Modeling the skin pattern of fishes

Complicated patterns showing various spatial scales have been obtained in the past by coupling Turing systems in such a way that the scales of the independent systems resonate. This produces superimposed patterns with different length scales. Here we propose a model consisting of two identical reaction-diffusion systems coupled together in such a way that one of them produces a simple Turing pattern of spots or stripes, and the other traveling wave fronts that eventually become stationary. The basic idea is to assume that one of the systems becomes fixed after some time and serves as a source of morphogens for the other system. This mechanism produces patterns very similar to the pigmentation patterns observed in different species of stingrays and other fishes. The biological mechanisms that support the realization of this model are discussed.

The Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS) - Part 2: Model sensitivity to the biomass burning

We describe an estimation technique for biomass burning emissions in South America based on a combination of remote-sensing fire products and field observations, the Brazilian Biomass Burning Emission Model (3BEM). For each fire pixel detected by remote sensing, the mass of the emitted tracer is calculated based on field observations of fire properties related to the type of vegetation burning. The burnt area is estimated from the instantaneous fire size retrieved by remote sensing, when available, or from statistical properties of the burn scars. The sources are then spatially and temporally distributed and assimilated daily by the Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS) in order to perform the prognosis of related tracer concentrations. Three other biomass burning inventories, including GFEDv2 and EDGAR, are simultaneously used to compare the emission strength in terms of the resultant tracer distribution. We also assess the effect of using the daily time resolution of fire emissions by including runs with monthly-averaged emissions. We evaluate the performance of the model using the different emission estimation techniques by comparing the model results with direct measurements of carbon monoxide both near-surface and airborne, as well as remote sensing derived products. The model results obtained using the 3BEM methodology of estimation introduced in this paper show relatively good agreement with the direct measurements and MOPITT data product, suggesting the reliability of the model at local to regional scales.

Cloud condensation nuclei in pristine tropical rainforest air of Amazonia: size-resolved measurements and modeling of atmospheric aerosol composition and CCN activity

Atmospheric aerosol particles serving as cloud condensation nuclei (CCN) are key elements of the hydrological cycle and climate. We have measured and characterized CCN at water vapor supersaturations in the range of S=0.10-0.82% in pristine tropical rainforest air during the AMAZE-08 campaign in central Amazonia. The effective hygroscopicity parameters describing the influence of chemical composition on the CCN activity of aerosol particles varied in the range of kappa approximate to 0.1-0.4 (0.16+/-0.06 arithmetic mean and standard deviation). The overall median value of kappa approximate to 0.15 was by a factor of two lower than the values typically observed for continental aerosols in other regions of the world. Aitken mode particles were less hygroscopic than accumulation mode particles (kappa approximate to 0.1 at D approximate to 50 nm; kappa approximate to 0.2 at D approximate to 200 nm), which is in agreement with earlier hygroscopicity tandem differential mobility analyzer (H-TDMA) studies. The CCN measurement results are consistent with aerosol mass spectrometry (AMS) data, showing that the organic mass fraction (f(org)) was on average as high as similar to 90% in the Aitken mode (D <= 100 nm) and decreased with increasing particle diameter in the accumulation mode (similar to 80% at D approximate to 200 nm). The kappa values exhibited a negative linear correlation with f(org) (R(2)=0.81), and extrapolation yielded the following effective hygroscopicity parameters for organic and inorganic particle components: kappa(org)approximate to 0.1 which can be regarded as the effective hygroscopicity of biogenic secondary organic aerosol (SOA) and kappa(inorg)approximate to 0.6 which is characteristic for ammonium sulfate and related salts. Both the size dependence and the temporal variability of effective particle hygroscopicity could be parameterized as a function of AMS-based organic and inorganic mass fractions (kappa(p)=kappa(org) x f(org)+kappa(inorg) x f(inorg)). The CCN number concentrations predicted with kappa(p) were in fair agreement with the measurement results (similar to 20% average deviation). The median CCN number concentrations at S=0.1-0.82% ranged from N(CCN,0.10)approximate to 35 cm(-3) to N(CCN,0.82)approximate to 160 cm(-3), the median concentration of aerosol particles larger than 30 nm was N(CN,30)approximate to 200 cm(-3), and the corresponding integral CCN efficiencies were in the range of N(CCN,0.10/NCN,30)approximate to 0.1 to N(CCN,0.82/NCN,30)approximate to 0.8. Although the number concentrations and hygroscopicity parameters were much lower in pristine rainforest air, the integral CCN efficiencies observed were similar to those in highly polluted megacity air. Moreover, model calculations of N(CCN,S) assuming an approximate global average value of kappa approximate to 0.3 for continental aerosols led to systematic overpredictions, but the average deviations exceeded similar to 50% only at low water vapor supersaturation (0.1%) and low particle number concentrations (<= 100 cm(-3)). Model calculations assuming aconstant aerosol size distribution led to higher average deviations at all investigated levels of supersaturation: similar to 60% for the campaign average distribution and similar to 1600% for a generic remote continental size distribution. These findings confirm earlier studies suggesting that aerosol particle number and size are the major predictors for the variability of the CCN concentration in continental boundary layer air, followed by particle composition and hygroscopicity as relatively minor modulators. Depending on the required and applicable level of detail, the information and parameterizations presented in this paper should enable efficient description of the CCN properties of pristine tropical rainforest aerosols of Amazonia in detailed process models as well as in large-scale atmospheric and climate models.

