Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, including such concepts as the small-world effect, degree distributions, clustering, network correlations, random graph models, models of network growth and preferential attachment, and dynamical processes taking place on networks.

Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding. q 2003 Published by Elsevier Ltd.

INTRODUCTION At the present time, the most commonly accepted definition of a complex system is that of a system containing many interdependent constituents which interact nonlinearly . Therefore, when we want to model a complex system, the first issue has to do with the connectivity properties of its network, the architecture of the wirings between the constituents. In fact, we have recently learned that the network structure can be as important as the nonlinear interactions between elements, and an accurate description of the coupling architecture and a characterization of the structural properties of the network can be of fundamental importance also to understand the dynamics of the system. The definition may seem somewhat fuzzy and generic: this is an indication that the notion of a complex system is still not precisely delineated and di#ers from author to author. On the other side, there is complete agreement that the "ideal" complex systems are the biological ones, especially

In this work we present a new methodology to study the structure of the configuration spaces of hard combinatorial problems. It consists in building the network that has as nodes the locally optimal configurations and as edges the weighted oriented transitions between their basins of attraction. We apply the approach to the detection of communities in the optima networks produced by two different classes of instances of a hard combinatorial optimization problem: the quadratic assignment problem (QAP). We provide evidence indicating that the two problem instance classes give rise to very different configuration spaces. For the so-called real-like class, the networks possess a clear modular structure, while the optima networks belonging to the class of random uniform instances are less well partitionable into clusters. This is convincingly supported by using several statistical tests. Finally, we shortly discuss the consequences of the findings for heuristically searching the corresponding problem spaces.

I investigate the effect of incomplete information on the growth process of scale-free networks- a situation that occurs frequently in real existing citation networks. I propose two mathematical models and solve those analytically for the scaling behavior of the connectivity distribution. These models show a varying scaling exponent with respect to the model parameters but no break-down of scaling thus introducing the first models that are scale-free networks in an environment of incomplete information. I compare to results from computer simulations and discuss the relevance for known data of real networks. 1

We propose a network characterization of combinatorial fitness landscapes by adapting the notion of inherent networks proposed for energy surfaces [5]. We use the well-known family of NK landscapes as an example. In our case the inherent network is the graph where the vertices are all the local maxima and edges mean basin adjacency between two maxima. We exhaustively extract such networks on representative small NK landscape instances, and show that they are ‘small-worlds’. However, the maxima graphs are not random, since their clustering coefficients are much larger than those of corresponding random graphs. Furthermore, the degree distributions are close to exponential instead of Poissonian. We also describe the nature of the basins of attraction and their relationship with the local maxima network.