Resilience of protein-protein interaction networks as determined by their large-scale topological features

The relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. Particularly, the structure of protein-protein interaction networks is related to important biological functions. In this work, we investigated how such a resilience is determined by the large scale features of the respective networks. Four species are taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements (degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of these networks. We verified that while they exhibit similar structural variations under random node removal, they differ significantly when subjected to intentional attacks (hub removal). As a matter of fact, more complex species tended to exhibit more robust networks. More specifically, we quantified how six important measurements of the networks topology (namely clustering coefficient, average degree of neighbors, average shortest path length, diameter, assortativity coefficient, and slope of the power law degree distribution) correlated with the two entropy measurements. Our results revealed that the fraction of hubs and the average neighbor degree contribute significantly for the resilience of networks. In addition, the topological analysis of the removed hubs indicated that the presence of alternative paths between the proteins connected to hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is underlain in networks and can be applied to the development of protein network models.

A large-scale synthesis of enantiomerically pure gamma-hydroxy-organochalcogenides

Enantiomerically pure (R)- and (S)-gamma-hydroxy-organochalcogenides are prepared using poly-[R]-3-hydroxybutanoate (PHB) as the starting material. (C) 2009 Elsevier Ltd. All rights reserved.

MAGNETOHYDRODYNAMIC SIMULATIONS OF RECONNECTION AND PARTICLE ACCELERATION: THREE-DIMENSIONAL EFFECTS

Magnetic fields can change their topology through a process known as magnetic reconnection. This process in not only important for understanding the origin and evolution of the large-scale magnetic field, but is seen as a possibly efficient particle accelerator producing cosmic rays mainly through the first-order Fermi process. In this work we study the properties of particle acceleration inserted in reconnection zones and show that the velocity component parallel to the magnetic field of test particles inserted in magnetohydrodynamic (MHD) domains of reconnection without including kinetic effects, such as pressure anisotropy, the Hall term, or anomalous effects, increases exponentially. Also, the acceleration of the perpendicular component is always possible in such models. We find that within contracting magnetic islands or current sheets the particles accelerate predominantly through the first-order Fermi process, as previously described, while outside the current sheets and islands the particles experience mostly drift acceleration due to magnetic field gradients. Considering two-dimensional MHD models without a guide field, we find that the parallel acceleration stops at some level. This saturation effect is, however, removed in the presence of an out-of-plane guide field or in three-dimensional models. Therefore, we stress the importance of the guide field and fully three-dimensional studies for a complete understanding of the process of particle acceleration in astrophysical reconnection environments.

Hydrodynamical simulations of Galactic fountains - I. Evolution of single fountains

The ejection of the gas out of the disc in late-type galaxies is related to star formation and is due mainly to Type II supernovae. In this paper, we studied in detail the development of the Galactic fountains in order to understand their dynamical evolution and their influence on the redistribution of the freshly delivered metals over the disc. To this aim, we performed a number of 3D hydrodynamical radiative cooling simulations of the gas in the Milky Way where the whole Galaxy structure, the Galactic differential rotation and the supernova explosions generated by a single OB association are considered. A typical fountain powered by 100 Type II supernovae may eject material up to similar to 2 kpc which than collapses back mostly in the form of dense, cold clouds and filaments. The majority of the gas lifted up by the fountains falls back on the disc remaining within a radial distance Delta R = 0.5 kpc from the place where the fountain originated. This localized circulation of disc gas does not influence the radial chemical gradients on large scale, as required by the chemical models of the Milky Way which reproduce the metallicity distribution without invoking large fluxes of metals. Simulations of multiple fountains fuelled by Type II supernovae of different OB associations will be presented in a companion paper.

Numerical evidence against a conjecture on the cover time of planar graphs

We investigate a conjecture on the cover times of planar graphs by means of large Monte Carlo simulations. The conjecture states that the cover time tau (G(N)) of a planar graph G(N) of N vertices and maximal degree d is lower bounded by tau (G(N)) >= C(d)N(lnN)(2) with C(d) = (d/4 pi) tan(pi/d), with equality holding for some geometries. We tested this conjecture on the regular honeycomb (d = 3), regular square (d = 4), regular elongated triangular (d = 5), and regular triangular (d = 6) lattices, as well as on the nonregular Union Jack lattice (d(min) = 4, d(max) = 8). Indeed, the Monte Carlo data suggest that the rigorous lower bound may hold as an equality for most of these lattices, with an interesting issue in the case of the Union Jack lattice. The data for the honeycomb lattice, however, violate the bound with the conjectured constant. The empirical probability distribution function of the cover time for the square lattice is also briefly presented, since very little is known about cover time probability distribution functions in general.

