1. Spatial network representation of complex living tissuesDean 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 "scalefree", with the powerlaw distribution of number of links per node, robust and modular with underlying selfsimilar 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 twophoton laser scanning microscopy of whole pancreas tissue slices, and cells conductances measured electrophysiologically using wholecell patchclamp. We find that the heterogeneity of beta cells in intact living islets induces scalefree topology of the tissue network. Furthermore, we show that the isletlike 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 Link to full text 
2. Encyclopedia of complexity and systems sciencedictionary, 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 selforganization, complex systems, synergetics, dynamical systems, turbulence, catastrophes, instabilities, nonlinearity, stochastic processes, chaos, neural networks, cellular automata, adaptive systems, and genetic algorithms. Examples of nearterm 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, selforganization, systems biology, systems science Published: 01.06.2012; Views: 1484; Downloads: 68 Link to full text 
3. Topologically determined optimal stochastic resonance responses of spatially embedded networksMarko 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 scalefree (SF) network with dominating longrange 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 longrange 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 longrange interactionsdominated network to a more latticelike network structure. Keywords: physics, stochastic resonance, complex networks Published: 07.06.2012; Views: 1025; Downloads: 166 Full text (2,08 MB) This document has many files! More...

4. Collective behavior and evolutionary gamesMatjaž Perc, Paolo Grigolini, 2013, original scientific article Keywords: kolektivni pojavi, evolucijske igre, fazni prehodi, kompleksne mreže, statistična fizika socioloških sistemov, collective phenomena, evolutionary games, phase transitions, complex networks, evolutionary statistical physics of social systems Published: 10.07.2015; Views: 581; Downloads: 18 Link to full text 
5. Evolution of interactions and cooperation in the spatial prisoner's dilemma gameChunyan 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 Full text (309,95 KB) This document has many files! More...

6. Pacemakerdriven stochastic resonance on diffusive and complex networks of bistable oscillatorsMatjaž Perc, Marko Gosak, 2008, original scientific article Abstract: We study the phenomenon of stochastic resonance on diffusive, smallworld and scalefree 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 pacemakerdriven 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 nearestneighbor interactions, thus being proportional to the square root of the coupling strength, whereas it becomes superdiffusive by an appropriate smallworld or scalefree topology of the interaction network. In particular, the scalefree 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 smallworld network to facilitate the outreach of the pacemakeremitted subthreshold rhythm. We additionally confirm these findings by using the FitzHughNagumo 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 Full text (2,18 MB) This document has many files! More...

7. Chimera states in uncoupled neurons induced by a multilayer structureSoumen 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. HindmarshRose 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 densitydependent 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 interlayer 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 Full text (1,40 MB) This document has many files! More...

8. Evolution of cooperation on scalefree networks subject to error and attackMatjaž Perc, 2009, original scientific article Abstract: We study the evolution of cooperation in the prisoner's dilemma and the snowdrift game on scalefree networks that are subjected to intentional and random removal of vertices. We show that, irrespective of the game type, cooperation on scalefree 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 scalefree 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 scalefree networks. Keywords: evolutionary game theory, social dilemma, spatial games, complex networks Published: 30.06.2017; Views: 589; Downloads: 154 Full text (684,60 KB) This document has many files! More...

9. Fast random rewiring and strong connectivity impair subthreshold signal detection in excitable networksVladislav 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 'functionfollowsform' principles for systems described within this framework. Keywords: neuronal dynamics, complex networks, coevolution, cognition Published: 03.07.2017; Views: 342; Downloads: 166 Full text (1,36 MB) 
10. Quantifying soil complexity using network models of soil porous structureMarko 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 nodenode 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 noncompact to compact phase of the network. Keywords: soil complexity, soil pore networks, complex systems Published: 21.07.2017; Views: 383; Downloads: 152 Full text (3,85 MB) This document has many files! More...
