Biomedical subjects

Alessandro P S de Moura

Publications and source records attributed to Alessandro P S de Moura.

14 recordsLinked to original sources

PubMed2006

Traffic of particles in complex networks.

The study of the information flow through communication networks, such as the Internet, is of great importance. In the Internet, information flows in discrete units ("packets"), and the capacity of storage and processing of information of computers is finite. Thus if there are many packets walking on the network at the same time, they will interfere with each other. To understand this, we propose an idealized model, in which many particles move randomly on the network, and the nodes support limited numbers of particles. The maximum number of packets supported by a node can be any positive integer, and can be different for each node. We analyze the statistical properties of this model, obtaining analytical expressions for the mean occupation of each node, for different network topologies. The analytical results are shown to be in agreement with numerical simulations.

Journal Article↗

PubMed2006

Finite-size effects on open chaotic advection.

We study the effects of finite-sizeness on small, neutrally buoyant, spherical particles advected by open chaotic flows. We show that, when observed in the configuration or physical space, the advected finite-size particles disperse about the unstable manifold of the chaotic saddle that governs the passive advection. Using a discrete-time system for the dynamics, we obtain an expression predicting the dispersion of the finite-size particles in terms of their Stokes parameter at the onset of the finite-size induced dispersion. We test our theory in a system derived from a flow and find remarkable agreement between our expression and the numerically measured dispersion.

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PubMed2006

Thin Watts-Strogatz networks.

A modified version of the Watts-Strogatz (WS) network model is proposed, in which the number of shortcuts scales with the network size N as Nalpha, with alpha < 1. In these networks, the ratio of the number of shortcuts to the network size approaches zero as N --> infinity, whereas in the original WS model, this ratio is constant. We call such networks "thin Watts-Strogatz networks." We show that even though the fraction of shortcuts becomes vanishingly small for large networks, they still cause a kind of small-world effect, in the sense that the length L of the network increases sublinearly with the size. We develop a mean-field theory for these networks, which predicts that the length scales as N1-alpha ln N for large N. We also study how a search using only local information works in thin WS networks. We find that the search performance is enhanced compared to the regular network, and we predict that the search time tau scales as N1-alpha/2. These theoretical results are tested using numerical simulations. We comment on the possible relevance of thin WS networks for the design of high-performance low-cost communication networks.

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PubMed2005

Fermi-Dirac statistics and traffic in complex networks.

We propose an idealized model for traffic in a network, in which many particles move randomly from node to node, following the network's links, and it is assumed that at most one particle can occupy any given node. This is intended to mimic the finite forwarding capacity of nodes in communication networks, thereby allowing the possibility of congestion and jamming phenomena. We show that the particles behave like free fermions, with appropriately defined energy-level structure and temperature. The statistical properties of this system are thus given by the corresponding Fermi-Dirac distribution. We use this to obtain analytical expressions for dynamical quantities of interest, such as the mean occupation of each node and the transport efficiency, for different network topologies and particle densities. We show that the subnetwork of free nodes always fragments into small isolated clusters for a sufficiently large number of particles, implying a communication breakdown at some density for all network topologies. These results are compared to direct simulations.

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PubMed2005

Inducing chaos by resonant perturbations: theory and experiment.

We propose a scheme to induce chaos in nonlinear oscillators that either are by themselves incapable of exhibiting chaos or are far away from parameter regions of chaotic behaviors. Our idea is to make use of small, judiciously chosen perturbations in the form of weak periodic signals with time-varying frequency and phase, and to drive the system into a hierarchy of nonlinear resonant states and eventually into chaos. We demonstrate this method by using numerical examples and a laboratory experiment with a Duffing type of electronic circuit driven by a phase-locked loop. The phase-locked loop can track the instantaneous frequency and phase of the Duffing circuit and deliver resonant perturbations to generate robust chaos.

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PubMed2005

Effective dynamics in Hamiltonian systems with mixed phase space.

An adequate characterization of the dynamics of Hamiltonian systems at physically relevant scales has been largely lacking. Here we investigate this fundamental problem and we show that the finite-scale Hamiltonian dynamics is governed by effective dynamical invariants, which are significantly different from the dynamical invariants that describe the asymptotic Hamiltonian dynamics. The effective invariants depend both on the scale of resolution and the region of the phase space under consideration, and they are naturally interpreted within a framework in which the nonhyperbolic dynamics of the Hamiltonian system is modeled as a chain of hyperbolic systems.

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PubMed2004

Reactions in flows with nonhyperbolic dynamics.

