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1.
Spatial network representation of complex living tissues
Dean Korošak, Marjan Rupnik, 2008, published scientific conference contribution

Abstract: Networks were widely used to describe organizational and functional principles of living organisms across various scales. The topology of such biological complex networks often turned out to be "scale-free", with the power-law distribution of number of links per node, robust and modular with underlying self-similar structure. However, the topology of cytoarchitecture in living tissues has not yet received wide attention from the network perspective. Here we discuss the spatial complex network model of coupled clusters of beta cells in pancreatic islets. Networks of cells in pancreatic islets were constructed from the 2D section images presenting fluorescently labelled intercellular spaces obtained by two-photon laser scanning microscopy of whole pancreas tissue slices, and cells conductances measured electrophysiologically using whole-cell patch-clamp. We find that the heterogeneity of beta cells in intact living islets induces scale-free topology of the tissue network. Furthermore, we show that the islet-like structures visually similar to 2D section images can be obtained using Voronoi diagrams of random points.
Keywords: pancreatic islets, betta cells, complex networks, cytoarchitecture
Published: 31.05.2012; Views: 1186; Downloads: 46
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2.
Encyclopedia of complexity and systems science
dictionary, encyclopaedia, lexicon, manual, atlas, map

Abstract: Encyclopedia of Complexity and Systems Science provides an authoritative single source for understanding and applying the concepts of complexity theory together with the tools and measures for analyzing complex systems in all fields of science and engineering. The science and tools of complexity and systems science include theories of self-organization, complex systems, synergetics, dynamical systems, turbulence, catastrophes, instabilities, nonlinearity, stochastic processes, chaos, neural networks, cellular automata, adaptive systems, and genetic algorithms. Examples of near-term problems and major unknowns that can be approached through complexity and systems science include: The structure, history and future of the universe; the biological basis of consciousness; the integration of genomics, proteomics and bioinformatics as systems biology; human longevity limits; the limits of computing; sustainability of life on earth; predictability, dynamics and extent of earthquakes, hurricanes, tsunamis, and other natural disasters; the dynamics of turbulent flows; lasers or fluids in physics, microprocessor design; macromolecular assembly in chemistry and biophysics; brain functions in cognitive neuroscience; climate change; ecosystem management; traffic management; and business cycles. All these seemingly quite different kinds of structure formation have a number of important features and underlying structures in common. These deep structural similarities can be exploited to transfer analytical methods and understanding from one field to another. This unique work will extend the influence of complexity and system science to a much wider audience than has been possible to date.
Keywords: cellular automata, complex networks, computational nanoscience, ecological complexity, ergodic theory, fractals, game theory, granular computing, graph theory, intelligent systems, perturbation theory, quantum information science, system dynamics, traffic management, chaos, climate modelling, complex systems, dynamical sistems, fuzzy theory systems, nonlinear systems, soft computing, stochastic processes, synergetics, self-organization, systems biology, systems science
Published: 01.06.2012; Views: 1484; Downloads: 68
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3.
Topologically determined optimal stochastic resonance responses of spatially embedded networks
Marko Gosak, Dean Korošak, Marko Marhl, 2011, original scientific article

Abstract: We have analyzed the stochastic resonance phenomenon on spatial networks of bistable and excitable oscillators, which are connected according to their location and the amplitude of external forcing. By smoothly altering the network topology from a scale-free (SF) network with dominating long-range connections to a network where principally only adjacent oscillators are connected, we reveal that besides an optimal noise intensity, there is also a most favorable interaction topology at which the best correlation between the response of the network and the imposed weak external forcing is achieved. For various distributions of the amplitudes of external forcing, the optimal topology is always found in the intermediate regime between the highly heterogeneous SF network and the strong geometric regime. Our findings thus indicate that a suitable number of hubs and with that an optimal ratio between short- and long-range connections is necessary in order to obtain the best global response of a spatial network. Furthermore, we link the existence of the optimal interaction topology to a critical point indicating the transition from a long-range interactions-dominated network to a more lattice-like network structure.
Keywords: physics, stochastic resonance, complex networks
Published: 07.06.2012; Views: 1025; Downloads: 166
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Evolution of interactions and cooperation in the spatial prisoner's dilemma game
Chunyan Zhang, Jianlei Zhang, Guangming Xie, Long Wang, Matjaž Perc, 2011, original scientific article

Abstract: We study the evolution of cooperation in the spatial prisoner's dilemma game where players are allowed to establish new interactions with others. By employing a simple coevolutionary rule entailing only two crucial parameters, we find that different selection criteria for the new interaction partners as well as their number vitally affect the outcome of the game. The resolution of the social dilemma is most probable if the selection favors more successful players and if their maximally attainable number is restricted. While the preferential selection of the best players promotes cooperation irrespective of game parametrization, the optimal number of new interactions depends somewhat on the temptation to defect. Our findings reveal that the "making of new friends" may be an important activity for the successful evolution of cooperation, but also that partners must be selected carefully and their number limited.
Keywords: evolutionary games, prisoner's dilemma, coevolution, complex networks, friendship
Published: 19.06.2017; Views: 222; Downloads: 183
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6.
Pacemaker-driven stochastic resonance on diffusive and complex networks of bistable oscillators
Matjaž Perc, Marko Gosak, 2008, original scientific article