Estimating wave spectra from the motions of moored vessels: Experimental validation

The practicability of estimating directional wave spectra based on a vessel`s 1st order response has been recently addressed by several researchers. Different alternatives regarding statistical inference methods and possible drawbacks that could arise from their application have been extensively discussed, with an apparent preference for estimations based on Bayesian inference algorithms. Most of the results on this matter, however, rely exclusively on numerical simulations or at best on few and sparse full-scale measurements, comprising a questionable basis for validation purposes. This paper discusses several issues that have recently been debated regarding the advantages of Bayesian inference and different alternatives for its implementation. Among those are the definition of the best set of input motions, the number of parameters required for guaranteeing smoothness of the spectrum in frequency and direction and how to determine their optimum values. These subjects are addressed in the light of an extensive experimental campaign performed with a small-scale model of an FPSO platform (VLCC hull), which was conducted in an ocean basin in Brazil. Tests involved long and short crested seas with variable levels of directional spreading and also bimodal conditions. The calibration spectra measured in the tank by means of an array of wave probes configured the paradigm for estimations. Results showed that a wide range of sea conditions could be estimated with good precision, even those with somewhat low peak periods. Some possible drawbacks that have been pointed out in previous works concerning the viability of employing large vessels for such a task are then refuted. Also, it is shown that a second parameter for smoothing the spectrum in frequency may indeed increase the accuracy in some situations, although the criterion usually proposed for estimating the optimum values (ABIC) demands large computational effort and does not seem adequate for practical on-board systems, which require expeditious estimations. (C) 2009 Elsevier Ltd. All rights reserved.

A new scale-invariant ratio and finite-size scaling for the stochastic susceptible-infected-recovered model

The critical behavior of the stochastic susceptible-infected-recovered model on a square lattice is obtained by numerical simulations and finite-size scaling. The order parameter as well as the distribution in the number of recovered individuals is determined as a function of the infection rate for several values of the system size. The analysis around criticality is obtained by exploring the close relationship between the present model and standard percolation theory. The quantity UP, equal to the ratio U between the second moment and the squared first moment of the size distribution multiplied by the order parameter P, is shown to have, for a square system, a universal value 1.0167(1) that is the same for site and bond percolation, confirming further that the SIR model is also in the percolation class.

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Scavenging processes of atmospheric particulate matter: a numerical modeling of case studies

Below cloud scavenging processes have been investigated considering a numerical simulation, local atmospheric conditions and particulate matter (PM) concentrations, at different sites in Germany. The below cloud scavenging model has been coupled with bulk particulate matter counter TSI (Trust Portacounter dataset, consisting of the variability prediction of the particulate air concentrations during chosen rain events. The TSI samples and meteorological parameters were obtained during three winter Campaigns: at Deuselbach, March 1994, consisting in three different events; Sylt, April 1994 and; Freiburg, March 1995. The results show a good agreement between modeled and observed air concentrations, emphasizing the quality of the conceptual model used in the below cloud scavenging numerical modeling. The results between modeled and observed data have also presented high square Pearson coefficient correlations over 0.7 and significant, except the Freiburg Campaign event. The differences between numerical simulations and observed dataset are explained by the wind direction changes and, perhaps, the absence of advection mass terms inside the modeling. These results validate previous works based on the same conceptual model.

