Evidence for nonrandom hydrophobicity structures in protein chains.

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistically significant way. By performing Fourier transforms on the random walks, one obtains additional evidence for nonrandomness of the distributions. We have also analyzed results from a synthetic model containing only two amino acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from some previous investigations using other methods, might have impact on how permissive with respect to sequence specificity protein folding process is-only sequences with nonrandom hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.

Can fractal-like spectra be experimentally observed in aperiodic superlattices?

We numerically investigate the effects of inhomogeneities in the energy spectrum of aperiodic semiconductor superlattices, focusing our attention on Thue-Morse and Fibonacci sequences. In the absence of disorder, the corresponding electronic spectra are self-similar. The presence of a certain degree of randomness, due to imperfections occurring during the growth processes, gives rise to a progressive loss of quantum coherence, smearing out the finer details of the energy spectra predicted for perfect aperiodic superlattices and spurring the onset of electron localization. However, depending on the degree of disorder introduced, a critical size for the system exists, below which peculiar transport properties, related to the pre-fractal nature of the energy spectrum, may be measured.

Excitations in Bose-Einstein condensates: collective modes, quantum turbulence and matter wave statistics

In this thesis, we present the generation and studies of a 87Rb Bose-Einstein condensate (BEC) perturbed by an oscillatory excitation. The atoms are trapped in a harmonic magnetic trap where, after an evaporative cooling process, we produce the BEC. In order to study the effect caused by oscillatory excitations, a quadrupole magnetic field time oscillatory is superimposed to the trapping potential. Through this perturbation, collective modes were observed. The dipole mode is excited even for low excitation amplitudes. However, a minimum excitation energy is needed to excite the condensate quadrupole mode. Observing the excited cloud in TOF expansion, we note that for excitation amplitude in which the quadrupole mode is excited, the cloud expands without invert its aspect ratio. By looking these clouds, after long time-of-flight, it was possible to see vortices and, sometimes, a turbulent state in the condensed cloud. We calculated the momentum distribution of the perturbed BECs and a power law behavior, like the law to Kolmogorov turbulence, was observed. Furthermore, we show that using the method that we have developed to calculate the momentum distribution, the distribution curve (including the power law exponent) exhibits a dependence on the quadrupole mode oscillation of the cloud. The randomness distribution of peaks and depletions in density distribution image of an expanded turbulent BEC, remind us to the intensity profile of a speckle light beam. The analogy between matter-wave speckle and light speckle is justified by showing the similarities in the spatial propagation (or time expansion) of the waves. In addition, the second order correlation function is evaluated and the same dependence with distance was observed for the both waves. This creates the possibility to understand the properties of quantum matter in a disordered state. The propagation of a three-dimensional speckle field (as the matter-wave speckle described here) creates an opportunity to investigate the speckle phenomenon existing in dimensions higher than 2D (the case of light speckle).

Modelagem estocástica da dispersão axial: aplicação em um reator tubular de polimerização.

Reatores tubulares de polimerização podem apresentar um perfil de velocidade bastante distorcido. Partindo desta observação, um modelo estocástico baseado no modelo de dispersão axial foi proposto para a representação matemática da fluidodinâmica de um reator tubular para produção de poliestireno. A equação diferencial foi obtida inserindo a aleatoriedade no parâmetro de dispersão, resultando na adição de um termo estocástico ao modelo capaz de simular as oscilações observadas experimentalmente. A equação diferencial estocástica foi discretizada e resolvida pelo método Euler-Maruyama de forma satisfatória. Uma função estimadora foi desenvolvida para a obtenção do parâmetro do termo estocástico e o parâmetro do termo determinístico foi calculado pelo método dos mínimos quadrados. Uma análise de convergência foi conduzida para determinar o número de elementos da discretização e o modelo foi validado através da comparação de trajetórias e de intervalos de confiança computacionais com dados experimentais. O resultado obtido foi satisfatório, o que auxilia na compreensão do comportamento fluidodinâmico complexo do reator estudado.

