Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation

The antimicrobial peptide indolicidin (IND) and the mutant CP10A in hydrated micelles were studied using molecular dynamics simulations in order to observe whether the molecular dynamics and experimental data could be sufficiently correlated and a detailed description of the interaction of the antimicrobial peptides with a model of the membrane provided by a hydrated micelle system could be obtained. In agreement with the experiments, the simulations showed that the peptides are located near the surface of the micelles. Peptide insertions agree with available experimental data, showing deeper insertion of the mutant compared with the peptide IND. Major insertion into the hydrophobic core of the micelle by all tryptophan and mutated residues of CP10A in relation to IND was observed. The charged residues of the terminus regions of both peptides present similar behavior, indicating that the major differences in the interactions with the micelles of the peptides IND and CP10A occur in the case of the hydrophobic residues.

Multifilter rotating shadowband radiometer calibration for spectral aerosol optical depth retrievals over Sao Paulo City, Brazil

Multifilter rotating shadowband radiometer (MFRSR) calibration values for aerosol optical depth (AOD) retrievals were determined by means of the general method formulated by Forgan [Appl. Opt. 33, 4841 (1994)] at a polluted urban site. The obtained precision is comparable with the classical method, the Langley plot, applied on clean mountaintops distant of pollution sources. The AOD retrieved over Sao Paulo City with both calibration procedures is compared with the Aerosol Robotic Network data. The observed results are similar, and, except for the shortest wavelength (415 nm), the MFRSR`s AOD is systematically overestimated by similar to 0.03. (c) 2008 Optical Society of America.

Fossil groups in the Millennium Simulation Evolution of the brightest galaxies

Aims. We create a catalogue of simulated fossil groups and study their properties, in particular the merging histories of their first-ranked galaxies. We compare the simulated fossil group properties with those of both simulated non-fossil and observed fossil groups. Methods. Using simulations and a mock galaxy catalogue, we searched for massive (>5 x 10(13) h(-1) M-circle dot) fossil groups in the Millennium Simulation Galaxy Catalogue. In addition, we attempted to identify observed fossil groups in the Sloan Digital Sky Survey Data Release 6 using identical selection criteria. Results. Our predictions on the basis of the simulation data are: (a) fossil groups comprise about 5.5% of the total population of groups/clusters with masses larger than 5 x 10(13) h(-1) M-circle dot. This fraction is consistent with the fraction of fossil groups identified in the SDSS, after all observational biases have been taken into account; (b) about 88% of the dominant central objects in fossil groups are elliptical galaxies that have a median R-band absolute magnitude of similar to-23.5-5 log h, which is typical of the observed fossil groups known in the literature; (c) first-ranked galaxies of systems with M > 5 x 10(13) h(-1) M-circle dot, regardless of whether they are either fossil or non-fossil, are mainly formed by gas-poor mergers; (d) although fossil groups, in general, assembled most of their virial masses at higher redshifts in comparison with non-fossil groups, first-ranked galaxies in fossil groups merged later, i.e. at lower redshifts, compared with their non-fossil-group counterparts. Conclusions. We therefore expect to observe a number of luminous galaxies in the centres of fossil groups that show signs of a recent major merger.

Fossil groups in the Millennium simulation Their environment and its evolution

Context. Fossil systems are defined to be X- ray bright galaxy groups ( or clusters) with a two- magnitude difference between their two brightest galaxies within half the projected virial radius, and represent an interesting extreme of the population of galaxy agglomerations. However, the physical conditions and processes leading to their formation are still poorly constrained. Aims. We compare the outskirts of fossil systems with that of normal groups to understand whether environmental conditions play a significant role in their formation. We study the groups of galaxies in both, numerical simulations and observations. Methods. We use a variety of statistical tools including the spatial cross- correlation function and the local density parameter Delta(5) to probe differences in the density and structure of the environments of "" normal"" and "" fossil"" systems in the Millennium simulation. Results. We find that the number density of galaxies surrounding fossil systems evolves from greater than that observed around normal systems at z = 0.69, to lower than the normal systems by z = 0. Both fossil and normal systems exhibit an increment in their otherwise radially declining local density measure (Delta(5)) at distances of order 2.5 r(vir) from the system centre. We show that this increment is more noticeable for fossil systems than normal systems and demonstrate that this difference is linked to the earlier formation epoch of fossil groups. Despite the importance of the assembly time, we show that the environment is different for fossil and non- fossil systems with similar masses and formation times along their evolution. We also confirm that the physical characteristics identified in the Millennium simulation can also be detected in SDSS observations. Conclusions. Our results confirm the commonly held belief that fossil systems assembled earlier than normal systems but also show that the surroundings of fossil groups could be responsible for the formation of their large magnitude gap.

