Biomedical subjects

A A Moreira

Publications and source records attributed to A A Moreira.

At least 19 recordsLinked to original sources

PubMed2005

Invasion percolation between two sites.

We investigate the process of invasion percolation between two sites (injection and extraction sites) separated by a distance r in two-dimensional lattices of size L. Our results for the nontrapping invasion percolation model indicate that the statistics of the mass of invaded clusters is significantly dependent on the local occupation probability (pressure) Pe at the extraction site. For Pe = 0, we show that the mass distribution of invaded clusters P(M) follows a power-law P(M) approximately M(-alpha) for intermediate values of the mass M, with an exponent alpha = 1.39+/-0.03. When the local pressure is set to Pe = Pc, where Pc corresponds to the site percolation threshold of the lattice topology, the distribution P(M) still displays a scaling region, but with an exponent alpha = 1.02+/-0.03. This last behavior is consistent with previous results for the cluster statistics in standard percolation. In spite of these differences, the results of our simulations indicate that the fractal dimension of the invaded cluster does not depend significantly on the local pressure Pe and it is consistent with the fractal dimension values reported for standard invasion percolation. Finally, we perform extensive numerical simulations to determine the effect of the lattice borders on the statistics of the invaded clusters and also to characterize the self-organized critical behavior of the invasion percolation process.

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PubMed2005

Mesoscopic modeling for nucleic acid chain dynamics.

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.

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PubMed2003

Statistics of the critical percolation backbone with spatial long-range correlations.

We study the statistics of the backbone cluster between two sites separated by distance r in two-dimensional percolation networks subjected to spatial long-range correlations. We find that the distribution of backbone mass follows the scaling ansatz, P(M(B)) approximately M(-(alpha+1))(B)f(M(B)/M(0)), where f(x)=(alpha+etax(eta))exp(-x(eta)) is a cutoff function and M0 and eta are cutoff parameters. Our results from extensive computational simulations indicate that this scaling form is applicable to both correlated and uncorrelated cases. We show that the exponent alpha can be directly related to the fractal dimension of the backbone d(B), and should therefore depend on the imposed degree of long-range correlations.

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PubMed2002

Traveling length and minimal traveling time for flow through percolation networks with long-range spatial correlations.

We study the distributions of traveling length l and minimal traveling time t(min) through two-dimensional percolation porous media characterized by long-range spatial correlations. We model the dynamics of fluid displacement by the convective movement of tracer particles driven by a pressure difference between two fixed sites ("wells") separated by Euclidean distance r. For strongly correlated pore networks at criticality, we find that the probability distribution functions P(l) and P(t(min)) follow the same scaling ansatz originally proposed for the uncorrelated case, but with quite different scaling exponents. We relate these changes in dynamical behavior to the main morphological difference between correlated and uncorrelated clusters, namely, the compactness of their backbones. Our simulations reveal that the dynamical scaling exponents d(l) and d(t) for correlated geometries take values intermediate between the uncorrelated and homogeneous limiting cases, where l(*) approximately r(d(l)) and t(*)(min) approximately r(d(t)), and l(*) and t(*)(min) are the most probable values of l and t(min), respectively.

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PubMed2002

Extended phase-space dynamics for the generalized nonextensive thermostatistics.

We apply a variant of the Nosé thermostat to derive the Hamiltonian of a nonextensive system that is compatible with the canonical ensemble of the generalized thermostatistics of Tsallis. This microdynamical approach provides a deterministic connection between the generalized nonextensive entropy and power-law behavior. For the case of a simple one-dimensional harmonic oscillator, we confirm by numerical simulation of the dynamics that the distribution of energy H follows precisely the canonical q statistics for different values of the parameter q. The approach is further tested for classical many-particle systems by means of molecular dynamics simulations. The results indicate that the intrinsic nonlinear features of the nonextensive formalism are capable of generating energy fluctuations that obey anomalous probability laws. For q<1 a broad distribution of energy is observed, while for q>1 the resulting distribution is confined to a compact support.

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PubMed2001

Flux front penetration in disordered superconductors.

We investigate flux front penetration in a disordered type-II superconductor by molecular dynamics simulations of interacting vortices and find scaling laws for the front position and the density profile. The scaling can be understood by performing a coarse graining of the system and writing a disordered nonlinear diffusion equation. Integrating numerically the equation, we observe a crossover from flat to fractal front penetration as the system parameters are varied. The value of the fractal dimension indicates that the invasion process is described by gradient percolation.

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PubMed2000