Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.

Temperature effects on the mechanism of time independent hydrogen assisted fatigue crack propagation in steels

The effects of temperature on hydrogen assisted fatigue crack propagation are investigated in three steels in the low-to-medium strength range; a low alloy structural steel, a super duplex stainless steel, and a super ferritic stainless steel. Significant enhancement of crack growth rates is observed in hydrogen gas at atmospheric pressure in all three materials. Failure occurs via a mechanism of time independent, transgranular, cyclic cleavage over a frequency range of 0.1-5 Hz. Increasing the temperature in hydrogen up to 80°C markedly reduces the degree of embrittlement in the structural and super ferritic steels. No such effect is observed in the duplex stainless steel until the temperature exceeds 120°C. The temperature response may be understood by considering the interaction between absorbed hydrogen and micro-structural traps, which are generated in the zone of intense plastic deformation ahead of the fatigue crack tip. © 1992.

Intragranular nucleation of austenite

The mechanism of intragranular nucleation of austenite in a duplex stainless steel (Fe-23.1 Cr-6.1 Ni-3.1 Mo-O.165 N-0.017 C, wt.%) weld metal and heat-affected zone (HAZ) has been examined. In the weld metal the acicular austenite is found to nucleate intragranularly on inclusions and subsequent plates form sympathetically resulting in a fine interlocked microstructure. Austenite plates adopt the Kurdjumov-Sachs orientation relationship with the ferrite matrix and grow with diffusion-controlled mechanism as evident from partitioning of substitutional alloying elements. At least one set of fine intrinsic dislocations on the austenite/ferrite interphase interfaces is observed suggesting that the boundaries are semi-coherent. The high cooling rates involved in the HAZ result in a supersaturated ferrite matrix where precipitation of intragranular austenite occurs as a result of reheating associated with subsequent passes. Austenite particles in the HAZ nucleate preferentially away from gain boundary austenite allotriomorphs indicating that intragranular precipitation is favoured by the supersaturated matrix.

Ergodic Rates of the Fast Rayleigh Fading Relay Channel for Different Cooperative Strategies

ACM Computing Classification System (1998): E.4, C.2.1.

Application of Regularized Discriminant Analysis

2000 Mathematics Subject Classification: 62H30, 62P99

Proposal and design of phase-modulated fiber gratings in transmission for pulse shaping

A novel approach to pulse shaping using a phase-modulated fiber Bragg grating (FBG) in transmission is proposed and designed. We show that phase-modulated FBGs can provide transmission responses suitable for pulse shaping applications, offering important technological feasibility benefits, since the coupling strength remains basically uniform in the grating. Moreover, this approach retains the substantial advantages of FBGs in transmission, such as optimum energy efficiency, no requirement for an optical circulator, and robustness against fabrication errors.

Recanto do vale do pium: condomínio de habitações com ênfase no baixo impacto ambiental e no desempenho térmico do ambiente construído

This work describes the design process of a small recreational gated community in Pium, Nísia Floresta/RN, from concept to final design stages, with emphasis on low environmental impact, thermal comfort and the spatial quality of housing. The process consisted in a review of the literature and relevant standards, studies of design references and architectural programming. The project development was initially focused on the project’s feasibility, with the definition of the number of units, implantation, size and location of the dwellings and the common areas of the development. Two types of houses (four low rise and five duplex units) have been proposed in order to attend the premises of architectural programming. The conception of the architectural design began with the rooms’ zoning according to the lots. This resulted in the pre-selection of three alternatives that were evaluated in terms of spatial quality and environmental performance. The development of sketches focused on the envelope consistent with the bioclimatic guidelines and on the language of the compatible proposal with the lowest possible environmental impact of the building system, which resulted in the selection of the eucalyptus wood type. During the working drawings, the Quality Technical Regulation for the Level of Energy Efficiency Residential Buildings (RTQ -R) was adopted for the evaluation of the envelope, which resulted in "B" level of efficiency for the first case. After minor adjustments, mainly in frames, the efficiency level rose to "A", demonstrating that early project decisions contributed to the envelope energy performance. Besides the design of the two types of units, the final proposal of the gated community includes the design of the equipment for the common areas (entrance, multipurpose room and support and service sector), and the descriptive texts explaining the project and construction’s details.