Numerical investigation of the three-dimensional secondary instabilities in the time-developing compressible mixing layer

Mixing layers are present in very different types of physical situations such as atmospheric flows, aerodynamics and combustion. It is, therefore, a well researched subject, but there are aspects that require further studies. Here the instability of two-and three-dimensional perturbations in the compressible mixing layer was investigated by numerical simulations. In the numerical code, the derivatives were discretized using high-order compact finite-difference schemes. A stretching in the normal direction was implemented with both the objective of reducing the sound waves generated by the shear region and improving the resolution near the center. The compact schemes were modified to work with non-uniform grids. Numerical tests started with an analysis of the growth rate in the linear regime to verify the code implementation. Tests were also performed in the non-linear regime and it was possible to reproduce the vortex roll-up and pairing, both in two-and three-dimensional situations. Amplification rate analysis was also performed for the secondary instability of this flow. It was found that, for essentially incompressible flow, maximum growth rates occurred for a spanwise wavelength of approximately 2/3 of the streamwise spacing of the vortices. The result demonstrated the applicability of the theory developed by Pierrehumbet and Widnall. Compressibility effects were then considered and the maximum growth rates obtained for relatively high Mach numbers (typically under 0.8) were also presented.

A positional FEM Formulation for geometrical non-linear analysis of shells

This work presents a fully non-linear finite element formulation for shell analysis comprising linear strain variation along the thickness of the shell and geometrically exact description for curved triangular elements. The developed formulation assumes positions and generalized unconstrained vectors as the variables of the problem, not displacements and finite rotations. The full 3D Saint-Venant-Kirchhoff constitutive relation is adopted and, to avoid locking, the rate of thickness variation enhancement is introduced. As a consequence, the second Piola-Kirchhoff stress tensor and the Green strain measure are employed to derive the specific strain energy potential. Curved triangular elements with cubic approximation are adopted using simple notation. Selected numerical simulations illustrate and confirm the objectivity, accuracy, path independence and applicability of the proposed technique.

The role of the observed tropical convection in the generation of frost events in the southern cone of South America

Based on previous results obtained from observations and linear wave theory analysis, the hypothesis that large-scale patterns can generate extreme cold events in southeast South America through the propagation of remotely excited Rossby waves was already suggested. This work will confirm these findings and extend their analysis through a series of numerical experiments using a primitive equation model where waves are excited by a thermal forcing situated in positions chosen according to observed convection anomalies over the equatorial region. The basic state used for these experiments is a composite of austral winters with maximum and minimum frequency of occurrence of generalized frosts that can affect a large area known as the Wet Pampas located in the central and eastern part of Argentina. The results suggest that stationary Rossby waves may be one important mechanism linking anomalous tropical convection with the extreme cold events in the Wet Pampas. The combination of tropical convection and a specific basic state can generate the right environment to guide the Rossby waves trigged by the tropical forcing towards South America. Depending on the phase of the waves entering the South American continent, they can favour the advection of anomalous wind at low levels from the south carrying cold and dry air over the whole southern extreme of the continent, producing a generalized frost in the Wet Pampa region. On the other hand, when a basic state based on the composites of minimum frosts is used, an anomalous anticyclone over the southern part of the continent generates a circulation with a south-southeast wind which brings maritime air and therefore humidity over the Wet Pampas region, creating negative temperature anomalies only over the northeastern part of the region. Under these conditions even if frosts occur they would not be generalized, as observed for the other basic state with maximum frequency of occurrence of generalized frosts.

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.

Transition to chaotic scattering: Signatures in the differential cross section

We show that bifurcations in chaotic scattering manifest themselves through the appearance of an infinitely fine-scale structure of singularities in the cross section. These ""rainbow singularities"" are created in a cascade, which is closely related to the bifurcation cascade undergone by the set of trapped orbits (the chaotic saddle). This cascade provides a signature in the differential cross section of the complex pattern of bifurcations of orbits underlying the transition to chaotic scattering. We show that there is a power law with a universal coefficient governing the sequence of births of rainbow singularities and we verify this prediction by numerical simulations.

EVOLUTION AND LIFETIME OF TRANSIENT CLUMPS IN THE TURBULENT INTERSTELLAR MEDIUM

We study the evolution of dense clumps and provide an argument that the existence of the clumps is not limited by their crossing times. We claim that the lifetimes of the clumps are determined by turbulent motions on a larger scale, and we predict the correlation of clump lifetime with column density. We use numerical simulations to successfully test this relation. In addition, we study the morphological asymmetry and the magnetization of the clumps as functions of their masses.