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Biomedical subjects

Oreste Piro

Publications and source records attributed to Oreste Piro.

15 recordsLinked to original sources

Embryonic nodal flow and the dynamics of nodal vesicular parcels.

We address with fluid-dynamical simulations using direct numerical techniques three important and fundamental questions with respect to fluid flow within the mouse node and left-right development. First, we consider the differences between what is experimentally observed when assessing cilium-induced fluid flow in the mouse node in vitro and what is to be expected in vivo. The distinction is that in vivo, the leftward fluid flow across the mouse node takes place within a closed system and is consequently confined, while this is no longer the case on removing the covering membrane and immersing the embryo in a fluid-filled volume to perform in vitro experiments. Although there is a central leftward flow in both instances, we elucidate some important distinctions about the closed in vivo situation. Second, we model the movement of the newly discovered nodal vesicular parcels (NVPs) across the node and demonstrate that the flow should indeed cause them to accumulate on the left side of the node, as required for symmetry breaking. Third, we discuss the rupture of NVPs. Based on the biophysical properties of these vesicles, we argue that the morphogens they contain are likely not delivered to the surrounding cells by their mechanical rupture either by the cilia or the flow, and rupture must instead be induced by an as yet undiscovered biochemical mechanism.

Animals↗

Control of particles in microelectrode devices.

The impact of the convective fluid motion induced by the electric fields on the dielectrophoretic manipulation of particles is investigated theoretically and experimentally. By means of a simplified model a channel with a periodic array of microelectrodes we show that electroconvective flows induce the formation of traps for particles, providing a dynamical mechanism to control microparticles in such devices. We demonstrate experimentally the theoretically predicted dynamical phenomena.

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Chiral symmetry breaking during crystallization: an advection-mediated nonlinear autocatalytic process.

When a chiral chemical compound crystallizes from solution or from its melt, stirring often results in the formation of crystals of just one of the two possible enantiomers, while without fluid advection both enantiomers are formed. We demonstrate with simulations of the dynamics of the system that secondary nucleation is a nonlinear autocatalytic phenomenon that can explain these observations. Furthermore, we present theoretical arguments and experimental results that suggest that at the microscale the mechanism of secondary nucleation is whisker crystal growth and dispersion in the fluid flow.

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Fluid-dynamical basis of the embryonic development of left-right asymmetry in vertebrates.

Experimental work in developmental biology has recently shown in mice that fluid flow driven by rotating cilia in the node, a structure present in the early stages of growth of vertebrate embryos, is responsible for determining the normal development of the left-right axis, with the heart on the left of the body, the liver on the right, and so on. The role of physics, in particular, of fluid dynamics, in the process is one of the important questions that remain to be answered. We show with an analysis of the fluid dynamics of the nodal flow in the developing embryo that the leftward flow that has been experimentally observed may be produced by the monocilia driving it being tilted toward the posterior. We propose a model for morphogen transport and mixing in the nodal flow and discuss how the development of left-right asymmetry might be initiated.

Animals↗

Thermo-optical "canard orbits" and excitable limit cycles.

We demonstrate experimentally and theoretically the existence of canard orbits and excitable quasiharmonic limit cycles in the thermo-optical dynamics of semiconductor optical amplifiers. We also observe the phase locking of the noise-induced spikes to the small-amplitude Hopf quasiharmonic oscillations, recently predicted by Makarov, Nekorkin, and Velarde [Phys. Rev. Lett. 86, 3431 (2001)]].

Biological Clocks↗

Effective dimensions and percolation in hierarchically structured scale-free networks.

We introduce appropriate definitions of dimensions in order to characterize the fractal properties of complex networks. We compute these dimensions in a hierarchically structured network of particular interest. In spite of the nontrivial character of this network that displays scale-free connectivity among other features, it turns out to be approximately one dimensional. The dimensional characterization is in agreement with the results on statistics of site percolation and other dynamical processes implemented on such a network.

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Experimental evidence of van der Pol-Fitzhugh-Nagumo dynamics in semiconductor optical amplifiers.

Thermo-optical pulsing in semiconductor amplifiers is experimentally shown to correspond to a very common excitable scenario (the van der Pol-Fitzhugh-Nagumo system). Self-sustained oscillations appear in the sequence predicted by this simple dynamical model as we change either the injection level or the bias current. Periodic modulation of these parameters leads to the characteristic phase-locking structure. Furthermore, coherence resonance is observed when external noise is added to the system.

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Bubbling and on-off intermittency in bailout embeddings.

We establish and investigate the conceptual connection between the dynamics of the bailout embedding of a Hamiltonian system and the dynamical regimes associated with the occurrence of bubbling and blowout bifurcations. The roles of the invariant manifold and the dynamics restricted to it, required in bubbling and blowout bifurcating systems, are played in the bailout embedding by the embedded Hamiltonian dynamical system. The Hamiltonian nature of the dynamics is precisely the distinctive feature of this instance of a bubbling or blowout bifurcation. The detachment of the embedding trajectories from the original ones can thus be thought of as transient on-off intermittency, and noise-induced avoidance of some regions of the embedded phase space can be recognized as Hamiltonian bubbling.