Distribution of Upper Cretaceous deep water agglutinated foraminifera in sediments of the North Atlantic and its marginal seas (Tab. 1)

The stratigraphic and biogeographic distribution of more than 170 species of deep-water agglutinated benthic foraminifers (DWAF) from the North Atlantic and adjacent marginal seas has been compared with paleoenvironmental data (e.g. paleobathymetry, oxygenation of the bottom waters, amount of terrigenous input and substrate disturbance). Six general types of assemblages, in which deep water agglutinated taxa occur, are defined from the Turonian to Maastrichtian times: 1. High latitude slope assemblages 2. Low to mid latitude slope assemblages 3. Flysch-type assemblages 4. Deep water limestone assemblages (,,Scaglia,,-type) 5. Abyssal mixed calcareous-agglutinated assemblages 6. Abyssal purely agglutinated assemblages Latitudinal differences in faunal composition are observed, the most important of which is the lack or extreme paucity of calcareous forms in high latitude assemblages. East-to-west differences appear to be of comparatively minor importance. Most DWAF species occur in all studied regions and are thus considered as cosmopolitan. Biostratigraphic turnovers in the taxonomic content of assemblages are observed in the lowermost Turonian, mid-Campanian and in the upper Maastrichtian to lowermost Paleocene. These datum levels correspond to inter-regional and time-constant paleooceanographic events, which probably also affected the deep-water benthic biota. This allows us to use deep-water agglutinated foraminifers for biostratigraphy in the North Atlantic sequences deposited below CCD and to geographically extend the currently used zonal schemes which have been established in the Carpathian and Alpine areas.

Visualizing Rare Watson-Crick-Like Tautomeric and Anionic Mismatches in DNA and RNA

The central dogma of molecular biology relies on the correct Watson-Crick (WC) geometry of canonical deoxyribonucleic acid (DNA) dG•dC and dA•dT base pairs to replicate and transcribe genetic information with speed and an astonishing level of fidelity. In addition, the Watson-Crick geometry of canonical ribonucleic acid (RNA) rG•rC and rA•rU base pairs is highly conserved to ensure that proteins are translated with high fidelity. However, numerous other potential nucleobase tautomeric and ionic configurations are possible that can give rise to entirely new pairing modes between the nucleotide bases. Very early on, James Watson and Francis Crick recognized their importance and in 1953 postulated that if bases adopted one of their less energetically disfavored tautomeric forms (and later ionic forms) during replication it could lead to the formation of a mismatch with a Watson-Crick-like geometry and could give rise to “natural mutations.”

Since this time numerous studies have provided evidence in support of this hypothesis and have expanded upon it; computational studies have addressed the energetic feasibilities of different nucleobases’ tautomeric and ionic forms in siico; crystallographic studies have trapped different mismatches with WC-like geometries in polymerase or ribosome active sites. However, no direct evidence has been given for (i) the direct existence of these WC-like mismatches in canonical DNA duplex, RNA duplexes, or non-coding RNAs; (ii) which, if any, tautomeric or ionic form stabilizes the WC-like geometry. This thesis utilizes nuclear magnetic resonance (NMR) spectroscopy and rotating frame relaxation dispersion (R1ρ RD) in combination with density functional theory (DFT), biochemical assays, and targeted chemical perturbations to show that (i) dG•dT mismatches in DNA duplexes, as well as rG•rU mismatches RNA duplexes and non-coding RNAs, transiently adopt a WC-like geometry that is stabilized by (ii) an interconnected network of rapidly interconverting rare tautomers and anionic bases. These results support Watson and Crick’s tautomer hypothesis, but additionally support subsequent hypotheses invoking anionic mismatches and ultimately tie them together. This dissertation shows that a common mismatch can adopt a Watson-Crick-like geometry globally, in both DNA and RNA, and whose geometry is stabilized by a kinetically linked network of rare tautomeric and anionic bases. The studies herein also provide compelling evidence for their involvement in spontaneous replication and translation errors.