Efeito da corrosão do chapeamento do fundo do casco sobre a confiabilidade estrutural de navios.

A engenharia é a ciência que transforma os conhecimentos das disciplinas básicas aplicadas a fatos reais. Nosso mundo está rodeado por essas realizações da engenharia, e é necessário que as pessoas se sintam confortáveis e seguras nas mesmas. Assim, a segurança se torna um fator importante que deve ser considerado em qualquer projeto. Na engenharia naval, um apropriado nível de segurança e, em consequência, um correto desenho estrutural é baseado, atualmente, em estudos determinísticos com o objetivo de obter estruturas capazes de suportar o pior cenário possível de solicitações durante um período de tempo determinado. A maior parte das solicitações na estrutura de um navio se deve à ação da natureza (ventos, ondas, correnteza e tempestades), ou, ainda, aos erros cometidos por humanos (explosões internas, explosões externas e colisões). Devido à aleatoriedade destes eventos, a confiabilidade estrutural de um navio deveria ser considerada como um problema estocástico sob condições ambientais bem caracterizadas. A metodologia probabilística, baseada em estatística e incertezas, oferece uma melhor perspectiva dos fenômenos reais que acontecem na estrutura dos navios. Esta pesquisa tem como objetivo apresentar resultados de confiabilidade estrutural em projetos e planejamento da manutenção para a chapa do fundo dos cascos dos navios, as quais são submetidas a esforços variáveis pela ação das ondas do mar e da corrosão. Foram estudados modelos estatísticos para a avaliação da estrutura da viga-navio e para o detalhe estrutural da chapa do fundo. Na avaliação da estrutura da viga-navio, o modelo desenvolvido consiste em determinar as probabilidades de ocorrência das solicitações na estrutura, considerando a deterioração por corrosão, com base numa investigação estatística da variação dos esforços em função das ondas e a deterioração em função de uma taxa de corrosão padrão recomendada pela DET NORSKE VERITAS (DNV). A abordagem para avaliação da confiabilidade dependente do tempo é desenvolvida com base nas curvas de resistências e solicitações (R-S) determinadas pela utilização do método de Monte Carlo. Uma variação estatística de longo prazo das adversidades é determinada pelo estudo estatístico de ondas em longo prazo e ajustada por uma distribuição com base numa vida de projeto conhecida. Constam no trabalho resultados da variação da confiabilidade ao longo do tempo de um navio petroleiro. O caso de estudo foi simplificado para facilitar a obtenção de dados, com o objetivo de corroborar a metodologia desenvolvida.

Effects of fiscal consolidations in Latin America

We use new data on cyclically adjusted primary balances for Latin America and the Caribbean to estimate e ects of scal consolidations on GDP and some of its components. Identi cation is conducted through a doubly-robust estimation procedure that controls for non-randomness in the "treatment assignment" by inverse probability weighting and impulse responses are generated by local projections. Results suggest output contraction by more than one percent on impact, with economy starting to recover from the second year on. Composition e ects indicate that revenue-based adjustments are way more contractionary than expenditure-based ones. Disentangling efects between demand components, we nd consumption being in general less responsive to consolidations than investment, although nonlinearities associated to initial levels of debt and taxation might play an important role.

