Automatic layout generation of static CMOS circuits targeting delay and power

The evolution of integrated circuits technologies demands the development of new CAD tools. The traditional development of digital circuits at physical level is based in library of cells. These libraries of cells offer certain predictability of the electrical behavior of the design due to the previous characterization of the cells. Besides, different versions of each cell are required in such a way that delay and power consumption characteristics are taken into account, increasing the number of cells in a library. The automatic full custom layout generation is an alternative each time more important to cell based generation approaches. This strategy implements transistors and connections according patterns defined by algorithms. So, it is possible to implement any logic function avoiding the limitations of the library of cells. Tools of analysis and estimate must offer the predictability in automatic full custom layouts. These tools must be able to work with layout estimates and to generate information related to delay, power consumption and area occupation. This work includes the research of new methods of physical synthesis and the implementation of an automatic layout generation in which the cells are generated at the moment of the layout synthesis. The research investigates different strategies of elements disposition (transistors, contacts and connections) in a layout and their effects in the area occupation and circuit delay. The presented layout strategy applies delay optimization by the integration with a gate sizing technique. This is performed in such a way the folding method allows individual discrete sizing to transistors. The main characteristics of the proposed strategy are: power supply lines between rows, over the layout routing (channel routing is not used), circuit routing performed before layout generation and layout generation targeting delay reduction by the application of the sizing technique. The possibility to implement any logic function, without restrictions imposed by a library of cells, allows the circuit synthesis with optimization in the number of the transistors. This reduction in the number of transistors decreases the delay and power consumption, mainly the static power consumption in submicrometer circuits. Comparisons between the proposed strategy and other well-known methods are presented in such a way the proposed method is validated.

Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis

Eukaryotic translation initiation factor 5A (eIF5A) is a protein that is highly conserved and essential for cell viability. This factor is the only protein known to contain the unique and essential amino acid residue hypusine. This work focused on the structural and functional characterization of Saccharomyces cerevisiae eIF5A. The tertiary structure of yeast eIF5A was modeled based on the structure of its Leishmania mexicana homologue and this model was used to predict the structural localization of new site-directed and randomly generated mutations. Most of the 40 new mutants exhibited phenotypes that resulted from eIF-5A protein-folding defects. Our data provided evidence that the C-terminal alpha-helix present in yeast eIF5A is an essential structural element, whereas the eIF5A N-terminal 10 amino acid extension not present in archaeal eIF5A homologs, is not. Moreover, the mutants containing substitutions at or in the vicinity of the hypusine modification site displayed nonviable or temperature-sensitive phenotypes and were defective in hypusine modification. Interestingly, two of the temperature-sensitive strains produced stable mutant eIF5A proteins - eIF5A(K56A) and eIF5A(Q22H,L93F)- and showed defects in protein synthesis at the restrictive temperature. Our data revealed important structural features of eIF5A that are required for its vital role in cell viability and underscored an essential function of eIF5A in the translation step of gene expression.

Análises estratigráfica e estrutural da Seção Rifte (Valanginiano ao Barremiano) na área do levantamento sísmico 3D de baixo vermelho, Bacia Potiguar emersa