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Excitable media in open and closed chaotic flows.

We investigate the response of an excitable medium to a localized perturbation in the presence of a two-dimensional smooth chaotic flow. Two distinct types of flows are numerically considered: open and closed. For both of them three distinct regimes are found, depending on the relative strengths of the stirring and the rate of the excitable reaction. In order to clarify and understand the role of the many competing mechanisms present, simplified models of the process are introduced. They are one-dimensional baker-map models for the flow and a one-dimensional approximation for the transverse profile of the filaments observed in the concentration patterns.

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Bailout embeddings and neutrally buoyant particles in three-dimensional flows.

We use the bailout embeddings of three-dimensional volume-preserving maps to study qualitatively the dynamics of small spherical neutrally buoyant impurities suspended in a time-periodic incompressible fluid flow. The accumulation of impurities in tubular vortical structures, the detachment of particles from fluid trajectories near hyperbolic invariant lines, and the formation of nontrivial three-dimensional structures in the distribution of particles are predicted.

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Subharmonic stochastic synchronization and resonance in neuronal systems.

We study the response of a model neuron, driven simultaneously by noise and at least two weak periodic signals. We focus on signals with frequencies components kf(0),(k+1)f(0),...(k+n)f(0) with k>1. The neuron's output is a sequence of pulses spaced at random interpulse intervals. We find an optimum input noise intensity for which the output pulses are spaced approximately 1/f(0), i.e., there is a stochastic resonance (SR) at a frequency missing in the input. Even higher noise intensities uncover additional, but weaker, resonances at frequencies present in the input. This is a different form of SR whereby the most robust resonance is the one enhancing a frequency, which is absent in the input, and which is not possible to recover via any linear processing. This can be important in understanding sensory systems including the neuronal mechanism for perception of complex tones.

Algorithms↗

Bailout embeddings, targeting of invariant tori, and the control of Hamiltonian chaos.

We introduce a technique, which we term bailout embedding, that can be used to target orbits having particular properties out of all orbits in a flow or map. We explicitly construct a bailout embedding for Hamiltonian systems so as to target invariant tori. We show how the bailout dynamics are able to lock onto extremely small regular islands in a chaotic sea.

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Noise- and inertia-induced inhomogeneity in the distribution of small particles in fluid flows.

The dynamics of small spherical neutrally buoyant particulate impurities immersed in a two-dimensional fluid flow are known to lead to particle accumulation in the regions of the flow in which vorticity dominates over strain, provided that the Stokes number of the particles is sufficiently small. If the flow is viewed as a Hamiltonian dynamical system, it can be seen that the accumulations occur in the nonchaotic parts of the phase space: the Kolmogorov-Arnold-Moser tori. This has suggested a generalization of these dynamics to Hamiltonian maps, dubbed a bailout embedding. In this paper we use a bailout embedding of the standard map to mimic the dynamics of neutrally buoyant impurities subject not only to drag but also to fluctuating forces modeled as white noise. We find that the generation of inhomogeneities associated with the separation of particle from fluid trajectories is enhanced by the presence of noise, so that they appear in much broader ranges of the Stokes number than those allowing spontaneous separation. (c) 2002 American Institute of Physics.

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Population dynamics advected by chaotic flows: A discrete-time map approach.

A discrete-time model of reacting evolving fields, transported by a bidimensional chaotic fluid flow, is studied. Our approach is based on the use of a Lagrangian scheme where fluid particles are advected by a two-dimensional symplectic map possibly yielding Lagrangian chaos. Each fluid particle carries concentrations of active substances which evolve according to its own reaction dynamics. This evolution is also modeled in terms of maps. Motivated by the question, of relevance in marine ecology, of how a localized distribution of nutrients or preys affects the spatial structure of predators transported by a fluid flow, we study a specific model in which the population dynamics is given by a logistic map with space-dependent coefficient, and advection is given by the standard map. Fractal and random patterns in the Eulerian spatial concentration of predators are obtained under different conditions. Exploiting the analogies of this coupled-map (advection plus reaction) system with a random map, some features of these patterns are discussed. (c) 2001 American Institute of Physics.

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Analytical and numerical studies of noise-induced synchronization of chaotic systems.

We study the effect that the injection of a common source of noise has on the trajectories of chaotic systems, addressing some contradictory results present in the literature. We present particular examples of one-dimensional maps and the Lorenz system, both in the chaotic region, and give numerical evidence showing that the addition of a common noise to different trajectories, which start from different initial conditions, leads eventually to their perfect synchronization. When synchronization occurs, the largest Lyapunov exponent becomes negative. For a simple map we are able to show this phenomenon analytically. Finally, we analyze the structural stability of the phenomenon. (c) 2001 American Institute of Physics.

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