Related papers: Duplication-divergence model of protein interactio…
We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also…
We introduce a growing network model in which a new node attaches to a randomly-selected node, as well as to all ancestors of the target node. This mechanism produces a sparse, ultra-small network where the average node degree grows…
Using a simple model with link removals as well as link additions, we show that an evolving network is scale free with a degree exponent in the range of (2, 4]. We then establish a relation between the network evolution and a set of…
In a recent work \cite{LiuJoladSchZia13}, we introduced dynamic networks with preferred degrees and presented simulation and analytic studies of a single, homogeneous system as well as two interacting networks. Here, we extend these studies…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Scale-free power law structure describes complex networks derived from a wide range of real world processes. The extensive literature focuses almost exclusively on networks with power law exponent strictly larger than 2, which can be…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
We propose a model for evolving networks by merging building blocks represented as complete graphs, reminiscent of modules in biological system or communities in sociology. The model shows power-law degree distributions, power-law…
Complex networks as the World Wide Web, the web of human sexual contacts or criminal networks often do not have an engineered architecture but instead are self-organized by the actions of a large number of individuals. From these local…
The degree distribution is a key statistical indicator in network theory, often used to understand how information spreads across connected nodes. In this paper, we focus on non-growing networks formed through a rewiring algorithm and…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
Traditionally, the evolution of cooperation has been studied on single, isolated networks. Yet a player, especially in human societies, will typically be a member of many different networks, and those networks will play a different role in…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
Here we introduce a model in which individuals differ in the rate at which they seek new interactions with others, making rational decisions modeled as general symmetric two-player games. Once a link between two individuals has formed, the…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
In complex networks the degrees of adjacent nodes may often appear dependent -- which presents a modelling challenge. We present a working framework for studying networks with an arbitrary joint distribution for the degrees of adjacent…
Users of social networks display diversified behavior and online habits. For instance, a user's tendency to reply to a post can depend on the user and the person posting. For convenience, we group users into aggregated behavioral patterns,…
Inspired by scientific collaboration networks, especially our empirical analysis of the network of econophysicists, an evolutionary model for weighted networks is proposed. Both degree-driven and weight-driven models are considered.…