THE SPECTRAL EVOLUTION AND EJECTA OF RECURRENT NOVA U Sco IN THE 2010 OUTBURST

Synoptic spectroscopic observations of the U Sco 2010 outburst from maximum light to quiescence as well as a contemporaneous X-ray observation are presented and analyzed. The X-ray spectrum 52 days after outburst indicates a hot source ( kT(bb) similar to 70 eV). Narrow-line components from the irradiated companion atmosphere were observed in hydrogen and helium optical recombination lines. The formation of a nebular spectrum is seen for the first time in this class of recurrent novae, allowing a detailed study of the ejecta using photoionization models. Unusual [O III] auroral-to-nebular line ratios were found and possible scenarios of their origin are discussed. The modeling of the emission line spectrum suggests highly heterogeneous ejecta with masses around or above 3 x 10(-6) M(sun).

HR Del REMNANT ANATOMY USING TWO-DIMENSIONAL SPECTRAL DATA AND THREE-DIMENSIONAL PHOTOIONIZATION SHELL MODELS

The HR Del nova remnant was observed with the IFU-GMOS at Gemini North. The spatially resolved spectral data cube was used in the kinematic, morphological, and abundance analysis of the ejecta. The line maps show a very clumpy shell with two main symmetric structures. The first one is the outer part of the shell seen in H alpha, which forms two rings projected in the sky plane. These ring structures correspond to a closed hourglass shape, first proposed by Harman & O'Brien. The equatorial emission enhancement is caused by the superimposed hourglass structures in the line of sight. The second structure seen only in the [O III] and [N II] maps is located along the polar directions inside the hourglass structure. Abundance gradients between the polar caps and equatorial region were not found. However, the outer part of the shell seems to be less abundant in oxygen and nitrogen than the inner regions. Detailed 2.5-dimensional photoionization modeling of the three-dimensional shell was performed using the mass distribution inferred from the observations and the presence of mass clumps. The resulting model grids are used to constrain the physical properties of the shell as well as the central ionizing source. A sequence of three-dimensional clumpy models including a disk-shaped ionization source is able to reproduce the ionization gradients between polar and equatorial regions of the shell. Differences between shell axial ratios in different lines can also be explained by aspherical illumination. A total shell mass of 9 x 10(-4) M(circle dot) is derived from these models. We estimate that 50%-70% of the shell mass is contained in neutral clumps with density contrast up to a factor of 30.

The young, tight, and low-mass binary TWA22AB: a new calibrator for evolutionary models? Orbit, spectral types, and temperature

Context. Tight binaries discovered in young, nearby associations are ideal targets for providing dynamical mass measurements to test the physics of evolutionary models at young ages and very low masses. Aims. We report the binarity of TWA22 for the first time. We aim at monitoring the orbit of this young and tight system to determine its total dynamical mass using an accurate distance determination. We also intend to characterize the physical properties (luminosity, effective temperature, and surface gravity) of each component based on near-infrared photometric and spectroscopic observations. Methods. We used the adaptive-optics assisted imager NACO to resolve the components, to monitor the complete orbit and to obtain the relative near-infrared photometry of TWA22 AB. The adaptive-optics assisted integral field spectrometer SINFONI was also used to obtain medium-resolution (R(lambda) = 1500-2000) spectra in JHK bands. Comparison with empirical and synthetic librairies were necessary for deriving the spectral type, the effective temperature, and the surface gravity for each component of the system. Results. Based on an accurate trigonometric distance (17.5 +/- 0.2 pc) determination, we infer a total dynamical mass of 220 +/- 21 M(Jup) for the system. From the complete set of spectra, we find an effective temperature T(eff) = 2900(-200)(+200) K for TWA22A and T(eff) = 2900(-100)(+200) for TWA22 B and surface gravities between 4.0 and 5.5 dex. From our photometry and an M6 +/- 1 spectral type for both components, we find luminosities of log(L/L(circle dot)) = -2.11 +/- 0.13 dex and log(L/L(circle dot)) = -2.30 +/- 0.16 dex for TWA22 A and B, respectively. By comparing these parameters with evolutionary models, we question the age and the multiplicity of this system. We also discuss a possible underestimation of the mass predicted by evolutionary models for young stars close to the substellar boundary.

