Computer simulation of packing of particles with size distributions produced by fragmentation processes

Fragmentation schemes inspired by theoretical results and conjectures of Kolmogorov are applied to produce particle size distributions of different natures, depending on fragmentation parameters. A two-dimensional computer simulation method of packing is applied to the resulting distributions and the void fraction is evaluated. The relationship between the void fraction and characteristic parameters of the fragmentation process is studied.

Intermittent pluri-sink model and the emergence of complex heterogeneity patterns: a simple paradigm for explaining complexity in soil chemical distributions

The spatial complexity of the distribution of organic matter, chemicals, nutrients, pollutants has been demonstrated to have multifractal nature (Kravchenco et al. [1]). This fact supports the possibility of existence of some emergent heterogeneity structure built under the evolution of the system. The aim of this note is providing a consistent explanation to the mentioned results via an extremely simple model.

Analysis of human cytochrome P450 3A4 cooperativity: Construction and characterization of a site-directed mutant that displays hyperbolic steroid hydroxylation kinetics

Cytochrome P450 3A4 is generally considered to be the most important human drug-metabolizing enzyme and is known to catalyze the oxidation of a number of substrates in a cooperative manner. An allosteric mechanism is usually invoked to explain the cooperativity. Based on a structure–activity study from another laboratory using various effector–substrate combinations and on our own studies using site-directed mutagenesis and computer modeling of P450 3A4, the most likely location of effector binding is in the active site along with the substrate. Our study was designed to test this hypothesis by replacing residues Leu-211 and Asp-214 with the larger Phe and Glu, respectively. These residues were predicted to constitute a portion of the effector binding site, and the substitutions were designed to mimic the action of the effector by reducing the size of the active site. The L211F/D214E double mutant displayed an increased rate of testosterone and progesterone 6β-hydroxylation at low substrate concentrations and a decreased level of heterotropic stimulation elicited by α-naphthoflavone. Kinetic analyses of the double mutant revealed the absence of homotropic cooperativity with either steroid substrate. At low substrate concentrations the steroid 6β-hydroxylase activity of the wild-type enzyme was stimulated by a second steroid, whereas L211F/D214E displayed simple substrate inhibition. To analyze L211F/D214E at a more mechanistic level, spectral binding studies were carried out. Testosterone binding by the wild-type enzyme displayed homotropic cooperativity, whereas substrate binding by L211F/D214E displayed hyperbolic behavior.

Mapping species distributions : A comparison of skilled naturalist and lay citizen science recording

Acknowledgements We are grateful to Elaine O’Mahony, Imogen Pearce, Richard Comont, Anthony McCluskey and other BBCT staff for the many hours of BeeWatch species identification and for all people who submitted sightings to BeeWatch, OPAL, BWARS and the various local recording schemes and societies. We thank the NBN for allowing us to download the bumblebee records without strings attached, and the Essex, Greater London, Cumbria and Sussex based recording centres for providing records upon request. Finally, we are indebted to Tom August and two anonymous reviewers for their valuable critique on an earlier version of this work.

Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting

Two variables define the topological state of closed double-stranded DNA: the knot type, K, and ΔLk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(ΔLk, K), is related to two conditional distributions: P(ΔLk|K), the distribution of ΔLk for a particular K, and P(K|ΔLk) and also to two simple distributions: P(ΔLk), the distribution of ΔLk irrespective of K, and P(K). We explored the relationships between these distributions. P(ΔLk, K), P(ΔLk), and P(K|ΔLk) were calculated from the simulated distributions of P(ΔLk|K) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(K|ΔLk), the distribution of knot types for a particular value of ΔLk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ΔLk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at |ΔLk| > 12, only one or two knot types dominate the P(K|ΔLk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed.

Invariant size–frequency distributions along a latitudinal gradient in marine bivalves

In the most extensive analysis of body size in marine invertebrates to date, we show that the size–frequency distributions of northeastern Pacific bivalves at the provincial level are surprisingly invariant in modal and median size as well as size range, despite a 4-fold change in species richness from the tropics to the Arctic. The modal sizes and shapes of these size–frequency distributions are consistent with the predictions of an energetic model previously applied to terrestrial mammals and birds. However, analyses of the Miocene–Recent history of body sizes within 82 molluscan genera show little support for the expectation that the modal size is an evolutionary attractor over geological time.

Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations

We describe and test a Markov chain model of microsatellite evolution that can explain the different distributions of microsatellite lengths across different organisms and repeat motifs. Two key features of this model are the dependence of mutation rates on microsatellite length and a mutation process that includes both strand slippage and point mutation events. We compute the stationary distribution of allele lengths under this model and use it to fit DNA data for di-, tri-, and tetranucleotide repeats in humans, mice, fruit flies, and yeast. The best fit results lead to slippage rate estimates that are highest in mice, followed by humans, then yeast, and then fruit flies. Within each organism, the estimates are highest in di-, then tri-, and then tetranucleotide repeats. Our estimates are consistent with experimentally determined mutation rates from other studies. The results suggest that the different length distributions among organisms and repeat motifs can be explained by a simple difference in slippage rates and that selective constraints on length need not be imposed.

The estimation of statistical parameters for local alignment score distributions

The distribution of optimal local alignment scores of random sequences plays a vital role in evaluating the statistical significance of sequence alignments. These scores can be well described by an extreme-value distribution. The distribution’s parameters depend upon the scoring system employed and the random letter frequencies; in general they cannot be derived analytically, but must be estimated by curve fitting. For obtaining accurate parameter estimates, a form of the recently described ‘island’ method has several advantages. We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects.

Characteristics of the deep ocean carbon system during the past 150,000 years: ΣCO2 distributions, deep water flow patterns, and abrupt climate change

Studies of carbon isotopes and cadmium in bottom-dwelling foraminifera from ocean sediment cores have advanced our knowledge of ocean chemical distributions during the late Pleistocene. Last Glacial Maximum data are consistent with a persistent high-ΣCO2 state for eastern Pacific deep water. Both tracers indicate that the mid-depth North and tropical Atlantic Ocean almost always has lower ΣCO2 levels than those in the Pacific. Upper waters of the Last Glacial Maximum Atlantic are more ΣCO2-depleted and deep waters are ΣCO2-enriched compared with the waters of the present. In the northern Indian Ocean, δ13C and Cd data are consistent with upper water ΣCO2 depletion relative to the present. There is no evident proximate source of this ΣCO2-depleted water, so I suggest that ΣCO2-depleted North Atlantic intermediate/deep water turns northward around the southern tip of Africa and moves toward the equator as a western boundary current. At long periods (>15,000 years), Milankovitch cycle variability is evident in paleochemical time series. But rapid millennial-scale variability can be seen in cores from high accumulation rate series. Atlantic deep water chemical properties are seen to change in as little as a few hundred years or less. An extraordinary new 52.7-m-long core from the Bermuda Rise contains a faithful record of climate variability with century-scale resolution. Sediment composition can be linked in detail with the isotope stage 3 interstadials recorded in Greenland ice cores. This new record shows at least 12 major climate fluctuations within marine isotope stage 5 (about 70,000–130,000 years before the present).

Distinct desmocollin isoforms occur in the same desmosomes and show reciprocally graded distributions in bovine nasal epidermis.

The adhesive core of the desmosome is composed of cadherin-like glycoproteins of two families, desmocollins and desmogleins. Three isoforms of each are expressed in a tissue-specific and developmentally regulated pattern. In bovine nasal epidermis, the three desmocollin (Dsc) isoforms are expressed in overlapping domains; Dsc3 expression is strongest in the basal layer, while Dsc2 and Dsc1 are strongly expressed in the suprabasal layers. Herein we have investigated whether different isoforms are assembled into the same or distinct desmosomes by performing double immunogold labeling using isoform-specific antibodies directed against Dsc1 and Dsc3. The results show that individual desmosomes harbor both isoforms in regions where their expression territories overlap. Quantification showed that the ratio of the proteins in each desmosome altered gradually from basal to immediately suprabasal and upper suprabasal layers, labeling for Dsc1 increasing and Dsc3 decreasing. Thus desmosomes are constantly modified as cells move up the epidermis, with continuing turnover of the desmosomal glycoproteins. Statistical analysis of the quantitative data showed a possible relationship between the distributions of the two isoforms. This gradual change in desmosomal composition may constitute a vertical adhesive gradient within the epidermis, having important consequences for cell positioning and differentiation.

