Slicing the metric space to provide quick indexing of complex data in the main memory

Searching in a dataset for elements that are similar to a given query element is a core problem in applications that manage complex data, and has been aided by metric access methods (MAMs). A growing number of applications require indices that must be built faster and repeatedly, also providing faster response for similarity queries. The increase in the main memory capacity and its lowering costs also motivate using memory-based MAMs. In this paper. we propose the Onion-tree, a new and robust dynamic memory-based MAM that slices the metric space into disjoint subspaces to provide quick indexing of complex data. It introduces three major characteristics: (i) a partitioning method that controls the number of disjoint subspaces generated at each node; (ii) a replacement technique that can change the leaf node pivots in insertion operations; and (iii) range and k-NN extended query algorithms to support the new partitioning method, including a new visit order of the subspaces in k-NN queries. Performance tests with both real-world and synthetic datasets showed that the Onion-tree is very compact. Comparisons of the Onion-tree with the MM-tree and a memory-based version of the Slim-tree showed that the Onion-tree was always faster to build the index. The experiments also showed that the Onion-tree significantly improved range and k-NN query processing performance and was the most efficient MAM, followed by the MM-tree, which in turn outperformed the Slim-tree in almost all the tests. (C) 2010 Elsevier B.V. All rights reserved.

Numerical solution of the eXtended Pom-Pom model for viscoelastic free surface flows

In this paper we present a finite difference method for solving two-dimensional viscoelastic unsteady free surface flows governed by the single equation version of the eXtended Pom-Pom (XPP) model. The momentum equations are solved by a projection method which uncouples the velocity and pressure fields. We are interested in low Reynolds number flows and, to enhance the stability of the numerical method, an implicit technique for computing the pressure condition on the free surface is employed. This strategy is invoked to solve the governing equations within a Marker-and-Cell type approach while simultaneously calculating the correct normal stress condition on the free surface. The numerical code is validated by performing mesh refinement on a two-dimensional channel flow. Numerical results include an investigation of the influence of the parameters of the XPP equation on the extrudate swelling ratio and the simulation of the Barus effect for XPP fluids. (C) 2010 Elsevier B.V. All rights reserved.

A Floating-point Extended Kalman Filter Implementation for Autonomous Mobile Robots

Localization and Mapping are two of the most important capabilities for autonomous mobile robots and have been receiving considerable attention from the scientific computing community over the last 10 years. One of the most efficient methods to address these problems is based on the use of the Extended Kalman Filter (EKF). The EKF simultaneously estimates a model of the environment (map) and the position of the robot based on odometric and exteroceptive sensor information. As this algorithm demands a considerable amount of computation, it is usually executed on high end PCs coupled to the robot. In this work we present an FPGA-based architecture for the EKF algorithm that is capable of processing two-dimensional maps containing up to 1.8 k features at real time (14 Hz), a three-fold improvement over a Pentium M 1.6 GHz, and a 13-fold improvement over an ARM920T 200 MHz. The proposed architecture also consumes only 1.3% of the Pentium and 12.3% of the ARM energy per feature.

Spectral absorption properties of aerosol particles from 350-2500nm

The aerosol spectral absorption efficiency (alpha(a) in m(2)/g) is measured over an extended wavelength range (350-2500 nm) using an improved calibrated and validated reflectance technique and applied to urban aerosol samples from Sao Paulo, Brazil and from a site in Virginia, Eastern US, that experiences transported urban/industrial aerosol. The average alpha(a) values (similar to 3m(2)/g at 550 nm) for Sao Paulo samples are 10 times larger than a a values obtained for aerosols in Virginia. Sao Paulo aerosols also show evidence of enhanced UV absorption in selected samples, probably associated with organic aerosol components. This extra UV absorption can double the absorption efficiency observed from black carbon alone, therefore reducing by up to 50% the surface UV fluxes, with important implications for climate, UV photolysis rates, and remote sensing from space. Citation: Martins, J.V., P. Artaxo, Y.J. Kaufman, A.D. Castanho, and L.A. Remer (2009), Spectral absorption properties of aerosol particles from 350-2500nm, Geophys. Res. Lett., 36, L13810, doi: 10.1029/2009GL037435.

