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A reconfiguration pattern for distributed embedded systems
Roman Gumzej, Matjaž Colnarič, Wolfgang A. Halang, 2007, original scientific article

Abstract: A reconfiguration pattern for UML-based projects of embedded (real-time) systems is defined. It enables to set up hardware/software configurations, and to specify conditions and methods for dynamic reconfiguration. The reconfiguration pattern was inspired by the reconfiguration management solution of the Specification PEARL methodology, which is based on the standard for Multiprocessor PEARL whose original idea it was to extend the language to enable the programming of distributed real-time applications in PEARL. In Specification PEARL, the possibility for abstract descriptions of hardware and software architectures and for defining mappings from software to hardware components has been enhanced in correspondence with the standard. Here, a UML pattern for reconfiguration management in distributed embedded applications based on concepts from Specification PEARL is presented. Its behavioural, structural and functional aspects are outlined. It addresses stereotype entities from the Specification PEARL language, which were joined in a UML profile, and outlines the related reconfiguration management mechanisms, which were carried over to the mentioned UML pattern. The proposed reconfiguration pattern is to facilitate the development of distributed embedded application in UML with consistent and temporally predictable reconfiguration support. It should also support and enhance the applicationsć flexibility and portability.
Keywords: real-time, distributed, embedded systems, dynamic reconfiguration, UML profiles and patterns, UML-RT, specification PEARL
Published: 31.05.2012; Views: 1320; Downloads: 76
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The dynamics of human gait
Matjaž Perc, 2005, original scientific article

Abstract: We analyse the dynamics of human gait with simple nonlinear time series analysis methods that are appropriate for undergraduate courses. We show that short continuous recordings of the human locomotory apparatus possess properties typical of deterministic chaotic systems. To facilitate interest and enable the reproduction of presented results, as well as to promote applications of nonlinear time series analysis to other experimental systems, we provide user-friendly programs for each implemented method. Thus, we provide new insights into the dynamics of human locomotion, and make an effort to ease the inclusion of nonlinear time series analysis methods into the curriculum at an early stage of the educational process.
Keywords: dynamic systems, chaotic systems, nonlinear dynamics, human gait, human locomotion
Published: 01.06.2012; Views: 1218; Downloads: 25
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Cellular diversity promotes intercellular Ca[sup]2+ wave propagation
Marko Gosak, 2009, original scientific article

Abstract: Calcium ions are an important second messenger in living cells. Calcium signals in form of waves serve as a means of intercellular communication and thus represent a vibrant subject for experimental and theoretical investigations. Here we study the role of cellular variability on the occurrence of ▫$Ca^{2+}$▫ wave propagation in a net of diffusively coupled cells. Dynamics of individual cells is simulated by a mathematical model for ▫$Ca^{2+}$▫ oscillations. Structural diversity of cells is introduced via variations of the bifurcation parameters, which signify cell sensitivity for external stimulation. Remarkably, for sufficient values of variability ▫$Ca^{2+}$▫ waves emerge, which are mostly ordered for intermediate variability strength. We analyze the spatial profile via the autocorrelation function, which confirms aresonance-like response due to the cellular variability. Thus, the reported phenomenon is a novel observation of diversity-induced spatial coherence resonance in a tissue-like media.
Keywords: dynamic systems, waves, calcium oscillations, resonance, diversity-induced resonance, cellular variability, coupled cells, intracellular processes
Published: 07.06.2012; Views: 1106; Downloads: 13
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Establishing the stochastic nature of intracellular calcium oscillations from experimental data
Matjaž Perc, Anne K. Green, C. Jane Dixon, Marko Marhl, 2008, original scientific article

Abstract: Calcium has been established as a key messenger in both intra- and intercellular signaling. Experimentally observed intracellular calcium responses to different agonists show a variety of behaviors from simple spiking to complex oscillatory regimes. Here we study typical experimental traces of calcium oscillations in hepatocytes obtained in response to phenylephrine and ATP. The traces were analyzed with methods of nonlinear time series analysis in order to determine the stochastic/deterministic nature of the intracellular calcium oscillations. Despite the fact that the oscillations appear, visually, to be deterministic yet perturbed by noise, our analyses provide strong evidence that the measured calcium traces in hepatocytes are prevalently of stochastic nature. In particular, bursting calcium oscillations are temporally correlated Gaussian series distorted by a monotonic, instantaneous, time-independent function, whilst the spiking behavior appears to have a dynamical nonlinear component whereby the overall determinism level is still low. The biological importance of this finding is discussed in relation to the mechanisms incorporated in mathematical models as well as the role of stochasticity and determinism at cellular and tissue levels which resemble typical statistical and thermodynamic effects in physics.
Keywords: dynamic systems, stochastic processes, cellular signaling, calcium oscillations, time series analyses, noise, temporal correlation
Published: 07.06.2012; Views: 1118; Downloads: 86
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Stochastic resonance in soft matter systems : combined effects of static and dynamic disorder
Matjaž Perc, Marko Gosak, Samo Kralj, 2008, original scientific article