Remote sensing the vertical profile of cloud droplet effective radius, thermodynamic phase, and temperature

Cloud-aerosol interaction is a key issue in the climate system, affecting the water cycle, the weather, and the total energy balance including the spatial and temporal distribution of latent heat release. Information on the vertical distribution of cloud droplet microphysics and thermodynamic phase as a function of temperature or height, can be correlated with details of the aerosol field to provide insight on how these particles are affecting cloud properties and their consequences to cloud lifetime, precipitation, water cycle, and general energy balance. Unfortunately, today's experimental methods still lack the observational tools that can characterize the true evolution of the cloud microphysical, spatial and temporal structure in the cloud droplet scale, and then link these characteristics to environmental factors and properties of the cloud condensation nuclei. Here we propose and demonstrate a new experimental approach (the cloud scanner instrument) that provides the microphysical information missed in current experiments and remote sensing options. Cloud scanner measurements can be performed from aircraft, ground, or satellite by scanning the side of the clouds from the base to the top, providing us with the unique opportunity of obtaining snapshots of the cloud droplet microphysical and thermodynamic states as a function of height and brightness temperature in clouds at several development stages. The brightness temperature profile of the cloud side can be directly associated with the thermodynamic phase of the droplets to provide information on the glaciation temperature as a function of different ambient conditions, aerosol concentration, and type. An aircraft prototype of the cloud scanner was built and flew in a field campaign in Brazil. The CLAIM-3D (3-Dimensional Cloud Aerosol Interaction Mission) satellite concept proposed here combines several techniques to simultaneously measure the vertical profile of cloud microphysics, thermodynamic phase, brightness temperature, and aerosol amount and type in the neighborhood of the clouds. The wide wavelength range, and the use of multi-angle polarization measurements proposed for this mission allow us to estimate the availability and characteristics of aerosol particles acting as cloud condensation nuclei, and their effects on the cloud microphysical structure. These results can provide unprecedented details on the response of cloud droplet microphysics to natural and anthropogenic aerosols in the size scale where the interaction really happens.

Thermodynamic origin of cooperativity in actomyosin interactions: The coupling of short-range interactions with actin bending stiffness in an Ising-like model

We present Monte Carlo simulations for a molecular motor system found in virtually all eukaryotic cells, the acto-myosin motor system, composed of a group of organic macromolecules. Cell motors were mapped to an Ising-like model, where the interaction field is transmitted through a tropomyosin polymer chain. The presence of Ca(2+) induces tropomyosin to block or unblock binding sites of the myosin motor leading to its activation or deactivation. We used the Metropolis algorithm to find the transient and the equilibrium states of the acto-myosin system composed of solvent, actin, tropomyosin, troponin, Ca(2+), and myosin-S1 at a given temperature, including the spatial configuration of tropomyosin on the actin filament surface. Our model describes the short- and long-range cooperativity during actin-myosin binding which emerges from the bending stiffness of the tropomyosin complex. We found all transition rates between the states only using the interaction energy of the constituents. The agreement between our model and experimental data also supports the recent theory of flexible tropomyosin.

Modeling the dichroic absorption band edge and light-induced magnetism in EuTe

The band-edge optical absorption in EuTe is studied in the framework of the 5d conduction band atomic model. Both relaxed antiferromagnetic order, and ferromagnetic order induced by an external magnetic field, were analyzed. For ferromagnetic arrangement, the absorption is characterized by a hugely dichroic doublet of narrow lines. In the antiferromagnetic order, the spectrum is blueshifted, becomes much broader and weaker, and dichroism is suppressed. These results are in excellent qualitative and quantitative agreement with experimental observations on EuTe and EuSe published by us previously [Phys. Rev. B 72, 155337 (2005)]. The possibility of inducing ferromagnetic order by illuminating the material at photon energies resonant with the band gap is also discussed.

