Thermodynamic Stabillity of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2046-2055, 2010

Head shape evolution in Tropidurinae lizards: does locomotion constrain diet?

Different components of complex integrated systems may be specialized for different functions, and thus the selective pressures acting on the system as a whole may be conflicting and can ultimately constrain organismal performance and evolution. The vertebrate cranial system is one of the most striking examples of a complex system with several possible functions, being associated to activities as different as locomotion, prey capture, display and defensive behaviours. Therefore, selective pressures on the cranial system as a whole are possibly complex and may be conflicting. The present study focuses on the influence of potentially conflicting selective pressures (diet vs. locomotion) on the evolution of head shape in Tropidurinae lizards. For example, the expected adaptations leading to flat heads and bodies in species living on vertical structures may conflict with the need for improved bite performance associated with the inclusion of hard or tough prey into the diet, a common phenomenon in Tropidurinae lizards. Body size and six variables describing head shape were quantified in preserved specimens of 23 species, and information on diet and substrate usage was obtained from the literature. No phylogenetic signal was observed in the morphological data at any branch length tested, suggesting adaptive evolution of head shape in Tropidurinae. This pattern was confirmed by both factor analysis and independent contrast analysis, which suggested adaptive co-variation between the head shape and the inclusion of hard prey into the diet. In contrast to our expectations, habitat use did not constrain or drive head shape evolution in the group.

Comparison of the interactomic networks of different species in terms of accessibility

Protein-protein interaction networks were investigated in terms of outward accessibility, which quantifies the effectiveness of each protein in accessing other proteins and is related to the internality of nodes. By comparing the accessibility between 144 ortholog proteins in yeast and the fruit fly, we found that the accessibility tends to be higher among proteins in the fly than in yeast. In addition, z-scores of the accessibility calculated for different species revealed that the protein networks of less evolved species tend to be more random than those of more evolved species. The accessibility was also used to identify the border of the yeast protein interaction network, which was found to be mainly composed of viable proteins.

The web of connections between tourism companies: Structure and dynamics

Tourism destination networks are amongst the most complex dynamical systems, involving a myriad of human-made and natural resources. In this work we report a complex network-based systematic analysis of the Elba (Italy) tourism destination network, including the characterization of its structure in terms of several traditional measurements, the investigation of its modularity, as well as its comprehensive study in terms of the recently reported superedges approach. In particular, structural (the number of paths of distinct lengths between pairs of nodes, as well as the number of reachable companies) and dynamical features (transition probabilities and the inward/outward activations and accessibilities) are measured and analyzed, leading to a series of important findings related to the interactions between tourism companies. Among the several reported results, it is shown that the type and size of the Companies influence strongly their respective activations and accessibilities, while their geographical position does not seem to matter. It is also shown that the Elba tourism network is largely fragmented and heterogeneous, so that it could benefit from increased integration. (C) 2009 Elsevier B.V. All rights reserved.

Electrification of precipitating systems over the Amazon: Physical processes of thunderstorm development

This study investigated the physical processes involved in the development of thunderstorms over southwestern Amazon by hypothesizing causalities for the observed cloud-to-ground lightning variability and the local environmental characteristics. Southwestern Amazon experiences every year a large variety of environmental factors, such as the gradual increase in atmospheric moisture, extremely high pollution due to biomass burning, and intense deforestation, which directly affects cloud development by differential surface energy partition. In the end of the dry period it was observed higher percentages of positive cloud-to-ground (+CG) lightning due to a relative increase in +CG dominated thunderstorms (positive thunderstorms). Positive (negative) thunderstorms initiated preferentially over deforested (forest) areas with higher (lower) cloud base heights, shallower (deeper) warm cloud depths, and higher (lower) convective potential available energy. These features characterized the positive (negative) thunderstorms as deeper (relatively shallower) clouds, stronger (relatively weaker) updrafts with enhanced (decreased) mixed and cold vertically integrated liquid. No significant difference between thunderstorms (negative and positive) and nonthunderstorms were observed in terms of atmospheric pollution, once the atmosphere was overwhelmed by pollution leading to an updraft-limited regime. However, in the wet season both negative and positive thunderstorms occurred during periods of relatively higher aerosol concentration and differentiated size distributions, suggesting an aerosol-limited regime where cloud electrification could be dependent on the aerosol concentration to suppress the warm and enhance the ice phase. The suggested causalities are consistent with the invoked hypotheses, but they are not observed facts; they are just hypotheses based on plausible physical mechanisms.

Confinement-induced phase transition in a DNA-lipid hydrated complex

We study the effect of the soft confinement by fluid lipid bilayers on the spatial organisation of DNA molecules in a DNA-zwitterionic lipid hydrated lamellar complex. The confinement is increased by dehydrating the complex in a controlled way, which leads to a decrease of the water channel thickness separating the periodically stacked bilayers. Using grazing-incidence small-angle X-ray scattering on an oriented thin film, we probe in situ as dehydration proceeds the structure of the DNA-lipid complex. A structural phase transition is evidenced, where an apparently disordered phase of DNA rods embedded within the one-dimensionally ordered lipid lamellar phase observed at high hydration is replaced by a 2D hexagonal structure of DNA molecules intercalated between the lipid bilayers. Copyright (C) EPLA, 2010

On the efficiency of transportation systems in large cities

We report an analysis of the accessibility between different locations in big cities, which is illustrated with respect to London and Paris. The effects of the respective underground systems in facilitating more uniform access to diverse places are also quantified and investigated. It is shown that London and Paris have markedly different patterns of accessibility, as a consequence of the number of bridges and large parks of London, and that in both cases the respective underground systems imply in general, thought in distinct manners, an increase of accessibility. Copyright (C) EPLA, 2010