We study the reaction dynamics of active particles that are advected passively by 2D incompressible open flows, whose motion is nonhyperbolic. This nonhyperbolicity is associated with the presence of persistent vortices near the wake, wherein fluid is trapped. We show that the fractal equilibrium distribution of the reactants is described by an effective dimension d(eff) , which is a finite resolution approximation to the fractal dimension. Furthermore, d(eff) depends on the resolution epsilon and on the reaction rate 1/tau . As tau is increased, the equilibrium distribution goes through a series of transitions where the effective dimension increases abruptly. These transitions are determined by the complex structure of Cantori surrounding the Kolmogorov-Arnold-Moser (KAM) islands.

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PubMed2004

Chemical and biological activity in three-dimensional flows.

We study the dynamics of active particles advected by three-dimensional (3D) open incompressible flows, both analytically and numerically. We find that 3D reactive flows have fundamentally different dynamical features from those in 2D systems. In particular, we show that the reaction's productivity per reaction step can be enhanced, with respect to the 2D case, while the productivity per unit time in some 3D flows goes to zero in the limit of high mixing rates, in contrast to the 2D behavior, in which the productivity goes to a finite constant. These theoretical predictions are validated by numerical simulations on a generic map model.

Biology↗

PubMed2004

Biased growth processes and the "rich-get-richer" principle.

We study a simple stochastic system with a "rich-get-richer" behavior, in which there are 2 states, and N particles that are successively assigned to one of the states, with a probability p(i) that depends on the states' occupation n(i) as p(i) = n(gamma)(i)/ n(gamma)(1) + n(gamma)(2)). We show that there is a phase transition as gamma crosses the critical value gamma(c) =1. For gamma<1, in the thermodynamic limit the occupations are approximately the same, n(1) approximately n(2). For gamma>1, however, a spontaneous symmetry breaking occurs, and the system goes to a highly clustered configuration, in which one of the states has almost all the particles. These results also hold for any finite number of states (not only two). We show that this "rich-get-richer" principle governs the growth dynamics in a simple model of gravitational aggregation, and we argue that the same is true in all growth processes mediated by long-range forces like gravity.

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PubMed2004

Reactive particles in random flows.

We study the dynamics of chemically or biologically active particles advected by open flows of chaotic time dependence, which can be modeled by a random time dependence of the parameters on a stroboscopic map. We develop a general theory for reactions in such random flows, and derive the reaction equation for this case. We show that there is a singular enhancement of the reaction in random flows, and this enhancement is increased as compared to the nonrandom case. We verify our theory in a model flow generated by four point vortices moving chaotically.

Models, Biological↗

PubMed2003

Searching in small-world networks.

We study the average time it takes to find a desired node in the Watts-Strogatz family of networks. We consider the case when the look-up time can be neglected and when it is important, where the look-up time is the time needed to choose one among all the neighboring nodes of a node at each step in the search. We show that in both cases, the search time is minimum in the small-world regime, when an appropriate distance between the nodes is defined. Through an analytical model, we show that the search time scales as N(1/D(D+1)) for small-world networks, where N is the number of nodes and D is the dimension of the underlying lattice. This model is shown to be in agreement with numerical simulations.

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PubMed2003

Signatures of small-world and scale-free properties in large computer programs.

A large computer program is typically divided into many hundreds or even thousands of smaller units, whose logical connections define a network in a natural way. This network reflects the internal structure of the program, and defines the "information flow" within the program. We show that (1) due to its growth in time this network displays a scale-free feature in that the probability of the number of links at a node obeys a power-law distribution, and (2) as a result of performance optimization of the program the network has a small-world structure. We believe that these features are generic for large computer programs. Our work extends the previous studies on growing networks, which have mostly been for physical networks, to the domain of computer software.

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PubMed2002

Topology of the conceptual network of language.

We define two words in a language to be connected if they express similar concepts. The network of connections among the many thousands of words that make up a language is important not only for the study of the structure and evolution of languages, but also for cognitive science. We study this issue quantitatively, by mapping out the conceptual network of the English language, with the connections being defined by the entries in a Thesaurus dictionary. We find that this network presents a small-world structure, with an amazingly small average shortest path, and appears to exhibit an asymptotic scale-free feature with algebraic connectivity distribution.

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PubMed2002

Rainbow transition in chaotic scattering.

We study the effects of classical chaotic scattering on the differential cross section, which is the measurable quantity in most scattering experiments. We show that the fractal set of singularities in the deflection function is not, in general, reflected on the differential cross section. We show that there are systems in which, as the energy (or some other parameter) crosses a critical value, the system's differential cross-section changes from a singular function having an infinite set of rainbow singularities with structure in all scales to a smooth function with no singularities, the scattering being chaotic on both sides of the transition. We call this metamorphosis the rainbow transition. We exemplify this transition with a physically relevant class of systems. These results have important consequences for the problem of inverse scattering in chaotic systems and for the experimental observation of chaotic scattering.

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