DISTRIBUTION OF CAPYBARAS IN AN AGROECOSYSTEM, SOUTHEASTERN BRAZIL, BASED ON ECOLOGICAL NICHE MODELING

Southeastern Brazil has seen dramatic landscape modifications in recent decades, due to expansion of agriculture and urban areas; these changes have influenced the distribution and abundance of vertebrates. We developed predictive models of ecological and spatial distributions of capybaras (Hydrochoerus hydrochaeris) using ecological niche modeling. Most Occurrences of capybaras were in flat areas with water bodies Surrounded by sugarcane and pasture. More than 75% of the Piracicaba River basin was estimated as potentially habitable by capybara. The models had low omission error (2.3-3.4%), but higher commission error (91.0-98.5%); these ""model failures"" seem to be more related to local habitat characteristics than to spatial ones. The potential distribution of capybaras in the basin is associated with anthropogenic habitats, particularly with intensive land use for agriculture.

MODELING SCIENTIFIC AGENTS FOR A BETTER SCIENCE

Science is a fundamental human activity and we trust its results because it has several error-correcting mechanisms. It is subject to experimental tests that are replicated by independent parts. Given the huge amount of information available and the information asymetry between producers and users of knowledge, scientists have to rely on the reports of others. This makes it possible for social effects to influence the scientific community. Here, an Opinion Dynamics agent model is proposed to describe this situation. The influence of Nature through experiments is described as an external field that acts on the experimental agents. We will see that the retirement of old scientists can be fundamental in the acceptance of a new theory. We will also investigate the interplay between social influence and observations. This will allow us to gain insight in the problem of when social effects can have negligible effects in the conclusions of a scientific community and when we should worry about them.

Thermodynamic and kinetic investigations of phosphate adsorption onto hydrous niobium oxide prepared by homogeneous solution method

The adsorption kinetics of phosphate onto Nb(2)O(5)center dot nH(2)O was investigated at initial phosphate concentrations 10 and 50 mg L(-1). The kinetic process was described by a pseudo second-order rate model very well. The adsorption thermodynamics was carried out at 298, 308, 318, 328 and 338 K. The positive values of both Delta H and Delta S suggest an endothermic reaction and increase in randomness at the solid-liquid interface during the adsorption. Delta G values obtained were negative indicating a spontaneous adsorption process. The Langmuir model described the data better than the Freundlich isotherm model. The peak appearing at 1050 cm(-1) in IR spectra after adsorption was attributed to the bending vibration of adsorbed phosphate. The effective desorption could be achieved using water at pH 12. (C) 2010 Elsevier B.V. All rights reserved.

Adsorption kinetic, thermodynamic and desorption studies of phosphate onto hydrous niobium oxide prepared by reverse microemulsion method

A type of Nb(2)O(5)center dot 3H(2)O was synthesized and its phosphate removal potential was investigated in this study. The kinetic study, adsorption isotherm, pH effect, thermodynamic study and desorption were examined in batch experiments. The kinetic process was described by a pseudo-second-order rate model very well. The phosphate adsorption tended to increase with a decrease of pH. The adsorption data fitted well to the Langmuir model with which the maximum P adsorption capacity was estimated to be 18.36 mg-Pg(-1). The peak appearing at 1050 cm(-1) in IR spectra after adsorption was attributed to the bending vibration of adsorbed phosphate. The positive values of both Delta H degrees and Delta S degrees suggest an endothermic reaction and increase in randomness at the solid-liquid interface during the adsorption. Delta G degrees values obtained were negative indicating a spontaneous adsorption process. A phosphate desorbability of approximately 68% was observed with water at pH 12, which indicated a relatively strong bonding between the adsorbed phosphate and the sorptive sites on the surface of the adsorbent. The immobilization of phosphate probably occurs by the mechanisms of ion exchange and physicochemical attraction. Due to its high adsorption capacity, this type of hydrous niobium oxide has the potential for application to control phosphorus pollution.