Bubbling transition to spatial mode excitation in an extended dynamical system

We investigated the transition to spatio-temporal chaos in spatially extended nonlinear dynamical systems possessing an invariant subspace with a low-dimensional attractor. When the latter is chaotic and the subspace is transversely stable we have a spatially homogeneous state only. The onset of spatio-temporal chaos, i.e. the excitation of spatially inhomogeneous modes, occur through the loss of transversal stability of some unstable periodic orbit embedded in the chaotic attractor lying in the invariant subspace. This is a bubbling transition, since there is a switching between spatially homogeneous and nonhomogeneous states with statistical properties of on-off intermittency. Hence the onset of spatio-temporal chaos depends critically both on the existence of a chaotic attractor in the invariant subspace and its being transversely stable or unstable. (C) 2008 Elsevier B.V. All rights reserved.

A portable Compton spectrometer for clinical X-ray beams in the energy range 20-150 keV

Primary beam spectra were obtained for an X-ray industrial equipment (40-150 kV), and for a clinical mammography apparatus (25-35 kV) from beams scattered at angles close to 90 degrees, measured with a CdTe Compton spectrometer. Actual scattering angles were determined from the Compton energy shift of characteristic X-rays or spectra end-point energy. Evaluated contribution of coherent scattering amounts to more than 15% of fluence in mammographic beams. This technique can be used in clinical environments. (C) 2010 Elsevier Ltd. All rights reserved.

Dielectric Dispersion of Water in the Frequency Range from 10 mHz to 30 MHz

We investigate the dielectric dispersion of water, specially in the low-frequency range, by using the impedance spectroscopy technique. The frequency dependencies of the real R and imaginary Z parts of the impedance Could not be explained by means of the Usual description of the dielectric properties of the water as all insulating liquid containing ions. This is due to the incomplete knowledge of the parameters entering in the fundamental equations describing the evolution of the system, and oil the mechanisms regulating the exchange of charge of the cell with the external circuit. We propose a simple description of our experimental data based on the model of Debye, by invoking a dc conductivity of the cell, related to the nonblocking character of the electrodes. A discussion on the electric Circuits able to simulate the cell under investigation, based oil bulk and Surface elements, is also reported. We find that the simple circuit formed by a series of two parallels of resistance and capacitance is able to reproduce the experimental data concerning the real and imaginary part of the electrical impedance of the cell for frequency larger than 1 Hz. According to this description, one of the parallels takes into account the electrical properties of interface between the electrode and water, and the other of the bulk. For frequency lower than 1 Hz, a good agreement with the experimental data is obtained by simulating the electrical properties of the interface by means of the constant phase element.

Percolation in a network with long-range connections: Implications for cytoskeletal structure and function

Cell shape, signaling, and integrity depend on cytoskeletal organization. In this study we describe the cytoskeleton as a simple network of filamentary proteins (links) anchored by complex protein structures (nodes). The structure of this network is regulated by a distance-dependent probability of link formation as P = p/d(s), where p regulates the network density and s controls how fast the probability for link formation decays with node distance (d). It was previously shown that the regulation of the link lengths is crucial for the mechanical behavior of the cells. Here we examined the ability of the two-dimensional network to percolate (i.e. to have end-to-end connectivity), and found that the percolation threshold depends strongly on s. The system undergoes a transition around s = 2. The percolation threshold of networks with s < 2 decreases with increasing system size L, while the percolation threshold for networks with s > 2 converges to a finite value. We speculate that s < 2 may represent a condition in which cells can accommodate deformation while still preserving their mechanical integrity. Additionally, we measured the length distribution of F-actin filaments from publicly available images of a variety of cell types. In agreement with model predictions, cells originating from more deformable tissues show longer F-actin cytoskeletal filaments. (C) 2008 Elsevier B.V. All rights reserved.