Abyssal community analysis from replicate box cores in the central North Pacific

A 0.25 m**2 United States Naval Electronics Laboratory box corer was used to take replicate samples from an oligotrophic bottom under the North Pacific Central Water Mass (~28°N, 155°W). The bottom is a red clay with manganese nodules at a depth of 5500-5800 m. Macrofaunal density ranges from 84 to 160 individuals per m**2 and is therefore much the same as in Northwest Atlantic Gyre waters. Of the macrofaunal taxa, polychaetes dominate (55 %), followed by tanaids (18 %), bivalves (7 %), and isopods (6 %). Meiofaunal taxa were only partially retained by the 297 µm screen used in washing. Even then, they are 1.5-3.9 times as abundant as the macrofaunal taxa, with nematodes being numerically dominant by far. Foraminifera seem to comprise an important portion of the community, but could not be assessed accurately because of the inability to discriminate living and dead tests. Remains of what are probably xenophyophoridans are also very important, but offer the same problem. Faunal diversity is extremely high, with deposit feeders comprising the overwhelming majority. Most species are rare, being encountered only once. The distributions of only three species show any significant deviation from randomness. The polychaete fauna from box cores collected from 90 miles to the north was not significantly different from that of the principal study locality. Concordance appeared at several taxonomic levels, from species through macrofaunal/meiofaunal relationships. As a result, the variation in total animal abundance shows aggregation among cores. We discuss Sokolova's concept of a deep-sea oligotrophic zone dominated by suspension feeders, and reconcile it with our present findings. The high diversity of the fauna combined with the low food level contradict theories that relate diversity directly with productivity.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.

Random vibration of the functionally graded laminates in thermal environments

This work deals with the random free vibration of functionally graded laminates with general boundary conditions and subjected to a temperature change, taking into account the randomness in a number of independent input variables such as Young's modulus, Poisson's ratio and thermal expansion coefficient of each constituent material. Based on third-order shear deformation theory, the mixed-type formulation and a semi-analytical approach are employed to derive the standard eigenvalue problem in terms of deflection, mid-plane rotations and stress function. A mean-centered first-order perturbation technique is adopted to obtain the second-order statistics of vibration frequencies. A detailed parametric study is conducted, and extensive numerical results are presented in both tabular and graphical forms for laminated plates that contain functionally graded material which is made of aluminum and zirconia, showing the effects of scattering in thermo-clastic material constants, temperature change, edge support condition, side-to-thickness ratio, and plate aspect ratio on the stochastic characteristics of natural frequencies. (c) 2005 Elsevier B.V. All rights reserved.

Testing the niche apportionment hypothesis with parasite communities: is random assortment always the rule?

Niche apportionment models have only been applied once to parasite communities. Only the random assortment model (RA), which indicates that species abundances are independent from each other and that interspecific competition is unimportant, provided a good fit to 3 out of 6 parasite communities investigated. The generality of this result needs to be validated, however. In this study we apply 5 niche apportionment models to the parasite communities of 14 fish species from the Great Barrier Reef. We determined which model fitted the data when using either numerical abundance or biomass as an estimate of parasite abundance, and whether the fit of niche apportionment models depends on how the parasite community is defined (e.g. ecto, endoparasites or all parasites considered together). The RA model provided a good fit for the whole community of parasites in 7 fish species when using biovolume (as a surrogate of biomass) as a measure of species abundance. The RA model also fitted observed data when ecto- and endoparasites were considered separately, using abundance or biovolume, but less frequently. Variation in fish sizes among species was not associated with the probability of a model fitting the data. Total numerical abundance and biovolume of parasites were not related across host species, suggesting that they capture different aspects of abundance. Biovolume is not only a better measurement to use with niche-orientated models, it should also be the preferred descriptor to analyse parasite community structure in other contexts. Most of the biological assumptions behind the RA model, i.e. randomness in apportioning niche space, lack of interspecific competition, independence of abundance among different species, and species with variable niches in changeable environments, are in accordance with some previous findings on parasite communities. Thus, parasite communities may generally be unsaturated with species, with empty niches, and interspecific interactions may generally be unimportant in determining parasite community structure.

Fibre slippage in cyclically perturbed fibrous assemblies

The dynamics of fibre slippage within general non-bonded fibrous assemblies is studied in the situation where the assembly is subjected to general small cyclic loads. Two models are proposed. The first is applicable when the general cyclic loading is complemented by an occasional tugging force on one end of a fibre, which causes it to gradually withdraw from the assembly, such as might occur during the pilling of a textile. The second considers the situation in which the cyclic perturbations act around a constant background load applied to the assembly. The dynamics is reminiscent of self-organized critical behaviour. This model is applied to predict the progressive elongation of a single yarn during weaving.

