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Emilio Hernandez-Garcia

Publications and source records attributed to Emilio Hernandez-Garcia.

At least 37 records · Page 2Linked to original sources
arXiv2010

Synchronization and entrainment of coupled circadian oscillators

Circadian rhythms in mammals are controlled by the neurons located in the suprachiasmatic nucleus of the hypothalamus. In physiological conditions, the system of neurons is very efficiently entrained by the 24-hour light-dark cycle. Most of the studies carried out so far emphasize the crucial role of the periodicity imposed by the light dark cycle in neuronal synchronization. Nevertheless, heterogeneity as a natural and permanent ingredient of these cellular interactions is seemingly to play a major role in these biochemical processes. In this paper we use a model that considers the neurons of the suprachiasmatic nucleus as chemically-coupled modified Goodwin oscillators, and introduce non-negligible heterogeneity in the periods of all neurons in the form of quenched noise. The system response to the light-dark cycle periodicity is studied as a function of the interneuronal coupling strength, external forcing amplitude and neuronal heterogeneity. Our results indicate that the right amount of heterogeneity helps the extended system to respond globally in a more coherent way to the external forcing. Our proposed mechanism for neuronal synchronization under external periodic forcing is based on heterogeneity-induced oscillators death, damped oscillators being more entrainable by the external forcing than the self-oscillating neurons with different periods.

physics.bio-ph↗
arXiv2009

How Gaussian competition leads to lumpy or uniform species distributions

A central model in theoretical ecology considers the competition of a range of species for a broad spectrum of resources. Recent studies have shown that essentially two different outcomes are possible. Either the species surviving competition are more or less uniformly distributed over the resource spectrum, or their distribution is 'lumped' (or 'clumped'), consisting of clusters of species with similar resource use that are separated by gaps in resource space. Which of these outcomes will occur crucially depends on the competition kernel, which reflects the shape of the resource utilization pattern of the competing species. Most models considered in the literature assume a Gaussian competition kernel. This is unfortunate, since predictions based on such a Gaussian assumption are not robust. In fact, Gaussian kernels are a border case scenario, and slight deviations from this function can lead to either uniform or lumped species distributions. Here we illustrate the non-robustness of the Gaussian assumption by simulating different implementations of the standard competition model with constant carrying capacity. In this scenario, lumped species distributions can come about by secondary ecological or evolutionary mechanisms or by details of the numerical implementation of the model. We analyze the origin of this sensitivity and discuss it in the context of recent applications of the model.

q-bio.PE↗
arXiv2009

Species competition: coexistence, exclusion and clustering

We present properties of Lotka-Volterra equations describing ecological competition among a large number of competing species. First we extend to the case of a non-homogeneous niche space stability conditions for solutions representing species coexistence. Second, we discuss mechanisms leading to species clustering and obtain an analytical solution for a lumped state in a specific instance of the system. We also discuss how realistic ecological interactions may result in different types of competition coefficients.

q-bio.PE↗
arXiv2009

Noisy continuous--opinion dynamics

We study the Deffuant et al. model for continuous--opinion dynamics under the influence of noise. In the original version of this model, individuals meet in random pairwise encounters after which they compromise or not depending of a confidence parameter. Free will is introduced in the form of noisy perturbations: individuals are given the opportunity to change their opinion, with a given probability, to a randomly selected opinion inside the whole opinion space. We derive the master equation of this process. One of the main effects of noise is to induce an order-disorder transition. In the disordered state the opinion distribution tends to be uniform, while for the ordered state a set of well defined opinion groups are formed, although with some opinion spread inside them. Using a linear stability analysis we can derive approximate conditions for the transition between opinion groups and the disordered state. The master equation analysis is compared with direct Monte-Carlo simulations. We find that the master equation and the Monte-Carlo simulations do not always agree due to finite-size induced fluctuations that we analyze in some detail.

physics.soc-ph↗
arXiv2009

Joint effects of nutrients and contaminants on the dynamics of a food chain in marine ecosystems

We analyze the joint effect of contaminants and nutrient loading on population dynamics of marine food chains by means of bifurcation analysis. Contaminant toxicity is assumed to alter mortality of some species with a sigmoidal dose-response relationship. A generic effect of pollutants is to delay transitions to complex dynamical states towards higher nutrient load values, but more counterintuitive consequences arising from indirect effects are described. In particular, the top predator seems to be the species more affected by pollutants, even when contaminant is toxic only to lower trophic levels.

q-bio.PE↗
arXiv2009

Simple models for scaling in phylogenetic trees

Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological species, are examples of trees for which such scaling is not observed. With this motivation, we analyze numerically two branching models leading to non-logarithmic scaling of the depth with the number of leaves. For Ford's alpha model, although a power-law scaling of the depth with tree size was established analytically, our numerical results illustrate that the asymptotic regime is approached only at very large tree sizes. We introduce here a new model, the activity model, showing analytically and numerically that it also displays a power-law scaling of the depth with tree size at a critical parameter value.

q-bio.QM↗
arXiv2008

Universal functions and exactly solvable chaotic systems

A universal differential equation is a nontrivial differential equation the solutions of which approximate to arbitrary accuracy any continuous function on any interval of the real line. On the other hand, there has been much interest in exactly solvable chaotic maps. An important problem is to generalize these results to continuous systems. Theoretical analysis would allow us to prove theorems about these systems and predict new phenomena. In the present paper we discuss the concept of universal functions and their relevance to the theory of universal differential equations. We present a connection between universal functions and solutions to chaotic systems. We will show the statistical independence between $X(t)$ and $X(t + τ)$ (when $τ$ is not equal to zero) and $X(t)$ is a solution to some chaotic systems. We will construct universal functions that behave as delta-correlated noise. We will construct universal dynamical systems with truly noisy solutions. We will discuss physically realizable dynamical systems with universal-like properties.