Approach to Equilibrium for a Class of Random Quantum Models of Infinite Range

We consider random generalizations of a quantum model of infinite range introduced by Emch and Radin. The generalizations allow a neat extension from the class l (1) of absolutely summable lattice potentials to the optimal class l (2) of square summable potentials first considered by Khanin and Sinai and generalised by van Enter and van Hemmen. The approach to equilibrium in the case of a Gaussian distribution is proved to be faster than for a Bernoulli distribution for both short-range and long-range lattice potentials. While exponential decay to equilibrium is excluded in the nonrandom l (1) case, it is proved to occur for both short and long range potentials for Gaussian distributions, and for potentials of class l (2) in the Bernoulli case. Open problems are discussed.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Extended analysis of the Al-like argon spectrum

A new analysis of the aluminium-like five times ionized argon (Ar VI) spectrum in the vacuum ultraviolet region is reported in this paper. Two adjusted and 14 new energy levels and 68 new classified lines between the configurations 3s(2)3p, 3p(3), 3s3p3d, 3s(2)4p and 3s3p(2), 3s(2)(3d + 4d + 5d), 3s(2)5s, 3p(2)3d, 3s3d(2) were obtained. Atomic calculation using the HFR program was also used in the analysis.

Static Hopfions in the extended Skyrme-Faddeev model

We construct static soliton solutions with non-zero Hopf topological charges to a theory which is an extension of the Skyrme-Faddeev model by the addition of a further quartic term in derivatives. We use an axially symmetric ansatz based on toroidal coordinates, and solve the resulting two coupled non-linear partial differential equations in two variables by a successive over-relaxation (SOR) method. We construct numerical solutions with Hopf charge up to four, and calculate their analytical behavior in some limiting cases. The solutions present an interesting behavior under the changes of a special combination of the coupling constants of the quartic terms. Their energies and sizes tend to zero as that combination approaches a particular special value. We calculate the equivalent of the Vakulenko and Kapitanskii energy bound for the theory and find that it vanishes at that same special value of the coupling constants. In addition, the model presents an integrable sector with an in finite number of local conserved currents which apparently are not related to symmetries of the action. In the intersection of those two special sectors the theory possesses exact vortex solutions (static and time dependent) which were constructed in a previous paper by one of the authors. It is believed that such model describes some aspects of the low energy limit of the pure SU(2) Yang-Mills theory, and our results may be important in identifying important structures in that strong coupling regime.

Exact vortex solutions in an extended Skyrme-Faddeev model

We construct exact vortex solutions in 3+1 dimensions to a theory which is an extension, due to Gies, of the Skyrme-Faddeev model, and that is believed to describe some aspects of the low energy limit of the pure SU(2) Yang-Mills theory. Despite the efforts in the last decades those are the first exact analytical solutions to be constructed for such type of theory. The exact vortices appear in a very particular sector of the theory characterized by special values of the coupling constants, and by a constraint that leads to an infinite number of conserved charges. The theory is scale invariant in that sector, and the solutions satisfy Bogomolny type equations. The energy of the static vortex is proportional to its topological charge, and waves can travel with the speed of light along them, adding to the energy a term proportional to a U(1) No ether charge they create. We believe such vortices may play a role in the strong coupling regime of the pure SU(2) Yang-Mills theory.

Protein lethality investigated in terms of long range dynamical interactions

The relationship between network structure/dynamics and biological function constitutes a fundamental issue in systems biology. However, despite many related investigations, the correspondence between structure and biological functions is not yet fully understood. A related subject that has deserved particular attention recently concerns how essentiality is related to the structure and dynamics of protein interactions. In the current work, protein essentiality is investigated in terms of long range influences in protein-protein interaction networks by considering simulated dynamical aspects. This analysis is performed with respect to outward activations, an approach which models the propagation of interactions between proteins by considering self-avoiding random walks. The obtained results are compared to protein local connectivity. Both the connectivity and the outward activations were found to be strongly related to protein essentiality.

Fast long-range connections in transportation networks

Multidimensional scaling is applied in order to visualize an analogue of the small-world effect implied by edges having different displacement velocities in transportation networks. Our findings are illustrated for two real-world systems, namely the London urban network (streets and underground) and the US highway network enhanced by some of the main US airlines routes. We also show that the travel time in these two networks is drastically changed by attacks targeting the edges with large displacement velocities. (C) 2011 Elsevier By. All rights reserved.