Sample-to-sample fluctuations of the overlap distributions in the three-dimensional Edwards-Anderson spin glass

We study the sample-to-sample fluctuations of the overlap probability densities from large-scale equilibrium simulations of the three-dimensional Edwards-Anderson spin glass below the critical temperature. Ultrametricity, stochastic stability, and overlap equivalence impose constraints on the moments of the overlap probability densities that can be tested against numerical data. We found small deviations from the Ghirlanda Guerra predictions, which get smaller as system size increases. We also focus on the shape of the overlap distribution, comparing the numerical data to a mean-field-like prediction in which finite-size effects are taken into account by substituting delta functions with broad peaks.

Finite-size scaling analysis of the distributions of pseudo-critical temperatures in spin glasses

Using the results of large scale numerical simulations we study the probability distribution of the pseudo critical temperature for the three dimensional Edwards Anderson Ising spin glass and for the fully connected Sherrington-Kirkpatrick model. We find that the behaviour of our data is nicely described by straightforward finitesize scaling relations.

Equações de onda generalizadas e quantização funtorial para teorias de campo escalar livre

Nesta dissertação apresentamos um método de quantização matemática e conceitualmente rigoroso para o campo escalar livre de interações. Trazemos de início alguns aspéctos importantes da Teoria de Distribuições e colocamos alguns pontos de geometria Lorentziana. O restante do trabalho é dividido em duas partes: na primeira, estudamos equações de onda em variedades Lorentzianas globalmente hiperbólicas e apresentamos o conceito de soluções fundamentais no contexto de equações locais. Em seguida, progressivamente construímos soluções fundamentais para o operador de onda a partir da distribuição de Riesz. Uma vez estabelecida uma solução para a equação de onda em uma vizinhança de um ponto da variedade, tratamos de construir uma solução global a partir da extensão do problema de Cauchy a toda a variedade, donde as soluções fundamentais dão lugar aos operadores de Green a partir da introdução de uma condição de contorno. Na última parte do trabalho, apresentamos um mínimo da Teoria de Categorias e Funtores para utilizar esse formalismo na contrução de um funtor de segunda quantização entre a categoria de variedades Lorentzianas globalmente hiperbólicas e a categoria de redes de álgebras C* satisfazendo os axiomas de Haag-Kastler. Ao fim, retomamos o caso particular do campo escalar quântico livre.

Low-resolution spectroscopy and spectral energy distributions of selected sources towards σ Orionis

Aims. We study in detail nine sources in the direction of the young σ Orionis cluster, which is considered to be a unique site for studying stellar and substellar formation. The nine sources were selected because of their peculiar properties, such as extremely-red infrared colours or excessively strong Hα emission for their blue optical colours. Methods. We acquired high-quality, low-resolution spectroscopy (R ∼ 500) of the nine targets with ALFOSC at the Nordic Optical Telescope. We also re-analysed [24]-band photometry from MIPS/Spitzer and compiled the highest quality photometric dataset available at the ViJHK_s passbands and the four IRAC/Spitzer channels, for constructing accurate spectral energy distributions between 0.55 and 24 μm. Results. The nine targets were classified into: one Herbig Ae/Be star with a scattering edge-on disc; two G-type stars; one X-ray flaring, early-M, young star with chromospheric Hα emission; one very low-mass, accreting, young spectroscopic binary; two young objects at the brown-dwarf boundary with the characteristics of classical T Tauri stars; and two emission-line galaxies, one undergoing star formation, and another whose spectral energy distribution is dominated by an active galactic nucleus. We also discovered three infrared sources associated with overdensities in a cold cloud of the cluster centre. Conclusions. Low-resolution spectroscopy and spectral energy distributions are a vital tool for measuring the physical properties and evolution of young stars and candidates in the σ Orionis cluster.

Dyakonons in hyperbolic metamaterials

We have analyzed surface-wave propagation that takes place at the boundary between an isotropic medium and a semi-infinite metal-dielectric periodic medium cut normally to the layers. In the range of frequencies where the periodic medium shows hyperbolic space dispersion, hybridization of surface waves (dyakonons) occurs. At low to moderate frequencies, dyakonons enable tighter confinement near the interface in comparison with pure SPPs. On the other hand, a distinct regime governs dispersion of dyakonons at higher frequencies.