arXiv subjects

T. Vicsek

Publications and source records attributed to T. Vicsek.

At least 19 recordsLinked to original sources

arXiv2011

Rotated multifractal network generator

The recently introduced multifractal network generator (MFNG), has been shown to provide a simple and flexible tool for creating random graphs with very diverse features. The MFNG is based on multifractal measures embedded in 2d, leading also to isolated nodes, whose number is relatively low for realistic cases, but may become dominant in the limiting case of infinitely large network sizes. Here we discuss the relation between this effect and the information dimension for the 1d projection of the link probability measure (LPM), and argue that the node isolation can be avoided by a simple transformation of the LPM based on rotation.

physics.data-an↗

arXiv2010

Multifractal Network Generator

We introduce a new approach to constructing networks with realistic features. Our method, in spite of its conceptual simplicity (it has only two parameters) is capable of generating a wide variety of network types with prescribed statistical properties, e.g., with degree- or clustering coefficient distributions of various, very different forms. In turn, these graphs can be used to test hypotheses, or, as models of actual data. The method is based on a mapping between suitably chosen singular measures defined on the unit square and sparse infinite networks. Such a mapping has the great potential of allowing for graph theoretical results for a variety of network topologies. The main idea of our approach is to go to the infinite limit of the singular measure and the size of the corresponding graph simultaneously. A very unique feature of this construction is that the complexity of the generated network is increasing with the size. We present analytic expressions derived from the parameters of the -- to be iterated-- initial generating measure for such major characteristics of graphs as their degree, clustering coefficient and assortativity coefficient distributions. The optimal parameters of the generating measure are determined from a simple simulated annealing process. Thus, the present work provides a tool for researchers from a variety of fields (such as biology, computer science, biology, or complex systems) enabling them to create a versatile model of their network data.

physics.data-an↗

arXiv2010

What makes a phase transition? Analysis of the random satisfiability problem

In the last 30 years it was found that many combinatorial systems undergo phase transitions. One of the most important examples of these can be found among the random k-satisfiability problems (often referred to as k-SAT), asking whether there exists an assignment of Boolean values satisfying a Boolean formula composed of clauses with k random variables each. The random 3-SAT problem is reported to show various phase transitions at different critical values of the ratio of the number of clauses to the number of variables. The most famous of these occurs when the probability of finding a satisfiable instance suddenly drops from 1 to 0. This transition is associated with a rise in the hardness of the problem, but until now the correlation between any of the proposed phase transitions and the hardness is not totally clear. In this paper we will first show numerically that the number of solutions universally follows a lognormal distribution, thereby explaining the puzzling question of why the number of solutions is still exponential at the critical point. Moreover we provide evidence that the hardness of the closely related problem of counting the total number of solutions does not show any phase transition-like behavior. This raises the question of whether the probability of finding a satisfiable instance is really an order parameter of a phase transition or whether it is more likely to just show a simple sharp threshold phenomenon. More generally, this paper aims at starting a discussion where a simple sharp threshold phenomenon turns into a genuine phase transition.

physics.data-an↗

arXiv2006

Community structure and ethnic preferences in school friendship networks

Recently developed concepts and techniques of analyzing complex systems provide new insight into the structure of social networks. Uncovering recurrent preferences and organizational principles in such networks is a key issue to characterize them. We investigate school friendship networks from the Add Health database. Applying threshold analysis, we find that the friendship networks do not form a single connected component through mutual strong nominations within a school, while under weaker conditions such interconnectedness is present. We extract the networks of overlapping communities at the schools (c-networks) and find that they are scale free and disassortative in contrast to the direct friendship networks, which have an exponential degree distribution and are assortative. Based on the network analysis we study the ethnic preferences in friendship selection. The clique percolation method we use reveals that when in minority, the students tend to build more densely interconnected groups of friends. We also find an asymmetry in the behavior of black minorities in a white majority as compared to that of white minorities in a black majority.

physics.soc-ph↗

arXiv2004

Auto-reverse nuclear migration in bipolar mammalian cells on micropatterned surfaces

A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and primary mouse fibroblast cells is diminished. Nevertheless, nuclei perform an unexpected auto-reverse motion: when a migrating nucleus approaches the leading edge, it decelerates, changes the direction of motion and accelerates to move toward the other end of the elongated cell. During this process cells show signs of polarization closely following the direction of nuclear movement. The observed nuclear movement requires a functioning microtubular system, as revealed by experiments disrupting the main cytoskeletal components with specific drugs. On the basis of our results we argue that auto-reverse nuclear migration is due to forces determined by the interplay of microtubule dynamics and the changing position of the microtubule organizing center as the nucleus reaches the leading edge. Our assay recapitulates specific features of nuclear migration (cell polarization, oscillatory nuclear movement), while allows the systematic study of a large number of individual cells. In particular, our experiments yielded the first direct evidence of reversive nuclear motion in mammalian cells, induced by attachment constraints.