Improved xylitol production in media containing phenolic aldehydes: application of response surface methodology for optimization and modeling of bioprocess

BACKGROUND: The combined effects of vanillin and syringaldehyde on xylitol production by Candida guilliermondii using response surface methodology (RSM) have been studied. A 2(2) full-factorial central composite design was employed for experimental design and analysis of the results. RESULTS: Maximum xylitol productivities (Q(p) = 0.74 g L(-1) h(-1)) and yields (Y(P/S) = 0.81 g g(-1)) can be attained by adding only vanillin at 2.0 g L(-1) to the fermentation medium. These data were closely correlated with the experimental results obtained (0.69 +/- 0.04 g L(-1) h(-1) and 0.77 +/- 0.01 g g(-1)) indicating a good agreement with the predicted value. C. guilliermondii was able to convert vanillin completely after 24 h of fermentation with 94% yield of vanillyl alcohol. CONCLUSIONS: The bioconversion of xylose into xylitol by C. guilliermondii is strongly dependent on the combination of aldehydes and phenolics in the fermentation medium. Vanillin is a source of phenolic compound able to improve xylitol production by yeast. The conversion of vanillin to alcohol vanilyl reveals the potential of this yeast for medium detoxification. (C) 2009 Society of Chemical Industry

Selection of new glass-forming compositions in Al-La system using a combination of topological instability and thermodynamic criteria

A combination of an extension of the topological instability ""lambda criterion"" and a thermodynamic criterion were applied to the Al-La system, indicating the best range of compositions for glass formation. Alloy compositions in this range were prepared by melt-spinning and casting in an arc-melting furnace with a wedge-section copper mold. The GFA of these samples was evaluated by X-ray diffraction, differential scanning calorimetry and scanning electron microscopy. The results indicated that the gamma* parameter of compositions with high GFA is higher, corresponding to a range in which the lambda parameter is greater than 0.1, which are compositions far from Al solid solution. A new alloy was identified with the best GFA reported so far for this system, showing a maximum thickness of 286 mu m in a wedge-section copper mold. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Modeling associations between genetic markers using Bayesian networks

Motivation: Understanding the patterns of association between polymorphisms at different loci in a population ( linkage disequilibrium, LD) is of fundamental importance in various genetic studies. Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure. GMs based in coalescent theory have been the most appealing because they link LD to evolutionary factors. Nevertheless, the inference and parameter estimation of such models is still computationally challenging. Results: We present a more practical method to build GM that describe LD. The method is based on learning weighted Bayesian network structures from haplotype data, extracting equivalence structure classes and using them to model LD. The results obtained in public data from the HapMap database showed that the method is a promising tool for modeling LD. The associations represented by the learned models are correlated with the traditional measure of LD D`. The method was able to represent LD blocks found by standard tools. The granularity of the association blocks and the readability of the models can be controlled in the method. The results suggest that the causality information gained by our method can be useful to tell about the conservability of the genetic markers and to guide the selection of subset of representative markers.

A Study on Unconditionally Stable FDTD Methods for the Modeling of Metamaterials

We assess the performance of three unconditionally stable finite-difference time-domain (FDTD) methods for the modeling of doubly dispersive metamaterials: 1) locally one-dimensional FDTD; 2) locally one-dimensional FDTD with Strang splitting; and (3) alternating direction implicit FDTD. We use both double-negative media and zero-index media as benchmarks.

Modeling and analysis of laminate composite plates with embedded active-passive piezoelectric networks

The objective of this work is to present the finite element modeling of laminate composite plates with embedded piezoelectric patches or layers that are then connected to active-passive resonant shunt circuits, composed of resistance, inductance and voltage source. Applications to passive vibration control and active control authority enhancement are also presented and discussed. The finite element model is based on an equivalent single layer theory combined with a third-order shear deformation theory. A stress-voltage electromechanical model is considered for the piezoelectric materials fully coupled to the electrical circuits. To this end, the electrical circuit equations are also included in the variational formulation. Hence, conservation of charge and full electromechanical coupling are guaranteed. The formulation results in a coupled finite element model with mechanical (displacements) and electrical (charges at electrodes) degrees of freedom. For a Graphite-Epoxy (Carbon-Fibre Reinforced) laminate composite plate, a parametric analysis is performed to evaluate optimal locations along the plate plane (xy) and thickness (z) that maximize the effective modal electromechanical coupling coefficient. Then, the passive vibration control performance is evaluated for a network of optimally located shunted piezoelectric patches embedded in the plate, through the design of resistance and inductance values of each circuit, to reduce the vibration amplitude of the first four vibration modes. A vibration amplitude reduction of at least 10 dB for all vibration modes was observed. Then, an analysis of the control authority enhancement due to the resonant shunt circuit, when the piezoelectric patches are used as actuators, is performed. It is shown that the control authority can indeed be improved near a selected resonance even with multiple pairs of piezoelectric patches and active-passive circuits acting simultaneously. (C) 2010 Elsevier Ltd. All rights reserved.