nlin.SI↗
arXiv2008

Network analysis identifies weak and strong links in a metapopulation system

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and of usual underlying hypothesis required for the interpretation of classical analysis, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens major perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial.

q-bio.PE↗
arXiv2008

Universal scaling in the branching of the Tree of Life

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.

q-bio.PE↗
arXiv2008

Diversity-induced resonance in a system of globally coupled linear oscillators

The purpose of this paper to analyze in some detail the arguably simplest case of diversity-induced reseonance: that of a system of globally-coupled linear oscillators subjected to a periodic forcing. Diversity appears as the parameters characterizing each oscillator, namely its mass, internal frequency and damping coefficient are drawn from a probability distribution. The main ingredients for the diversity-induced-resonance phenomenon are present in this system as the oscillators display a variability in the individual responses but are induced, by the coupling, to synchronize their responses. A steady state solution for this model is obtained. We also determine the conditions under which it is possible to find a resonance effect.

nlin.AO↗
arXiv2007

Species clustering in competitive Lotka-Volterra models

We study the properties of Lotka-Volterra competitive models in which the intensity of the interaction among species depends on their position along an abstract niche space through a competition kernel. We show analytically and numerically that the properties of these models change dramatically when the Fourier transform of this kernel is not positive definite, due to a pattern forming instability. We estimate properties of the species distributions, such as the steady number of species and their spacings, for different types of kernels.

q-bio.PE↗
arXiv2007

Spectrum of genetic diversity and networks of clonal organisms

Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations was examined using a combination of new tools to analyze microsatellite data in the marine angiosperm Posidonia oceanica. These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. The properties and topology of networks based on genetic distances showed a "small-world" topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in sub-families of closely related individuals. Keywords: genetic networks; small-world networks; genetic diversity; clonal organisms

q-bio.PE↗
arXiv2006

Lagrangian transport through an ocean front in the North-Western Mediterranean Sea

We analyze with the tools of lobe dynamics the velocity field from a numerical simulation of the surface circulation in the Northwestern Mediterranean Sea. We identify relevant hyperbolic trajectories and their manifolds, and show that the transport mechanism known as the `turnstile', previously identified in abstract dynamical systems and simplified model flows, is also at work in this complex and rather realistic ocean flow. In addition nonlinear dynamics techniques are shown to be powerful enough to identify the key geometric structures in this part of the Mediterranean. In particular the North Balearic Front, the westernmost part of the transition zone between saltier and fresher waters in the Western Mediterranean is interpreted in terms of the presence of a semipermanent ``Lagrangian barrier'' across which little transport occurs. Our construction also reveals the routes along which this transport happens. Topological changes in that picture, associated with the crossing by eddies and that may be interpreted as the breakdown of the front, are also observed during the simulation.

physics.ao-ph↗
arXiv2006

Kinematic studies of transport across an island wake, with application to the Canary islands

Transport from nutrient-rich coastal upwellings is a key factor influencing biological activity in surrounding waters and even in the open ocean. The rich upwelling in the North-Western African coast is known to interact strongly with the wake of the Canary islands, giving rise to filaments and other mesoscale structures of increased productivity. Motivated by this scenario, we introduce a simplified two-dimensional kinematic flow describing the wake of an island in a stream, and study the conditions under which there is a net transport of substances across the wake. For small vorticity values in the wake, it acts as a barrier, but there is a transition when increasing vorticity so that for values appropriate to the Canary area, it entrains fluid and enhances cross-wake transport.

nlin.CD↗
arXiv2005

Birth, death and diffusion of interacting particles

Individual-based models of chemical or biological dynamics usually consider individual entities diffusing in space and performing a birth-death type dynamics. In this work we study the properties of a model in this class where the birth dynamics is mediated by the local, within a given distance, density of particles. Groups of individuals are formed in the system and in this paper we concentrate on the study of the properties of these clusters (lifetime, size, and collective diffusion). In particular, in the limit of the interaction distance approaching the system size, a unique cluster appears which helps to understand and characterize the clustering dynamics of the model.

cond-mat.stat-mech↗
arXiv2004

Leaking method approach to surface transport in the Mediterranean Sea from a numerical ocean model

We use Lagrangian diagnostics (the leaking and the exchange methods) to characterize surface transport out of and between selected regions in the Western Mediterranean. Velocity fields are obtained from a numerical model. Residence times of water of Atlantic origin in the Algerian basin, with a strong seasonal dependence, are calculated. Exchange rates between these waters and the ones occupying the northern basin are also evaluated. At surface, northward transport is dominant, and involves filamental features and eddy structures that can be identified with the Algerian eddies. The impact on these results of the presence of small scale turbulent motions is evaluated by adding Lagrangian diffusion.

physics.ao-ph↗
arXiv2004

Fluctuations impact on a pattern-forming model of population dynamics with non-local interactions

A model of interacting random walkers is presented and shown to give rise to patterns consisting in periodic arrangements of fluctuating particle clusters. The model represents biological individuals that die or reproduce at rates depending on the number of neighbors within a given distance. We evaluate the importance of the discrete and fluctuating character of this particle model on the pattern forming process. To this end, a deterministic mean-field description, including a linear stability and a weakly nonlinear analysis, is given and compared with the particle model. The deterministic approach is shown to reproduce some of the features of the discrete description, in particular, the existence of a finite-wavelength instability. Stochasticity in the particle dynamics, however, has strong effects in other important aspects such as the parameter values at which pattern formation occurs, or the nature of the homogeneous phase.

cond-mat.stat-mech↗