q-bio.CB↗

arXiv2004

A Tractable Complex Network Model based on the Stochastic Mean-field Model of Distance

Much recent research activity has been devoted to empirical study and theoretical models of complex networks (random graphs) with three qualitative features: power-law degree distribution, local clustering of edges, and small diameter. We point out a new (in this context) platform for such models -- the stochastic mean-field model of distance -- and within this platform study a simple two-parameter proportional attachment model. The model is mathematicallly natural, permits a wide variety of explicit calculations, has the desired three qualitative features, and fits the complete range of degree scaling exponents and clustering parameters; in these respects it compares favorably to existing models.

cond-mat.dis-nn↗

arXiv2004

Global organization of metabolic fluxes in the bacterium, Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions. We implement a flux balance analysis of the E. coli MG1655 metabolism, finding that the network utilization is highly uneven: while most metabolic reactions have small fluxes, the metabolism's activity is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high flux backbone. The identified behavior likely represents a universal feature of metabolic activity in all cells, with potential implications to metabolic engineering.

q-bio.MN↗

arXiv2003

Networks in life: Scaling properties and eigenvalue spectra

We analyse growing networks ranging from collaboration graphs of scientists to the network of similarities defined among the various transcriptional profiles of living cells. For the explicit demonstration of the scale-free nature and hierarchical organization of these graphs, a deterministic construction is also used. We demonstrate the use of determining the eigenvalue spectra of sparse random graph models for the categorization of small measured networks.

cond-mat.stat-mech↗

arXiv2002

Critical Discussion of "Synchronized Flow", Simulation of Pedestrian Evacuation, and Optimization of Production Processes

We critically discuss the concept of ``synchronized flow'' from a historical, empirical, and theoretical perspective. Problems related to the measurement of vehicle data are highlighted, and questionable interpretations are identified. Moreover, we propose a quantitative and consistent theory of the empirical findings based on a phase diagram of congested traffic states, which is universal for all conventional traffic models having the same instability diagram and a fundamental diagram. New empirical and simulation data supporting this approach are presented as well. We also give a short overview of the various phenomena observed in panicking pedestrian crowds relevant from the point of evacuation of buildings, ships, and stadia. Some of these can be applied to the optimization of production processes, e.g. the ``slower-is-faster effect''.

cond-mat.stat-mech↗

arXiv2002

The topology of the transcription regulatory network in the yeast, S. cerevisiae

MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene activity coupled with the assessment of perturbed transcriptome (i. e., global mRNA expression) patterns represents one approach toward this goal, and may provide a backbone into which other measurements can be later integrated. RESULT: We use microarray data on 287 single gene deletion Saccharomyces cerevisiae mutant strains to elucidate generic relationships among perturbed transcriptomes. Their comparison with a method that preferentially recognizes distinct expression subpatterns allows us to pair those transcriptomes that share localized similarities. Analyses of the resulting transcriptome similarity network identify a continuum hierarchy among the deleted genes, and in the frequency of local similarities that establishes the links among their reorganized transcriptomes. We also find a combinatorial utilization of shared expression subpatterns within individual links, with increasing quantitative similarity among those that connect transcriptome states induced by the deletion of functionally related gene products. This suggests a distinct hierarchical and combinatorial organization of the S. cerevisiae transcriptional activity, and may represent a pattern that is generic to the transcriptional organization of all eukaryotic organisms. AVAILABILITY: Detailed analyses of the comparison method and free software are available from the authors and at http://angel.elte.hu/bioinf

cond-mat.stat-mech↗

arXiv2002

Avalanche Dynamics in Wet Granular Media

A detailed characterization of avalanche dynamics of wet granular media in a rotating drum apparatus is presented. The results confirm the existence of the three wetness regimes observed previously: the granular, the correlated and the viscoplastic regime. These regimes show qualitatively different dynamic behaviors which are reflected in all the investigated quantities. We discuss the effect of interstitial liquid on the characteristic angles of the material and on the avalanche size distribution. These data also reveal logarithmic aging and allow us to map out the phase diagram of the dynamical behavior as a function of liquid content and flow rate. Via quantitative measurements of the flow velocity and the granular flux during avalanches, we characterize novel avalanche types unique to wet media. We also explore the details of viscoplastic flow (observed at the highest liquid contents) in which there are lasting contacts during flow, leading to coherence across the entire sample. This coherence leads to a velocity independent flow depth at high rotation rates and novel robust pattern formation in the granular surface.