Spectral dependence of aerosol light absorption over the Amazon Basin

In this study, we examine the spectral dependence of aerosol absorption at different sites and seasons in the Amazon Basin. The analysis is based on measurements performed during three intensive field experiments at a pasture site (Fazenda Nossa Senhora, Rondonia) and at a primary forest site (Cuieiras Reserve, Amazonas), from 1999 to 2004. Aerosol absorption spectra were measured using two Aethalometers: a 7-wavelength Aethalometer (AE30) that covers the visible (VIS) to near-infrared (NIR) spectral range, and a 2-wavelength Aethalometer (AE20) that measures absorption in the UV and in the NIR. As a consequence of biomass burning emissions, about 10 times greater absorption values were observed in the dry season in comparison to the wet season. Power law expressions were fitted to the measurements in order to derive the absorption Angstrom exponent, defined as the negative slope of absorption versus wavelength in a log-log plot. At the pasture site, about 70% of the absorption Angstrom exponents fell between 1.5 and 2.5 during the dry season, indicating that biomass burning aerosols have a stronger spectral dependence than soot carbon particles. Angstrom exponents decreased from the dry to the wet season, in agreement with the shift from biomass burning aerosols, predominant in the fine mode, to biogenic and dust aerosols, predominant in the coarse mode. The lowest absorption Angstrom exponents (90% of data below 1.5) were observed at the forest site during the dry season. Also, results indicate that low absorption coefficients were associated with low Angstrom exponents. This finding suggests that biogenic aerosols from Amazonia have a weaker spectral dependence for absorption than biomass burning aerosols, contradicting our expectations of biogenic particles behaving as brown carbon. In a first order assessment, results indicate a small (<1 %) effect of variations in absorption Angstrom exponents on 24-h aerosol forcings, at least in the spectral range of 450-880 nm. Further studies should be taken to assess the corresponding impact in the UV spectral range. The assumption that soot spectral properties represent all ambient light absorbing particles may cause a misjudgment of absorption towards the UV, especially in remote areas. Therefore, it is recommended to measure aerosol absorption at several wavelengths to accurately assess the impact of non-soot aerosols on climate and on photochemical atmospheric processes.

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation,first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

Bilayer graphene dual-gate nanodevice: An ab initio simulation

We study the electronic transport properties of a dual-gated bilayer graphene nanodevice via first-principles calculations. We investigate the electric current as a function of gate length and temperature. Under the action of an external electrical field we show that even for gate lengths up 100 angstrom, a nonzero current is exhibited. The results can be explained by the presence of a tunneling regime due the remanescent states in the gap. We also discuss the conditions to reach the charge neutrality point in a system free of defects and extrinsic carrier doping.

