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Search Results: 1 - 10 of 485532 matches for " Emilio Hernández-García "
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Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle
Marco Patriarca ,Svetlana Postnova,Hans A. Braun,Emilio Hernández-García,Raúl Toral
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002650
Abstract: Recent advances in sleep neurobiology have allowed development of physiologically based mathematical models of sleep regulation that account for the neuronal dynamics responsible for the regulation of sleep-wake cycles and allow detailed examination of the underlying mechanisms. Neuronal systems in general, and those involved in sleep regulation in particular, are noisy and heterogeneous by their nature. It has been shown in various systems that certain levels of noise and diversity can significantly improve signal encoding. However, these phenomena, especially the effects of diversity, are rarely considered in the models of sleep regulation. The present paper is focused on a neuron-based physiologically motivated model of sleep-wake cycles that proposes a novel mechanism of the homeostatic regulation of sleep based on the dynamics of a wake-promoting neuropeptide orexin. Here this model is generalized by the introduction of intrinsic diversity and noise in the orexin-producing neurons, in order to study the effect of their presence on the sleep-wake cycle. A simple quantitative measure of the quality of a sleep-wake cycle is introduced and used to systematically study the generalized model for different levels of noise and diversity. The model is shown to exhibit a clear diversity-induced resonance: that is, the best wake-sleep cycle turns out to correspond to an intermediate level of diversity at the synapses of the orexin-producing neurons. On the other hand, only a mild evidence of stochastic resonance is found, when the level of noise is varied. These results show that disorder, especially in the form of quenched diversity, can be a key-element for an efficient or optimal functioning of the homeostatic regulation of the sleep-wake cycle. Furthermore, this study provides an example of a constructive role of diversity in a neuronal system that can be extended beyond the system studied here.
Wikipedia Information Flow Analysis Reveals the Scale-Free Architecture of the Semantic Space
Adolfo Paolo Masucci,Alkiviadis Kalampokis,Victor Martínez Eguíluz,Emilio Hernández-García
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017333
Abstract: In this paper we extract the topology of the semantic space in its encyclopedic acception, measuring the semantic flow between the different entries of the largest modern encyclopedia, Wikipedia, and thus creating a directed complex network of semantic flows. Notably at the percolation threshold the semantic space is characterised by scale-free behaviour at different levels of complexity and this relates the semantic space to a wide range of biological, social and linguistics phenomena. In particular we find that the cluster size distribution, representing the size of different semantic areas, is scale-free. Moreover the topology of the resulting semantic space is scale-free in the connectivity distribution and displays small-world properties. However its statistical properties do not allow a classical interpretation via a generative model based on a simple multiplicative process. After giving a detailed description and interpretation of the topological properties of the semantic space, we introduce a stochastic model of content-based network, based on a copy and mutation algorithm and on the Heaps' law, that is able to capture the main statistical properties of the analysed semantic space, including the Zipf's law for the word frequency distribution.
Scaling properties of protein family phylogenies
Alejandro Herrada, Víctor M Eguíluz, Emilio Hernández-García, Carlos M Duarte
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-155
Abstract: The comparative analysis between protein and species phylogenies shows that both sets of phylogenies share a remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees.The invariance of the scaling properties at levels spanning from genes to species suggests that rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.During the last century, an important effort has been devoted to the understanding of diversification patterns and processes in terms of branching evolutionary trees [1-7]. Tempo and mode of genetic change, and their connections with tempo and mode of speciation is an important issue in this context. In that sense, we address the question of whether similar forces act across the gene level and species-level evolution [8-10], through a comparative analysis of the topological behavior of protein and species phylogenies.Previous analyses of the topological properties of phylogenies have revealed universal patterns of phylogenetic differentiation [3,6,7,11,12]. This means that the impact of evolutionary forces shaping the diversity of life on Earth on the shape of phylogenetic trees is, at least to the level of detail captured by the descriptors used, similar across a broad range of scales, from macro-evolution to speciation and population differentiation, and across diverse organisms such as eukaryotes, eubacteria, archaea or viruses, thereby. This together with the fact that evolutionary forces work at molecular lev
Burridge-Knopoff Models as Elastic Excitable Media
Julyan H. E. Cartwright,Emilio Hernández-García,Oreste Piro
Physics , 1997, DOI: 10.1103/PhysRevLett.79.527
Abstract: We construct a model of an excitable medium with elastic rather than the usual diffusive coupling. We explore the dynamics of elastic excitable media, which we find to be dominated by low dimensional structures, including global oscillations, period-doubled pacemakers, and propagating fronts. We suggest that examples of elastic excitable media are to be found in such diverse physical systems as Burridge-Knopoff models of frictional sliding, electronic transmission lines, and active optical waveguides.
