抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The emergence of order in natural systems is a constant source of inspiration for both physical and biological sciences. While the spatial order characterizing for example the crystals has been the basis of many advances in contemporary physics, most complex systems in nature do not offer such high degree of order. Many of these systems form complex networks whose nodes are the elements of the system and edges represent the interactions between them. 
Traditionally complex networks have been described by the random graph theory founded in 1959 by Paul Erdohs and Alfred Renyi. One of the defining features of random graphs is that they are statistically homogeneous, and their degree distribution (characterizing the spread in the number of edges starting from a node) is a Poisson distribution. In contrast, recent empirical studies, including the work of our group, indicate that the topology of real networks is much richer than that of random graphs. In particular, the degree distribution of real networks is a power-law, indicating a heterogeneous topology in which the majority of the nodes have a small degree, but there is a significant fraction of highly connected nodes that play an important role in the connectivity of the network. 
The scale-free topology of real networks has very important consequences on their functioning. For example, we have discovered that scale-free networks are extremely resilient to the random disruption of their nodes. On the other hand, the selective removal of the nodes with highest degree induces a rapid breakdown of the network to isolated subparts that cannot communicate with each other. 
The non-trivial scaling of the degree distribution of real networks is also an indication of their assembly and evolution. Indeed, our modeling studies have shown us that there are general principles governing the evolution of networks. Most networks start from a small seed and grow by the addition of new nodes which attach to the nodes already in the system. This process obeys preferential attachment: the new nodes are more likely to connect to nodes with already high degree. We have proposed a simple model based on these two principles wich was able to reproduce the power-law degree distribution of real networks. Perhaps even more importantly, this model paved the way to a new paradigm of network modeling, trying to capture the evolution of networks, not just their static topology.

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Statistical mechanics of complex networks

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.

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The Structure and Function of Complex Networks

A number of recent studies have focused on the statistical properties of networked systems such as social networks and the Worldwide Web. Researchers have concentrated particularly on a few properties that seem to be common to many networks: the small-world property, power-law degree distributions, and network transitivity. In this article, we highlight another property that is found in many networks, the property of community structure, in which network nodes are joined together in tightly knit groups, between which there are only looser connections. We propose a method for detecting such communities, built around the idea of using centrality indices to find community boundaries. We test our method on computer-generated and real-world graphs whose community structure is already known and find that the method detects this known structure with high sensitivity and reliability. We also apply the method to two networks whose community structure is not well known—a collaboration network and a food web—and find that it detects significant and informative community divisions in both cases.

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Community structure in social and biological networks

We propose and study a set of algorithms for discovering community structure in networks-natural divisions of network nodes into densely connected subgroups. Our algorithms all share two definitive features: first, they involve iterative removal of edges from the network to split it into communities, the edges removed being identified using any one of a number of possible "betweenness" measures, and second, these measures are, crucially, recalculated after each removal. We also propose a measure for the strength of the community structure found by our algorithms, which gives us an objective metric for choosing the number of communities into which a network should be divided. We demonstrate that our algorithms are highly effective at discovering community structure in both computer-generated and real-world network data, and show how they can be used to shed light on the sometimes dauntingly complex structure of networked systems.

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Finding and evaluating community structure in networks.

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

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Evolution of networks

The combination of the compactness of networks, featuring small diameters, and their complex architectures results in a variety of critical effects dramatically different from those in cooperative systems on lattices. In the last few years, important steps have been made toward understanding the qualitatively new critical phenomena in complex networks. The results, concepts, and methods of this rapidly developing field are reviewed. Two closely related classes of these critical phenomena are considered, namely, structural phase transitions in the network architectures and transitions in cooperative models on networks as substrates. Systems where a network and interacting agents on it influence each other are also discussed. A wide range of critical phenomena in equilibrium and growing networks including the birth of the giant connected component, percolation, $k$-core percolation, phenomena near epidemic thresholds, condensation transitions, critical phenomena in spin models placed on networks, synchronization, and self-organized criticality effects in interacting systems on networks are mentioned. Strong finite-size effects in these systems and open problems and perspectives are also discussed.

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Critical phenomena in complex networks

Only recently did mankind realise that it resides in a world of networks. The Internet and World Wide Web are changing our life. Our physical existence is based on various biological networks. We have recently learned that the term "network" turns out to be a central notion in our time, and the consequent explosion of interest in networks is a social and cultural phenomenon. The principles of the complex organization and evolution of networks, natural and artificial, are the topic of this book, which is written by physicists and is addressed to all involved researchers and students. The aim of the text is to understand networks and the basic principles of their structural organization and evolution. The ideas are presented in a clear and a pedagogical way, with minimal mathematics, so even students without a deep knowledge of mathematics and statistical physics will be able to rely on this as a reference. Special attention is given to real networks, both natural and artifical. Collected empirical data and numerous real applications of existing theories are discussed in detail, as well as the topical problems of communication networks. Available in OSO: http://www.oxfordscholarship.com/oso/public/content/physics/9780198515906/toc.html

Evolution of Networks: From Biological Nets to the Internet and WWW

Evolution of Networks: From Biological Nets to the Internet and WWW (Physics)

The model of growing networks with the preferential attachment of new links is generalized to include initial attractiveness of sites. We find the exact form of the stationary distribution of the number of incoming links of sites in the limit of long times, $P(q)$, and the long-time limit of the average connectivity $\overline{q}(s,t)$ of a site $s$ at time $t$ (one site is added per unit of time). At long times, $P(q)\ensuremath{\sim}{q}^{\ensuremath{-}\ensuremath{\gamma}}$ at $q\ensuremath{\rightarrow}\ensuremath{\infty}$ and $\overline{q}(s,t)\ensuremath{\sim}(s/t{)}^{\ensuremath{-}\ensuremath{\beta}}$ at $s/t\ensuremath{\rightarrow}0$, where the exponent $\ensuremath{\gamma}$ varies from $2$ to $\ensuremath{\infty}$ depending on the initial attractiveness of sites. We show that the relation $\ensuremath{\beta}(\ensuremath{\gamma}\ensuremath{-}1)\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1$ between the exponents is universal.

Sergey N. Dorogovtsev

Papers

Evolution of networks

Critical phenomena in complex networks

Evolution of Networks: From Biological Nets to the Internet and WWW

Evolution of Networks: From Biological Nets to the Internet and WWW (Physics)

Structure of growing networks with preferential linking.