Baixo Vermelho area, situated on the northern portion of Umbuzeiro Graben (onshore Potiguar Basin), represents a typical example of a rift basin, characterized, in subsurface, by the sedimentary rift sequence, correlated to Pendência Formation (Valanginian-Barremian), and by the Carnaubais fault system. In this context, two main goals, the stratigraphic and the structural analysis, had guided the research. For this purpose, it was used the 3D seismic volume and eight wells located in the study area and adjacencies. The stratigraphic analysis of the Valanginian-Barremian interval was carried through in two distinct phases, 1D and 2D, in which the basic concepts of the sequence stratigraphy had been adapted. In these phases, the individual analysis of each well and the correlation between them, allowed to recognize the main lithofacies, to interpret the effective depositional systems and to identify the genetic units and key-surfaces of chronostratigraphic character. The analyzed lithofacies are represented predominantly by conglomerates, sandstones, siltites and shales, with carbonate rocks and marls occurring subordinately. According to these lithofacies associations, it is possible to interpret the following depositional systems: alluvial fan, fluvio-deltaic and lacustrine depositional systems. The alluvial fan system is mainly composed by conglomerates deposits, which had developed, preferentially in the south portion of the area, being directly associated to Carnaubais fault system. The fluvial-deltaic system, in turn, was mainly developed in the northwest portion of the area, at the flexural edge, being characterized by coarse sandstones with shales and siltites intercalated. On the other hand, the lacustrine system, the most dominant one in the study area, is formed mainly by shales that could occur intercalated with thin layers of fine to very fine sandstones, interpreted as turbidite deposits. The recognized sequence stratigraphy units in the wells are represented by parasequence sets, systems tracts and depositional sequences. The parasequence sets, which are progradational or retrogradational, had been grouped and related to the systems tracts. The predominance of the progradation parasequence sets (general trend with coarsening-upward) characterizes the Regressive Systems Tract, while the occurrence, more frequently, of the retrogradation parasequence sets (general trend with finning-upward) represents the Transgressive System Tract. In the seismic stratigraphic analysis, the lithofacies described in the wells had been related to chaotic, progradational and parallel/subparallel seismic facies, which are associated, frequently, to the alluvial fans, fluvial-deltaic and lacustrine depositional systems, respectively. In this analysis, it was possible to recognize fifteen seismic horizons that correspond to sequence boundaries and to maximum flooding surfaces, which separates Transgressive to Regressive systems tracts. The recognition of transgressive-regressive cycles allowed to identify nine, possibly, 3a order deposicional sequences, related to the tectonic-sedimentary cycles. The structural analysis, in turn, was done at Baixo Vermelho seismic volume, which shows, clearly, the structural complexity printed in the area, mainly related to Carnaubais fault system, acting as an important fault system of the rift edge. This fault system is characterized by a main arrangement of normal faults with trend NE-SO, where Carnaubais Fault represents the maximum expression of these lineations. Carnaubais Fault corresponds to a fault with typically listric geometry, with general trend N70°E, dipping to northwest. It is observed, throughout all the seismic volume, with variations in its surface, which had conditioned, in its evolutive stages, the formation of innumerable structural features that normally are identified in Pendencia Formation. In this unit, part of these features is related to the formation of longitudinal foldings (rollover structures and distentional folding associated), originated by the displacement of the main fault plan, propitiating variations in geometry and thickness of the adjacent layers, which had been deposited at the same time. Other structural features are related to the secondary faultings, which could be synthetic or antithetic to Carnaubais Fault. In a general way, these faults have limited lateral continuity, with listric planar format and, apparently, they play the role of the accomodation of the distentional deformation printed in the area. Thus, the interaction between the stratigraphic and structural analysis, based on an excellent quality of the used data, allowed to get one better agreement on the tectonicsedimentary evolution of the Valanginian-Barremian interval (Pendência Formation) in the studied area

Análise da deformação pós-Rifte na Bacia do Araripe, Nordeste do Brasil

The Araripe Basin is located over Precambrian terrains of the Borborema Province, being part of Northeast Brazil inner basins. Its origin is related to the fragmentation of the Gondwana supercontinent and consequently opening of South Atlantic during early Cretaceous. The basin has a sedimentary infill encompassing four distinct evolution stages, comprising Paleozoic syneclisis, pre-rift, rift and post-rift. The target of this study comprises the post-rift section of the basin focusing deformational styles which affect evaporates from Ipubi Member of the Santana Formation, which is composed by gypsum and anidrite layers interbedded with shales. These units occur widespread across the basin. In the central part of the basin, near Nova Olinda-Santana do Cariri, evaporites are affected by an essentialy brittle deformation tipified by fibrous gypsum filled fractures, cutting massive layers of gypsum and anidrite. Veins with variable orientations and dips are observed in the region distributed over three main populations: i) a dominant NWSE with shallow to moderate NE dipping population, consisting of gypsum filled veins in which fibers are normal to vein walls; i) NE-SW veins with moderate SE dips containing subhorizontal growth fibers; and iii) N-S veins with shallow E-W dips with fibers oblique to vein walls. In the west portion of the basin, near Trindade-Ipubi-Araripina towns, evaporate layers are dominantly constituted by gypsum/anidrite finely stratified, showing a minor density of veins. These layers are affected by a unique style of deformation, more ductile, typified by gentle to open horizontal normal folding with several tens of meters length and with double plunging NW-SE or NE-SW hinges, configuring domic features. In detail, gypsum/anidrite laminae are affected by metre to decimeter scale close to tight folding, usually kinked, with broken hinges, locally turning into box folds. Veins show NE-SW main directions with shallow NE dips, growth fibers are parallel to vein walls, constituting slickenfibers. This region is marked by faults that affect Araripina Formation with NW-SE, NE-SW and E-W directions. The main structural styles and general orientations of structures which affected the post-rift section of Araripe Basin yielded important kinematic information analysis which led us to infer a E-W to NE-SW extension direction to the northeastern part of the Basin, whereas in the southeastern part, extension occurred in N-S direction. Thus, it was possible to determine a regional kinematic setting, through this analysis, characterizing a NE-SW to ENE-WSW system for the post-rift section, which is compatible with the tension settings for the Sout American Plate since Albian. Local variations at the fluid pressure linked (or not) to sedimentary overload variation define local tension settings. This way, at the northeastern portion of the basin, the post-rift deformation was governed by a setting which σ 1 is sub-horizontal trending NE-SW and, σ 3 is sub-vertical, emphasizing a reverse fault situation. At the southwestern portion however there was characterized a strike slip fault setting, featuring σ 1 trending ENEWSW and σ3 trending NNW-SSE

Aplicação da modelagem estrutural computacional direta na análise da geometria de falhas: exemplo da falha de Baixa Grande (Bacia Potiguar - NE do Brasil)