cond-mat.dis-nn↗

arXiv2002

Synchronization of oscillators with long range interaction: phase transition and anomalous finite size effects

Synchronization in a lattice of a finite population of phase oscillators with algebraically decaying, non-normalized coupling is studied by numerical simulations. A critical level of decay is found, below which full locking takes place if the population contains a sufficiently large number of elements. For large number of oscillators and small coupling constant, numerical simulations and analytical arguments indicate that a phase transition separating synchronization from incoherence appears at a decay exponent value equal to the number of dimensions of the lattice. In contrast with earlier results on similar systems with normalized coupling, we have indication that for the decay exponent less than the dimensions of the lattice and for large populations, synchronization is possible even if the coupling is arbitarily weak. This finding suggests that in organisms interacting through slowly decaying signals like light or sound, collective oscillations can always be established if the population is sufficiently large.

cond-mat.stat-mech↗

arXiv2002

Avalanche Dynamics in Wet Granular Materials

We have studied the dynamics of avalanching wet granular media in a rotating drum apparatus. Quantitative measurements of the flow velocity and the granular flux during avalanches allow us to characterize novel avalanche types unique to wet media. We also explore the details of viscoplastic flow (observed at the highest liquid contents) in which there are lasting contacts during flow, leading to coherence across the entire sample. This coherence leads to a velocity independent flow depth at high rotation rates and novel robust pattern formation in the granular surface.

cond-mat.dis-nn↗

arXiv2001

Collective dynamics of two-mode stochastic oscillators

We study a system of two-mode stochastic oscillators coupled through their collective output. As a function of a relevant parameter four qualitatively distinct regimes of collective behavior are observed. In an extended region of the parameter space the periodicity of the collective output is enhanced by the considered coupling. This system can be used as a new model to describe synchronization-like phenomena in systems of units with two or more oscillation modes. The model can also explain how periodic dynamics can be generated by coupling largely stochastic units. Similar systems could be responsible for the emergence of rhythmic behavior in complex biological or sociological systems.

cond-mat.stat-mech↗

arXiv2001

Evolution of the social network of scientific collaborations

The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer the dynamic and the structural mechanisms that govern the evolution and topology of this complex system. First, empirical measurements allow us to uncover the topological measures that characterize the network at a given moment, as well as the time evolution of these quantities. The results indicate that the network is scale-free, and that the network evolution is governed by preferential attachment, affecting both internal and external links. However, in contrast with most model predictions the average degree increases in time, and the node separation decreases. Second, we propose a simple model that captures the network's time evolution. Third, numerical simulations are used to uncover the behavior of quantities that could not be predicted analytically.

cond-mat.soft↗

arXiv2001

Stick-Slip Fluctuations in Granular Drag

We study fluctuations in the drag force experienced by an object moving through a granular medium. The successive formation and collapse of jammed states give a stick-slip nature to the fluctuations which are periodic at small depths but become "stepped" at large depths, a transition which we interpret as a consequence of the long-range nature of the force chains and the finite size of our experiment. Another important finding is that the mean force and the fluctuations appear to be independent of the properties of the contact surface between the grains and the dragged object. These results imply that the drag force originates in the bulk properties of the granular sample.

cond-mat.dis-nn↗

arXiv2000

Transitions in the Horizontal Transport of Vertically Vibrated Granular Layers

Motivated by recent advances in the investigation of fluctuation-driven ratchets and flows in excited granular media, we have carried out experimental and simulational studies to explore the horizontal transport of granular particles in a vertically vibrated system whose base has a sawtooth-shaped profile. The resulting material flow exhibits novel collective behavior, both as a function of the number of layers of particles and the driving frequency; in particular, under certain conditions, increasing the layer thickness leads to a reversal of the current, while the onset of transport as a function of frequency occurs gradually in a manner reminiscent of a phase transition. Our experimental findings are interpreted here with the help of extensive, event driven Molecular Dynamics simulations. In addition to reproducing the experimental results, the simulations revealed that the current may be reversed as a function of the driving frequency as well. We also give details about the simulations so that similar numerical studies can be carried out in a more straightforward manner in the future.

cond-mat.stat-mech↗

arXiv2000

Physics of the rhythmic applause

We discuss in detail a human scale example of the synchronization phenomenon, namely the dynamics of the rhythmic applause. After a detailed experimental investigation, we describe the phenomenon with an approach based on the classical Kuramoto model. Computer simulations based on the theoretical assumptions, reproduce perfectly the observed dynamics. We argue that a frustration present in the system is responsible for the interesting interplay between synchronized and unsynchronized regimes

cond-mat.stat-mech↗