Measuring the spatial arrangement patterns of pathological lesions in histological sections of brain tissue

The development of abnormal protein aggregates in the form of extracellular plaques and intracellular inclusions is a characteristic feature of many neurodegenerative diseases such as Alzheimer's disease (AD), Creutzfeldt-Jakob disease (CJD) and the fronto-temporal dementias (FTD). An important aspect of a pathological protein aggregate is its spatial topography in the tissue. Lesions may not be randomly distributed within a histological section but exhibit spatial pattern, a departure from randomness either towards regularity or clustering. Information on the spatial pattern of a lesion may be useful in elucidating its pathogenesis and in studying the relationships between different lesions. This article reviews the methods that have been used to study the spatial topography of lesions. These include simple tests of whether the distribution of a lesion departs significantly from random using randomized points or sample fields, and more complex methods that employ grids or transects of contiguous fields and which can detect the intensity of aggregation and the sizes, distribution and spacing of the clusters. The usefulness of these methods in elucidating the pathogenesis of protein aggregates in neurodegenerative disease is discussed.

Methods of studying the planar distribution of objects in histological sections of brain tissue

This article reviews the statistical methods that have been used to study the planar distribution, and especially clustering, of objects in histological sections of brain tissue. The objective of these studies is usually quantitative description, comparison between patients or correlation between histological features. Objects of interest such as neurones, glial cells, blood vessels or pathological features such as protein deposits appear as sectional profiles in a two-dimensional section. These objects may not be randomly distributed within the section but exhibit a spatial pattern, a departure from randomness either towards regularity or clustering. The methods described include simple tests of whether the planar distribution of a histological feature departs significantly from randomness using randomized points, lines or sample fields and more complex methods that employ grids or transects of contiguous fields, and which can detect the intensity of aggregation and the sizes, distribution and spacing of clusters. The usefulness of these methods in understanding the pathogenesis of neurodegenerative diseases such as Alzheimer's disease and Creutzfeldt-Jakob disease is discussed. © 2006 The Royal Microscopical Society.

What does the study of the spatial patterns of pathological lesions tell us about the pathogenesis of neurodegenerative disorders?

Discrete pathological lesions, which include extracellular protein deposits, intracellular inclusions and changes in cell morphology, occur in the brain in the majority of neurodegenerative disorders. These lesions are not randomly distributed in the brain but exhibit a spatial pattern, that is, a departure from randomness towards regularity or clustering. The spatial pattern of a lesion may reflect pathological processes affecting particular neuroanatomical structures and, therefore, studies of spatial pattern may help to elucidate the pathogenesis of a lesion and of the disorders themselves. The present article reviews first, the statistical methods used to detect spatial patterns and second, the types of spatial patterns exhibited by pathological lesions in a variety of disorders which include Alzheimer's disease, Down syndrome, dementia with Lewy bodies, Creutzfeldt-Jakob disease, Pick's disease and corticobasal degeneration. These studies suggest that despite the morphological and molecular diversity of brain lesions, they often exhibit a common type of spatial pattern (i.e. aggregation into clusters that are regularly distributed in the tissue). The pathogenic implications of spatial pattern analysis are discussed with reference to the individual disorders and to studies of neurodegeneration as a whole.

Rhetoric in organized anarchies

This empirical case study of a business school internationalisation process investigates the relationship between rhetoric, ambiguity and strategic action in a garbage can context. Our data showed that rhetoric structured the garbage can and reduced the randomness of the strategy-making process in two ways. First, rhetoric enabled actors to distinguish between two uses of ambiguity - maximising ambiguity to avoid action, and minimising ambiguity to enact action. Rhetorics that maximised ambiguity were most frequent at the start of the strategy process; rhetorics that minimised ambiguity were most common later in the strategy process. Second, rhetoric provided structure by linking solutions, problems and participants to choice opportunities to enable action and by negating links between solutions, problems and participants and choice opportunities in order to enable inaction.