The Baixa grande fault is located on the edge of the S-SW Potiguar Rift. It limits the south part of Umbuzeiro Graben and the Apodi Graben. Although a number of studies have associated the complex deformation styles in the hanging wall of the Baixa Grande Fault with geometry and displacement variations, none have applied the modern computational techniques such as geometrical and kinematic validations to address this problem. This work proposes a geometric analysis of the Baixa Fault using seismic interpretation. The interpretation was made on 3D seismic data of the Baixa Grande fault using the software OpendTect (dGB Earth Sciences). It was also used direct structural modeling, such as Analog Direct Modeling know as Folding Vectors and, 2D and 3D Direct Computational Modeling. The Folding Vectors Modeling presented great similarity with the conventional structural seismic interpretations of the Baixa Grande Fault, thus, the conventional interpretation was validated geometrically. The 2D direct computational modeling was made on some sections of the 3D data of the Baixa Grande Fault on software Move (Midland Valley Ltd) using the horizon modeling tool. The modeling confirms the influence of fault geometry on the hanging wall. The Baixa Grande Fault ramp-flat-ramp geometry generates synform on the concave segments of the fault and antiform in the convex segments. On the fault region that does not have segments angle change, the beds are dislocated without deformation, and on the listric faults occur rollover. On the direct 3D computational modeling, structural attributes were obtained as horizons on the hanging wall of the main fault, after the simulation of several levels of deformation along the fault. The occurrence of structures that indicates shortening in this modeling, also indicates that the antiforms on the Baixa Grande Fault were influenced by fault geometry

Propriedades mecânicas do cimento ósseo e da poliuretana de mamona com e sem catalisador

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural alterations in the seminiferous tubules of rats treated with immunosuppressor tacrolimus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular characterization and phylogenetic analysis of JussuMP-I: A RGD-P-III class hemorrhagic metalloprotease from Bothrops jararacussu snake venom

Snake venom metalloproteases (SVMPs) embody zinc-dependent multidomain enzymes responsible for a relevant pathophysiology in envenomation. including local and systemic hemorrhage. The molecular features responsible for hemorrhagic potency of SVMPs have been associated with their multidomains structures which can target these proteins them to several receptors of different tissues and cellular types. BjussuMP-I. a SVMP isolated from the Bothrops jararacussu venom, has been characterized as a P-III hemorrhagic metalloprotease. The complete cDNA sequence of BjussuMP-I with 1641bp encodes open reading frames of 547 amino acid residues, which conserve the common domains of P-III high molecular weight hemorrhagic metalloproteases: (i) pre-pro-peptide, (ii) metalloprotease, (iii) disintegrin-like and (iv) rich cysteine domain. BjussuMP-I induced lyses in fibrin clots and inhibited collagen- and ADP-induced platelet aggregation. We are reporting, for the first time, the primary structure of an RGD-P-III class snake venom metalloprotease. A phylogenetic analysis of the BjussuMP-1 metalloprotease/catalytic domain was performed to get new insights into the molecular evolution of the metalloproteases. A theoretical molecular model of this domain was built through folding recognition (threading) techniques and refined by molecular dynamics simulation. Then, the final BjussuMP-I catalytic domain model was compared to other SVMPs and Reprolysin family proteins in order to identify eventual structural differences, which could help to understand the biochemical activities of these enzymes. The presence of large hydrophobic areas and some conserved surface charge-positive residues were identified as important features of the SVMPs and other metalloproteases. (C) 2006 Elsevier B.V. All rights reserved.

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

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

Crystallographic structure of PNP from Mycobacterium tuberculosis at 1.9 angstrom resolution

Even being a bacterial purine nucleoside phosphorylase (PNP), which normally shows hexameric folding, the Mycobacterium tuberculosis PNP (MtPNP) resembles the mammalian trimeric structure. The crystal structure of the MtPNP apoenzyme was solved at 1.9 Angstrom resolution. The present work describes the first structure of MtPNP in complex with phosphate. In order to develop new insights into the rational drug design, conformational changes were profoundly analyzed and discussed. Comparisons over the binding sites were specially studied to improve the discussion about the selectivity of potential new drugs. (C) 2004 Elsevier B.V. All rights reserved.

Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

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

The phylogenetic relationships of the charismatic poster frogs, Phyllomedusinae (Anura, Hylidae)

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

Nonlocal description of the nuclear interaction

Extensive systematizations of theoretical and experimental nuclear densities and of optical potential strengths extracted from heavy-ion elastic scattering data analyses at low and intermediate energies are presented. The energy-dependence of the nuclear potential is accounted for within a model based on the nonlocal nature of the interaction. The systematics indicates that the heavy-ion nuclear potential can be described in a simple global way through a double-folding shape, which basically depends only on the density of nucleons of the partners in the collision. The possibility of extracting information about the nucleon-nucleon interaction from the heavy-ion potential is investigated.