Abstract: We study the phenomenon of stochastic resonance on diffusive, small-world and scale-free networks consisting of bistable overdamped oscillators. Important thereby is the fact that the external subthreshold periodic forcing is introduced only to a single oscillator of the network. Hence, the forcing acts as a pacemaker trying to impose its rhythm on the whole network through the unit to which it is introduced. Without the addition of additive spatiotemporal noise, however, the whole network, including the unit that is directly exposed to the pacemaker, remains trapped forever in one of the two stable steady states of the local dynamics. We show that the correlation between the frequency of subthreshold pacemaker activity and the response of the network is resonantly dependent on the intensity of additive noise. The reported pacemaker-driven stochastic resonance depends most significantly on the coupling strength and the underlying network structure. Namely, the outreach of the pacemaker obeys the classic diffusion law in the case of nearest-neighbor interactions, thus being proportional to the square root of the coupling strength, whereas it becomes superdiffusive by an appropriate small-world or scale-free topology of the interaction network. In particular, the scale-free topology is identified as being optimal for the dissemination of localized rhythmic activity across the whole network. Also, we show that the ratio between the clustering coefficient and the characteristic path length is the crucial quantity defining the ability of a small-world network to facilitate the outreach of the pacemaker-emitted subthreshold rhythm. We additionally confirm these findings by using the FitzHugh-Nagumo excitable system as an alternative to the bistable overdamped oscillator.
Keywords: noise, bistable dynamics, stochastic simulations, complex networks
Published: 03.07.2017; Views: 318; Downloads: 197
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7.
Chimera states in uncoupled neurons induced by a multilayer structure
Soumen Majhi, Matjaž Perc, Dibakar Ghosh, 2016, original scientific article

Abstract: Spatial coexistence of coherent and incoherent dynamics in network of coupled oscillators is called a chimera state. We study such chimera states in a network of neurons without any direct interactions but connected through another medium of neurons, forming a multilayer structure. The upper layer is thus made up of uncoupled neurons and the lower layer plays the role of a medium through which the neurons in the upper layer share information among each other. Hindmarsh-Rose neurons with square wave bursting dynamics are considered as nodes in both layers. In addition, we also discuss the existence of chimera states in presence of inter layer heterogeneity. The neurons in the bottom layer are globally connected through electrical synapses, while across the two layers chemical synapses are formed. According to our research, the competing effects of these two types of synapses can lead to chimera states in the upper layer of uncoupled neurons. Remarkably, we find a density-dependent threshold for the emergence of chimera states in uncoupled neurons, similar to the quorum sensing transition to a synchronized state. Finally, we examine the impact of both homogeneous and heterogeneous inter-layer information transmission delays on the observed chimera states over a wide parameter space.
Keywords: complex networks, computational biophysics, nonlinear phenomena, statistical physics
Published: 23.06.2017; Views: 224; Downloads: 191
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8.
Evolution of cooperation on scale-free networks subject to error and attack
Matjaž Perc, 2009, original scientific article

Abstract: We study the evolution of cooperation in the prisoner's dilemma and the snowdrift game on scale-free networks that are subjected to intentional and random removal of vertices. We show that, irrespective of the game type, cooperation on scale-free networks is extremely robust against random deletionof vertices, but declines quickly if vertices with the maximal degree are targeted. In particular, attack tolerance is lowest if the temptation to defect is largest, whereby a small fraction of removed vertices suffices to decimate cooperators. The decline of cooperation can be directly linked to the decrease of heterogeneity of scale-free networks that sets in due to the removal of high degree vertices. We conclude that the evolution of cooperation is characterized by similar attack and error tolerance as was previously reported for information readiness and spread of viruses on scale-free networks.
Keywords: evolutionary game theory, social dilemma, spatial games, complex networks
Published: 30.06.2017; Views: 589; Downloads: 154
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9.
Fast random rewiring and strong connectivity impair subthreshold signal detection in excitable networks
Vladislav Volman, Matjaž Perc, 2010, original scientific article

Abstract: We study dynamical responses in locally paced networks consisting of diffusively coupled excitable units with dynamically adjusted connectivity. It is shown that for weak subthreshold pacing, excessive or strong connectivity impairs the reliable response of a network to the stimulus. Fast random dynamic rewiring of the network also acts detrimentally on signal detection by enforcing a faster relaxation upon the paced unit. Our results indicate that efficient signal processing on excitable complex networks requires tight correspondence between the dynamics of connectivity and the dynamical processes taking place on the network. This, in turn, suggests the existence of 'function-follows-form' principles for systems described within this framework.
Keywords: neuronal dynamics, complex networks, coevolution, cognition
Published: 03.07.2017; Views: 342; Downloads: 166
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10.
Quantifying soil complexity using network models of soil porous structure
Marko Samec, A. Santiago, J. P. Cardenas, R. M. Benito, A. M. Tarquis, Sacha Jon Mooney, Dean Korošak, 2013, original scientific article

Abstract: This paper describes an investigation into the properties of spatially embedded complex networks representing the porous architecture of soil systems. We suggest an approach to quantify the complexity of soil pore structure based on the node-node link correlation properties of the networks. We show that the complexity depends on the strength of spatial embedding of the network and that this is related to the transition from a non-compact to compact phase of the network.
Keywords: soil complexity, soil pore networks, complex systems
Published: 21.07.2017; Views: 383; Downloads: 152
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