Oceanic three-dimensional Lagrangian Coherent Structures: A study of a mesoscale eddy in the Benguela ocean region
Jo?o H. Bettencourt,Cristóbal López,Emilio Hernández-García
Physics , 2011, DOI: 10.1016/j.ocemod.2012.04.004
Abstract: We study three dimensional oceanic Lagrangian Coherent Structures (LCSs) in the Benguela region, as obtained from an output of the ROMS model. To do that we first compute Finite-Size Lyapunov exponent (FSLE) fields in the region volume, characterizing mesoscale stirring and mixing. Average FSLE values show a general decreasing trend with depth, but there is a local maximum at about 100 m depth. LCSs are extracted as ridges of the calculated FSLE fields. They present a "curtain-like" geometry in which the strongest attracting and repelling structures appear as quasivertical surfaces. LCSs around a particular cyclonic eddy, pinched off from the upwelling front are also calculated. The LCSs are confirmed to provide pathways and barriers to transport in and out of the eddy.
Synchronization, quantum correlations and entanglement in oscillator networks
Gonzalo Manzano,Fernando Galve,Gian Luca Giorgi,Emilio Hernández-García,Roberta Zambrini
Physics , 2013, DOI: 10.1038/srep01439
Abstract: Synchronization is one of the paradigmatic phenomena in the study of complex systems. It has been explored theoretically and experimentally mostly to understand natural phenomena, but also in view of technological applications. Although several mechanisms and conditions for synchronous behavior in spatially extended systems and networks have been identified, the emergence of this phenomenon has been largely unexplored in quantum systems until very recently. Here we discuss synchronization in quantum networks of different harmonic oscillators relaxing towards a stationary state, being essential the form of dissipation. By local tuning of one of the oscillators, we establish the conditions for synchronous dynamics, in the whole network or in a motif. Beyond the classical regime we show that synchronization between (even unlinked) nodes witnesses the presence of quantum correlations and entanglement. Furthermore, synchronization and entanglement can be induced between two different oscillators if properly linked to a random network.
Hydrodynamic provinces and oceanic connectivity from a transport network help designing marine reserves
Vincent Rossi,Enrico Ser-Giacomi,Cristóbal López,Emilio Hernández-García
Physics , 2014, DOI: 10.1002/2014GL059540
Abstract: Oceanic dispersal and connectivity have been identified as crucial factors for structuring marine populations and designing Marine Protected Areas (MPAs). Focusing on larval dispersal by ocean currents, we propose an approach coupling Lagrangian transport and new tools from Network Theory to characterize marine connectivity in the Mediterranean basin. Larvae of different pelagic durations and seasons are modeled as passive tracers advected in a simulated oceanic surface flow from which a network of connected areas is constructed. Hydrodynamical provinces extracted from this network are delimited by frontiers which match multi-scale oceanographic features. By examining the repeated occurrence of such boundaries, we identify the spatial scales and geographic structures that would control larval dispersal across the entire seascape. Based on these hydrodynamical units, we study novel connectivity metrics for existing reserves. Our results are discussed in the context of ocean biogeography and MPAs design, having ecological and managerial implications.
