Pós-Traumático (TEPT) é classificado como um transtorno de ansiedade que se caracteriza por gerar uma classe de comportamentos inadequados a situações que não representam perigo real. Em geral, este transtorno está relacionado à ocorrência de algum evento traumático de grande magnitude no passado. Vários trabalhos foram desenvolvidos utilizando ambientes virtuais tridimensionais (3D) para tratar e diagnosticar este distúrbio. Entretanto, percebe-se uma carência de sistemas que consigam controlar o nível de dificuldade das atividades desenvolvidas nesses ambientes. Nesse caso, esta dissertação tem por objetivo descrever o desenvolvimento e avaliar o potencial de utilização de dois sistemas: um que explora a Realidade Virtual (ARVET) para oferecer cenas virtuais que simulem os estímulos geradores de ansiedade similares aqueles da vida real; e outro que explora a Lógica Fuzzy (SAPTEPT) para classificar os níveis de ansiedade do paciente, possibilitando a análise quali-quantitativa de dados psicofisiológicos e psicométricos. As avaliações realizadas com especialistas na área mostraram que o ARVET pode proporcionar um alto grau de estímulos ansiogênicos e a integração com o SAPTEPT ocorreu de forma satisfatória mostrando o potencial que os sistemas têm de serem utilizados em pacientes reais.

Sources of variability in the free-ball micro-scale abrasion test

In the 'free-ball' version of the micro-scale abrasion or ball-cratering test the rotating ball rests against a tilted sample and a grooved drive shaft. Tests under nominally identical conditions with different apparatus commonly show small but significant differences in measured wear rate. An indirect method has been developed and demonstrated for continuous on-line measurement of the coefficient of friction in the free-ball test. Experimental investigation of the effects of sample tilt angle and drive shaft groove width shows that both these factors influence the stability of the rotation of the ball, and the shape of the abrasive slurry pool, which in turn affect the coefficient of friction in the wear scar area and the measured wear rate. It is suggested that in order to improve the reproducibility of this method the geometry of the apparatus should be specified. For the apparatus used in this work with a steel ball of 25 mm diameter, a sample tilt angle of 60-75° and a shaft groove width of about 10mm provided the most stable ball motion and a wear rate which showed least variability. © 2004 Elsevier B.V. All rights reserved.

Síntese de árvores de padrões Fuzzy através de Programação Genética Cartesiana.

Esta dissertação apresenta um sistema de indução de classificadores fuzzy. Ao invés de utilizar a abordagem tradicional de sistemas fuzzy baseados em regras, foi utilizado o modelo de Árvore de Padrões Fuzzy(APF), que é um modelo hierárquico, com uma estrutura baseada em árvores que possuem como nós internos operadores lógicos fuzzy e as folhas são compostas pela associação de termos fuzzy com os atributos de entrada. O classificador foi obtido sintetizando uma árvore para cada classe, esta árvore será uma descrição lógica da classe o que permite analisar e interpretar como é feita a classificação. O método de aprendizado originalmente concebido para a APF foi substituído pela Programação Genética Cartesiana com o intuito de explorar melhor o espaço de busca. O classificador APF foi comparado com as Máquinas de Vetores de Suporte, K-Vizinhos mais próximos, florestas aleatórias e outros métodos Fuzzy-Genéticos em diversas bases de dados do UCI Machine Learning Repository e observou-se que o classificador APF apresenta resultados competitivos. Ele também foi comparado com o método de aprendizado original e obteve resultados comparáveis com árvores mais compactas e com um menor número de avaliações.

