Fundamental statistical features and self-similar properties of tagged networks (2008)
Palla, Gergely, Farkas, Illes J., Pollner, Peter, Derenyi, Imre, Vicsek, Tamas
We investigate the fundamental statistical features of tagged (or annotated) networks having a rich variety of attributes associated with their nodes. Tags (attributes, annotations, properties,...
Centrality properties of directed module members in social networks (2008)
Pollner, Peter, Palla, Gergely, Abel, Daniel, Vicsek, Andras, Farkas, Illes J., Derenyi, Imre, ...
Several recent studies of complex networks have suggested algorithms for locating network communities, also called modules or clusters, which are mostly defined as groups of nodes with dense internal...
The relevance of neck linker docking in the motility of kinesin (2008)
Czovek, Andras, Szollosi, Gergely J., Derenyi, Imre
Conventional kinesin is a motor protein, which is able to walk along a microtubule processively. The exact mechanism of the stepping motion and force generation of kinesin is still far from clear. In...
The Effect of Recombination on the Neutral Evolution of Genetic Robustness (2008)
Szollosi, Gergely J., Derenyi, Imre
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary...
Evolutionary games on minimally structured populations (2007)
Szollosi, Gergely J, Derenyi, Imre
Population structure induced by both spatial embedding and more general networks of interaction, such as model social networks, have been shown to have a fundamental effect on the dynamics and...
Directed network modules (2007)
Palla, Gergely, Farkas, Illes J., Pollner, Peter, Derenyi, Imre, Vicsek, Tamas
A search technique locating network modules, i.e., internally densely connected groups of nodes in directed networks is introduced by extending the Clique Percolation Method originally proposed for...
The critical point of k-clique percolation in the Erdos-Renyi graph (2006)
Palla, Gergely, Derenyi, Imre, Vicsek, Tamas
Motivated by the success of a k-clique percolation method for the identification of overlapping communities in large real networks, here we study the k-clique percolation problem in the Erdos-Renyi...
The maintenance of sex in bacteria is ensured by its potential to reload genes (2006)
Szollosi, Gergely J., Derenyi, Imre, Vellai, Tibor
Why sex is maintained in nature is a fundamental question in biology. Natural genetic transformation (NGT) is a sexual process by which bacteria actively take up exogenous DNA and use it to replace...
Dynamic Response of Adhesion Complexes: Beyond the Single-Path Picture (2006)
Bartolo, Denis, Derenyi, Imre, Ajdari, Armand
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the...
CFinder: Locating cliques and overlapping modules in biological networks (2006)
Adamcsek, Balazs, Palla, Gergely, Farkas, Illes J., Derenyi, Imre, Vicsek, Tamas
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear...
Reversible mesoscopic model of protein adsorption: From equilibrium to dynamics (2005)
Szollosi, Gergely J., Derenyi, Imre, Voros, Janos
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution...
Uncovering the overlapping community structure of complex networks in nature and society (2005)
Palla, Gergely, Derenyi, Imre, Farkas, Illes, Vicsek, Tamas
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the...
Clique percolation in random networks (2005)
Derenyi, Imre, Palla, Gergely, Vicsek, Tamas
The notion of k-clique percolation in random graphs is introduced, where k is the size of the complete subgraphs whose large scale organizations are analytically and numerically investigated. For the...
Reverse engineering of linking preferences from network restructuring (2004)
Palla, Gergely, Farkas, Illes, Derenyi, Imre, Barabasi, Albert-Laszlo, Vicsek, Tamas
We provide a method to deduce the preferences governing the restructuring dynamics of a network from the observed rewiring of the edges. Our approach is applicable for systems in which the...
Statistical mechanics of topological phase transitions in networks (2003)
Palla, Gergely, Derenyi, Imre, Farkas, Illes, Vicsek, Tamas
We provide a phenomenological theory for topological transitions in restructuring networks. In this statistical mechanical approach energy is assigned to the different network topologies and...
Effects of intermediate bound states in dynamic force spectroscopy (2003)
Derenyi, Imre, Bartolo, Denis, Ajdari, Armand
We revisit here some aspects of the interpretation of dynamic force spectroscopy experiments. The standard theory predicts a typical unbinding force $f^*$ linearly proportional to the logarithm of...
Topological phase transitions of random networks (2003)
Derenyi, Imre, Farkas, Illes, Palla, Gergely, Vicsek, Tamas
To provide a phenomenological theory for the various interesting transitions in restructuring networks we employ a statistical mechanical approach with detailed balance satisfied for the transitions...
DNA uptake into nuclei: Numerical and analytical results (2002)
Farkas, Zeno, Derenyi, Imre, Vicsek, Tamas
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to...
Formation and Interaction of Membrane Tubes (2002)
Derenyi, Imre, Julicher, Frank, Prost, Jacques
We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly non-trivial and involves first order shape transitions. The force...
Dynamic Response of Adhesion Complexes: Beyond the Single-Path Picture (2001)
Bartolo, Denis, Derenyi, Imre, Ajdari, Armand
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the...
Spectra of "Real-World" Graphs: Beyond the Semi-Circle Law (2001)
Farkas, Illes J., Derenyi, Imre, Barabasi, Albert-Laszlo, Vicsek, Tamas
Many natural and social systems develop complex networks, that are usually modelled as random graphs. The eigenvalue spectrum of these graphs provides information about their structural properties....
Dynamic Response of Adhesion Complexes: Beyond the Single-Path Picture (2001)
Bartolo, Denis, Derenyi, Imre, Ajdari, Armand
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the...
Dynamic Response of Adhesion Complexes: Beyond the Single-Path Picture (2001)
Bartolo, Denis, Derenyi, Imre, Ajdari, Armand
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the...
Reducing vortex density in superconductors using the ratchet effect (1999)
Lee, Choongseop, Janko, Boldizsar, Derenyi, Imre, Barabasi, Albert-Laszlo
A serious obstacle that impedes the application of low and high temperature superconductor (SC) devices is the presence of trapped flux. Flux lines or vortices are induced by fields as small as the...
A Chemically Reversible Brownian Motor: Application to Kinesin and Ncd (1999)
R. Dean Astumian, Imre Derenyi
Kinesin and nonclaret disjunctional protein (ncd) are two microtubule-based molecular motors that use energy from ATP hydrolysis to drive motion in opposite directions. They are structurally very...
Realistic Models of Biological Motion (1998)
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament,...
Cooperative Transport of Brownian Particles (1998)
We consider the collective motion of finite-sized, overdamped Brownian particles (e.g., motor proteins) in a periodic potential. Simulations of our model have revealed a number of novel cooperative...
The kinesin walk: a dynamic model with elastically coupled heads (1998)
Recently individual two-headed kinesin molecules have been studied in in vitro motility assays revealing a number of their peculiar transport properties. In this paper we propose a simple and robust...
Ratchet Effect in Surface Electromigration: Smoothing Surfaces by an ac Field (1998)
Derenyi, Imre, Lee, Choongseop, Barabasi, Albert-Laszlo
We demonstrate that for surfaces that have a nonzero Schwoebel barrier the application of an ac field parallel to the surface induces a net electro- migration current that points in the descending...