Abstract: We study the impact of static and dynamic disorder on the phenomenon of stochastic resonance (SR) in a representative soft matter system. Due to their extreme susceptibility to weak perturbations, soft matter systems appear to be excellent candidates for the observation of SR. Indeed, we derive generic SR equations from a polymer-stabilized ferroelectric liquid crystal (LC) cell, which is a typical soft matter representative constituting one of the basic components in several electro-optic applications. We generalize these equations further in order to study an even broader class of qualitatively different systems, especially disclosing the influence of different types of static disorder and interaction ranges amongst LC molecules on the SR response. We determine the required conditions for the observation of SR in the examined system, and moreover, reveal that a random field type static disorder yields qualitatively different responses with respect to random dilution, random bond and spin glass universality classes. In particular, while the latter three decrease the level of dynamic disorder (Gaussian noise) warranting the optimal response, the former evokes exactly the opposite effect, hence increasing the optimal noise level that is needed to resonantly fine-tune the system's response in accordance with the weak deterministic electric field. These observations are shown to be independent of the system size and range of interactions, thus implying their general validity and potentially wide applicability also within other similar settings. We argue that soft matter systems might be particularly adequate as a base for different SR-based sensitive detectors and thus potent candidates for additional theoretical as well as experimental research in the presently outlined direction.
Keywords: dynamic systems, stochastic processes, stochastic resonance, nonlinear dynamical systems, soft-matter systems, static disorder, dynamic disorder
Published: 07.06.2012; Views: 1182; Downloads: 59
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Noise-guided evolution within cyclical interactions
Matjaž Perc, Attila Szolnoki, 2007, original scientific article

Abstract: We study a stochastic predator-prey model on a square lattice, where each of the six species has two superior and two inferior partners. The invasion probabilities between species depend on the predator-prey pair and are supplemented by Gaussian noise. Conditions are identified that warrant the largest impact of noise on the evolutionary process, and the results of Monte Carlo simulations are qualitatively reproduced by a four-point cluster dynamical mean-field approximation. The observed noise-guided evolution is deeply routed in short-range spatial correlations, which is supported by simulations on other host lattice topologies. Our findings are conceptually related to the coherence resonance phenomenon in dynamical systems via the mechanism of threshold duality. We also show that the introduced concept of noise-guided evolution via the exploitation of threshold duality is not limited to predator-prey cyclical interactions, but may apply to models of evolutionary game theory as well, thus indicating its applicability in several different fields of research.
Keywords: dynamic systems, stochastic processes, cyclical interactions, evolutionary rules, flow simulations, Monte Carlo simulations
Published: 07.06.2012; Views: 1278; Downloads: 272
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Coherence resonance in a spatial prisoner's dilemma game
Matjaž Perc, 2006, original scientific article

Abstract: We study effects of additive spatiotemporal random variations, introduced to the payoffs of a spatial prisoner's dilemma game, on the evolution of cooperation. In the absence of explicit payoff variations the system exhibits a phase transition from a mixed state of cooperators and defectors to a homogenous state of defectors belonging to the directed percolation universality class. By introducing nonzero random variations to the payoffs, this phase transition can be reverted in a resonance-like manner depending on the variance of noise, thus marking coherence resonance in the system. We argue that explicit random payoff variations present a viable mechanism that promotes cooperation for defection temptation values substantially exceeding the one marking the transition point to homogeneity by deterministic payoffs.
Keywords: dynamic systems, noise, spatiotemporal noise, intensity, spatial resonance, inherent spatial resonance, spatial decoherence, excitable media
Published: 07.06.2012; Views: 1066; Downloads: 288
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Thoughts out of noise
Matjaž Perc, 2006, original scientific article

Abstract: We study the effects of additive Gaussian noise on the behaviour of a simple spatially extended system, which is locally modelled by a nonlinear two-dimensional iterated map describing neuronal dynamics. In particular, we focus on the ability of noise to induce spatially ordered patterns, i. e. the so-called noise-induced pattern formation. For intermediate noise intensities, the spatially extended system exhibits ordered circular waves, thereby clearly manifesting the constructive role of random perturbations. The emergence of observed noise-induced patterns is explained with simple arguments that are obtained by analysing the typical spatial scale of patterns evoked by various diffusion coefficients. Since discrete-time systems are straightforward to implement and require modest computational capabilities, the present study describes one of the most fascinating and visually compelling examples of noise-induced self-organization in nonlinear systems in an accessible way for graduate or even advanced undergraduate students attending a nonlinear dynamics course.
Keywords: dynamic systems, chaotic systems, nonlinear dynamics, nonlinear systems, noise, nonlinear analyses
Published: 07.06.2012; Views: 921; Downloads: 23
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Evolutionary and dynamical coherence resonances in the pair approximated prisoner's dilemma game
Matjaž Perc, Marko Marhl, 2006, original scientific article

Abstract: Stochasticity has recently emerged as being a potent promoter of cooperative behaviour in systems developed under the framework of evolutionary game theory. In the spatial prisoner's dilemma game, the fitness of players adopting the cooperative strategy was found to be resonantly dependent on the intensity of payoff fluctuations. Evidently, the phenomenon resembles classical coherence resonance, whereby the noise-induced order, or coherence, of the dynamics is substituted with the noise-induced prevalence of the 'good' strategy, thus marking a constructive effect of noise on the system. The connection between the former 'dynamical' coherence resonance and the latter so-called 'evolutionary' coherence resonance, however, has not yet been established. The two different definitions of coherence resonance appear to provoke some discomfort. The goal of the present paper is therefore, on one hand, to draw a clear line between the two different perceptions of coherence resonance, and on the other, to show that the two apparently disjoint phenomena, that are currently related only by name, can in fact be observed simultaneously, sharing an identical mechanism of emergence.
Keywords: dynamic systems, noise, spatiotemporal noise, intensity, spatial resonance, inherent spatial resonance, spatial decoherence, excitable media
Published: 07.06.2012; Views: 1263; Downloads: 246
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