Evolution of the tectogene concept, 1930-1965

The tectogene, or crustal downbuckle, was proposed in the early 1930s by F.A. Vening Meinesz to explain the unexpected belts of negative gravity anomalies in island arcs. He attributed the isostatic imbalance to a deep sialic root resulting from the action of subcrustal convection currents. Vening Meinesz's model was initially corroborated experimentally by P.H. Kuenen, but additional experiments by D.T. Griggs and geological analysis by H.H. Hess in the late 1930s led to substantial revision in detail. As modified, the tectogene provided a plausible model for the evolution of island arcs into alpine mountain belts for another two decades. Additional revisions became necessary in the early 1950s to accommodate the unexpected absence of sialic crust in the Caribbean and the marginal seas of the western Pacific. By 1960 the cherished analogy between island arcs and alpine mountain belts had collapsed under the weight of the detailed field investigations by Hess and his students in the Caribbean region. Hess then incorporated a highly modified form of the tectogene into his sea-floor spreading hypothesis. Ironically, this final incarnation of the concept preserved some of the weaker aspects of the 1930s original, such as the ad hoc explanation for the regular geometry of island arcs.

The calculation of acoustic shielding of engine noise by the Silent Aircraft Airframe

The Silent Aircraft airframe has a flying wing design with a large wing planform and a propulsion system embedded in the rear of the airframe with intake on the upper surface of the wing. In the present paper, boundary element calculations are presented to evaluate acoustic shielding at low frequencies. Besides the three-dimensional geometry of the Silent Aircraft airframe, a few two-dimensional problems are considered that provide some physical insight into the shielding calculations. Mean flow refraction effects due to forward flight motion are accounted for by a simple time transformation that decouples the mean-flow and acoustic-field calculations. It is shown that significant amount of shielding can be obtained in the shadow region where there is no direct line of sight between the source and observer. The boundary element solutions are restricted to low frequencies. We have used a simple physically-based model to extend the solution to higher frequencies. Based on this model, using a monopole acoustic source, we predict at least an 18 dBA reduction in the overall sound pressure level of forward-propagating fan noise because of shielding.

The development of turbine exit flow in a swan-necked inter-stage diffuser

This paper describes both the migration and dissipation of flow phenomena downstream of a transonic high-pressure turbine stage. The geometry of the HP stage exit duct considered is a swan-necked diffuser similar to those likely to be used in future engine designs. The paper contains results both from an experimental programme in a turbine test facility and from numerical predictions. Experimental data was acquired using three fast-response aerodynamic probes capable of measuring Mach number, whirl angle, pitch angle, total pressure and static pressure. The probes were used to make time-resolved area traverses at two axial locations downstream of the rotor trailing edge. A 3D time-unsteady viscous Navier-Stokes solver was used for the numerical predictions. The unsteady exit flow from a turbine stage is formed from rotordependent phenomena (such as the rotor wake, the rotor trailing edge recompression shock, the tip-leakage flow and the hub secondary flow) and vane-rotor interaction dependant phenomena. This paper describes the time-resolved behaviour and three-dimensional migration paths of both of these phenomena as they convect downstream. It is shown that the inlet flow to a downstream vane is dominated by two corotating vortices, the first caused by the rotor tip-leakage flow and the second by the rotor hub secondary flow. At the inlet plane of the downstream vane the wake is extremely weak and the radial pressure gradient is shown to have caused the majority of the high loss wake fluid to be located between the mid-height of the passage and the casing wall. The structure of the flow indicates that between a high pressure stage and a downstream vane simple two-dimensional blade row interaction does not occur. The results presented in this paper indicate that the presence of an upstream stage is likely to significantly alter the structure of the secondary flow within a downstream vane. The paper also shows that vane-rotor interaction within the upstream stage causes a 10° circumferential variation in the inlet flow angle of the 2nd stage vane.

Development of blade profiles for low pressure turbine applications

This paper describes a program of work, largely experimental, which was undertaken with the objective of developing an improved blade profile for the low-pressure turbine in aero-engine applications. Preliminary experiments were conducted using a novel technique. An existing cascade of datum blades was modified to enable the pressure distribution on the suction surface of one of the blades to be altered. Various means, such as shaped inserts, an adjustable flap at the trailing edge, and changing stagger were employed to change the geometry of the passage. These experiments provided boundary layer and lift data for a wide range of suction surface pressure distributions. The data was then used as a guide for the development of new blade profiles. The new blade profiles were then investigated in a low-speed cascade that included a set of moving bars upstream of the cascade of blades to simulate the effect of the incoming wakes from the previous blade row in a multistage turbine environment.