Characterization of coherent structures in three-dimensional flows using the finite-size Lyapunov exponent
Jo?o H Bettencourt,Cristóbal López,Emilio Hernández-García
Physics , 2012, DOI: 10.1088/1751-8113/46/25/254022
Abstract: In this paper we use the finite size Lyapunov Exponent (FSLE) to characterize Lagrangian coherent structures in three-dimensional (3d) turbulent flows. Lagrangian coherent structures act as the organizers of transport in fluid flows and are crucial to understand their stirring and mixing properties. Generalized maxima (ridges) of the FSLE fields are used to locate these coherent structures. Three-dimensional FSLE fields are calculated in two phenomenologically distinct turbulent flows: a wall-bounded flow (channel flow) and a regional oceanic flow obtained by numerical solution of the primitive equations where two-dimensional turbulence dominates. In the channel flow, autocorrelations of the FSLE field show that the structure is substantially different from the near wall to the mid-channel region and relates well to the more widely studied Eulerian coherent structure of the turbulent channel flow. The ridges of the FSLE field have complex shapes due to the 3d character of the turbulent fluctuations. In the oceanic flow, strong horizontal stirring is present and the flow regime is similar to that of 2d turbulence where the domain is populated by coherent eddies that interact strongly. This in turn results in the presence of high FSLE lines throughout the domain leading to strong non-local mixing. The ridges of the FSLE field are quasi-vertical surfaces, indicating that the horizontal dynamics dominates the flow. Indeed, due to rotation and stratification, vertical motions in the ocean are much less intense than horizontal ones. This suppression is absent in the channel flow, as the 3d character of the FSLE ridges shows.
How reliable are Finite-Size Lyapunov Exponents for the assessment of ocean dynamics?
Ismael Hernández-Carrasco,Emilio Hernández-García,Cristóbal López,Antonio Turiel
Physics , 2010, DOI: 10.1016/j.ocemod.2010.12.006
Abstract: Much of atmospheric and oceanic transport is associated with coherent structures. Lagrangian methods are emerging as optimal tools for their identification and analysis. An important Lagrangian technique which is starting to be widely used in oceanography is that of Finite-Size Lyapunov Exponents (FSLEs). Despite this growing relevance there are still many open questions concerning the reliability of the FSLEs in order to analyse the ocean dynamics. In particular, it is still unclear how robust they are when confronted with real data. In this paper we analyze the effect on this Lagrangian technique of the two most important effects when facing real data, namely noise and dynamics of unsolved scales. Our results, using as a benchmarch data from a primitive numerical model of the Mediterranean Sea, show that even when some dynamics is missed the FSLEs results still give an accurate picture of the oceanic transport properties.
The reduction of plankton biomass induced by mesoscale stirring: a modeling study in the Benguela upwelling
Ismael Hernández-Carrasco,Vincent Rossi,Emilio Hernández-García,Veronique Gar?on,Cristóbal López
Physics , 2011, DOI: 10.1016/j.dsr.2013.09.003
Abstract: Recent studies, both based on remote sensed data and coupled models, showed a reduction of biological productivity due to vigorous horizontal stirring in upwelling areas. In order to better understand this phenomenon, we consider a system of oceanic flow from the Benguela area coupled with a simple biogeochemical model of Nutrient-Phyto-Zooplankton (NPZ) type. For the flow three different surface velocity fields are considered: one derived from satellite altimetry data, and the other two from a regional numerical model at two different spatial resolutions. We compute horizontal particle dispersion in terms of Lyapunov Exponents, and analyzed their correlations with phytoplankton concentrations. Our modelling approach confirms that in the south Benguela there is a reduction of biological activity when stirring is increased. Two-dimensional offshore advection and latitudinal difference in Primary Production, also mediated by the flow, seem to be the dominant processes involved. We estimate that mesoscale processes are responsible for 30 to 50% of the offshore fluxes of biological tracers. In the northern area, other factors not taken into account in our simulation are influencing the ecosystem. We suggest explanations for these results in the context of studies performed in other eastern boundary upwelling areas.
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