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624408]

Simulation of sugarcane residue decomposition and aboveground growth

Due to the worldwide increase in demand for biofuels, the area cultivated with sugarcane is expected to increase. For environmental and economic reasons, an increasing proportion of the areas are being harvested without burning, leaving the residues on the soil surface. This periodical input of residues affects soil physical, chemical and biological properties, as well as plant growth and nutrition. Modeling can be a useful tool in the study of the complex interactions between the climate, residue quality, and the biological factors controlling plant growth and residue decomposition. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of aboveground phytomass and litter decomposition, and to validate the model through field experiment data. When studying aboveground growth, burned and unburned harvest systems were compared, as well as the effect of mineral fertilizer and organic residue applications. The simulations were performed with data from experiments with different durations, from 12 months to 60 years, in Goiana, TimbaA(0)ba and Pradpolis, Brazil; Harwood, Mackay and Tully, Australia; and Mount Edgecombe, South Africa. The differentiation of two pools in the litter, with different decomposition rates, was found to be a relevant factor in the simulations made. Originally, the model had a basically unlimited layer of mulch directly available for decomposition, 5,000 g m(-2). Through a parameter optimization process, the thickness of the mulch layer closer to the soil, more vulnerable to decomposition, was set as 110 g m(-2). By changing the layer of mulch at any given time available for decomposition, the sugarcane residues decomposition simulations where close to measured values (R (2) = 0.93), contributing to making the CENTURY model a tool for the study of sugarcane litter decomposition patterns. The CENTURY model accurately simulated aboveground carbon stalk values (R (2) = 0.76), considering burned and unburned harvest systems, plots with and without nitrogen fertilizer and organic amendment applications, in different climates and soil conditions.

Simulation of Soil Carbon Dynamics under Sugarcane with the CENTURY Model

Currently there is a trend for the expansion of the area cropped with sugarcane (Saccharum officinarum L.), driven by an increase in the world demand for biofuels, due to economical, environmental, and geopolitical issues. Although sugarcane is traditionally harvested by burning dried leaves and tops, the unburned, mechanized harvest has been progressively adopted. The use of process based models is useful in understanding the effects of plant litter in soil C dynamics. The objective of this work was to use the CENTURY model in evaluating the effect of sugarcane residue management in the temporal dynamics of soil C. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of soil C, validating the model through field experiment data, and finally to make predictions in the long term regarding soil C. The main focus of this work was the comparison of soil C stocks between the burned and unburned litter management systems, but the effect of mineral fertilizer and organic residue applications were also evaluated. The simulations were performed with data from experiments with different durations, from 1 to 60 yr, in Goiana and Timbauba, Pernambuco, and Pradopolis, Sao Paulo, all in Brazil; and Mount Edgecombe, Kwazulu-Natal, South Africa. It was possible to simulate the temporal dynamics of soil C (R(2) = 0.89). The predictions made with the model revealed that there is, in the long term, a trend for higher soil C stocks with the unburned management. This increase is conditioned by factors such as climate, soil texture, time of adoption of the unburned system, and N fertilizer management.

Energy systems contributions in 2,000 m race simulation: a comparison among rowing ergometers and water

This study investigated the energy system contributions of rowers in three different conditions: rowing on an ergometer without and with the slide and rowing in the water. For this purpose, eight rowers were submitted to 2,000 m race simulations in each of the situations defined above. The fractions of the aerobic (W(AER)), anaerobic alactic (W(PCR)) and anaerobic lactic (W([La-])) systems were calculated based on the oxygen uptake, the fast component of excess post-exercise oxygen uptake and changes in net blood lactate, respectively. In the water, the metabolic work was significantly higher [(851 (82) kJ] than during both ergometer [674 (60) kJ] and ergometer with slide [663 (65) kJ] (P <= 0.05). The time in the water [515 (11) s] was higher (P < 0.001) than in the ergometers with [398 (10) s] and without the slide [402 (15) s], resulting in no difference when relative energy expenditure was considered: in the water [99 (9) kJ min(-1)], ergometer without the slide [99.6 (9) kJ min(-1)] and ergometer with the slide [100.2 (9.6) kJ min(-1)]. The respective contributions of the WAER, WPCR and W[La-] systems were water = 87 (2), 7 (2) and 6 (2)%, ergometer = 84 (2), 7 (2) and 9 (2)%, and ergometer with the slide = 84 (2), 7 (2) and 9 (1)%. (V) over dotO(2), HR and lactate were not different among conditions. These results seem to indicate that the ergometer braking system simulates conditions of a bigger and faster boat and not a single scull. Probably, a 2,500 m test should be used to properly simulate in the water single-scull race.