Effect of size, morphology and crystallinity of seed crystal on the nucleation and growth of single grain Y-Ba-Cu-O

The effect of size, morphology and crystallinity of seed crystals on the nucleation and growth of large grain Y-Ba-Cu-O (YBCO) bulk superconductors fabricated by top seeded melt growth (TSMG) has been investigated. Seeding bulk samples with small, square shaped seed crystals leads to point nucleation and growth of the superconducting YBa2Cu3O7-y (Y-123) phase that exhibits the usual square habitual growth symmetry. The use of triangular and circular shaped seed crystals, however, modifies significantly the growth habit geometry of the grain. The use of large area seeds both increases the rate of epitaxial nucleation of the Y-123 phase and produces relatively large crystals in the incongruent melt, which decreases significantly the processing times of large grain samples. The present study is relevant to decrease processing times of samples with both preferred or no growth sectors and for multiple seeding of large grain samples which contain clean grain boundaries. © 2005 Published by Elsevier Ltd.

A new alternative for reduction of secondary flows in low pressure turbines

This paper describes a new flow mechanism for the reduction of secondary flows in Low Pressure Turbines using the benefit of contoured endwalls. The extensive application of contoured endwalls in recent years has provided a deeper understanding of the physical phenomenon that governs the reduction of secondary flows. Based on this understanding, the endwall geometry of a linear cascade of solid-thin profiles typical of Low Pressure Turbines has been redesigned. Experimental data are presented for the validation of this new solution. Based on these data, a reduction of 72% in the SKEH and 20% in the mixed-out endwall losses can be obtained. CFD simulations are also presented to illustrate the effect of the new endwall on the secondary flows. Furthermore, an explanation of the flow mechanism that governs the reduction of the SKEH and the losses is given. Copyright © 2006 by ASME.

Design, development, and evaluation of a simple blackbody radiative source

This paper presents a simple design and the testing of a blackbody prototype. The physical properties and geometry of the cavity produce a radiator or blackbody with an emissivity greater than 0.99. The prototype has the advantages of having a traditional spherical cavity made of alumina refractory cement and a radiative emission very close to that of an ideal blackbody. The prototype can be used as a calibration standard for other radiation measuring instruments or sensors. Experimental measurements of radiant flux of the prototype measured with a calibrated infrared radiometer and a wide spectrum radiometer are also presented. The prototype is easy to construct and the material required are available to most research centers, laboratories, industries, and universities. © 2010 American Institute of Physics.

A comparison of two models for the vibration response of piled foundations to inertial and underground-railway-induced loadings

The vibration response of piled foundations due to ground-borne vibration produced by an underground railway is a largely-neglected area in the field of structural dynamics. However, this continues to be an important aspect of research as it is expected that the presence of piled foundations can have a significant influence on the propagation and transmission of the wavefield produced by the underground railway. This paper presents a comparison of two methods that can be employed in calculating the vibration response of a piled foundation: an efficient semi-analytical model, and a Boundary Element model. The semi-analytical model uses a column or an Euler beam to model the pile, and the soil is modelled as a linear, elastic continuum that has the geometry of a thick-walled cylinder with an infinite outer radius and an inner radius equal to the radius of the pile. The boundary element model uses a constant-element BEM formulation for the halfspace, and a rectangular discretisation of the circular pile-soil interface. The piles are modelled as Timoshenko beams. Pile-soil-pile interactions are inherently accounted for in the BEM equations, whereas in the semi-analytical model these are quantified using the superposition of interaction factors. Both models use the method of joining subsystems to incorporate the incident wavefield generated by the underground railway into the pile model. Results are computed for a single pile subject to an inertial loading, pile-soil-pile interactions, and a pile group subjected to excitation from an underground railway. The two models are compared in terms of accuracy, computation time, versatility and applicability, and guidelines for future vibration prediction models involving piled foundations are proposed.