23,607 research outputs found
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
Modularity and anti-modularity in networks with arbitrary degree distribution
Networks describing the interaction of the elements that constitute a complex
system grow and develop via a number of different mechanisms, such as the
addition and deletion of nodes, the addition and deletion of edges, as well as
the duplication or fusion of nodes. While each of these mechanisms can have a
different cause depending on whether the network is biological, technological,
or social, their impact on the network's structure, as well as its local and
global properties, is similar. This allows us to study how each of these
mechanisms affects networks either alone or together with the other processes,
and how they shape the characteristics that have been observed. We study how a
network's growth parameters impact the distribution of edges in the network,
how they affect a network's modularity, and point out that some parameters will
give rise to networks that have the opposite tendency, namely to display
anti-modularity. Within the model we are describing, we can search the space of
possible networks for parameter sets that generate networks that are very
similar to well-known and well-studied examples, such as the brain of a worm,
and the network of interactions of the proteins in baker's yeast.Comment: 23 pages. 13 figures, 1 table. Includes Supplementary tex
Evolution of networks
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 artificial networks of such a kind came into existence
recently. This opens a wide field for the study of their topology, evolution,
and complex processes occurring 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 large sizes of these
networks, the distances between most their vertices are short -- a feature
known as the ``small-world'' effect. We discuss how growing networks
self-organize into scale-free structures and the role of the mechanism of
preferential linking. We consider the topological and structural properties of
evolving networks, and percolation in these networks. We present a number of
models demonstrating the main features of evolving networks and discuss current
approaches for their simulation and analytical study. Applications of the
general results to particular networks in Nature are discussed. We demonstrate
the generic connections of the network growth processes with the general
problems of non-equilibrium physics, econophysics, evolutionary biology, etc.Comment: 67 pages, updated, revised, and extended version of review, submitted
to Adv. Phy
Skeleton and fractal scaling in complex networks
We find that the fractal scaling in a class of scale-free networks originates
from the underlying tree structure called skeleton, a special type of spanning
tree based on the edge betweenness centrality. The fractal skeleton has the
property of the critical branching tree. The original fractal networks are
viewed as a fractal skeleton dressed with local shortcuts. An in-silico model
with both the fractal scaling and the scale-invariance properties is also
constructed. The framework of fractal networks is useful in understanding the
utility and the redundancy in networked systems.Comment: 4 pages, 2 figures, final version published in PR
Growing network model for community with group structure
We propose a growing network model for a community with a group structure.
The community consists of individual members and groups, gatherings of members.
The community grows as a new member is introduced by an existing member at each
time step. The new member then creates a new group or joins one of the groups
of the introducer. We investigate the emerging community structure analytically
and numerically. The group size distribution shows a power law distribution for
a variety of growth rules, while the activity distribution follows an
exponential or a power law depending on the details of the growth rule. We also
present an analysis of empirical data from on the online communities, the
``Groups'' in \url{http://www.yahoo.com} and the ``Cafe'' in
\url{http://www.daum.net}, which shows a power law distribution for a wide
range of group sizes.Comment: 5 figures and 1 tabl
Graphene Grown on Ge(001) from Atomic Source
Among the many anticipated applications of graphene, some - such as
transistors for Si microelectronics - would greatly benefit from the
possibility to deposit graphene directly on a semiconductor grown on a Si
wafer. We report that Ge(001) layers on Si(001) wafers can be uniformly covered
with graphene at temperatures between 800{\deg}C and the melting temperature of
Ge. The graphene is closed, with sheet resistivity strongly decreasing with
growth temperature, weakly decreasing with the amount of deposited C, and
reaching down to 2 kOhm/sq. Activation energy of surface roughness is low
(about 0.66 eV) and constant throughout the range of temperatures in which
graphene is formed. Density functional theory calculations indicate that the
major physical processes affecting the growth are: (1) substitution of Ge in
surface dimers by C, (2) interaction between C clusters and Ge monomers, and
(3) formation of chemical bonds between graphene edge and Ge(001), and that the
processes 1 and 2 are surpassed by CH surface diffusion when the C atoms
are delivered from CH. The results of this study indicate that graphene
can be produced directly at the active region of the transistor in a process
compatible with the Si technology
Dynamic interactions of a conserved enterotoxigenic Escherichia coli adhesin with intestinal mucins govern epithelium engagement and toxin delivery
At present, there is no vaccine for enterotoxigenic Escherichia coli (ETEC), an important cause of diarrheal illness. Nevertheless, recent microbial pathogenesis studies have identified a number of molecules produced by ETEC that contribute to its virulence and are novel antigenic targets to complement canonical vaccine approaches. EtpA is a secreted two-partner adhesin that is conserved within the ETEC pathovar. EtpA interacts with the tips of ETEC flagella to promote bacterial adhesion, toxin delivery, and intestinal colonization by forming molecular bridges between the bacteria and the epithelial surface. However, the nature of EtpA interactions with the intestinal epithelium remains poorly defined. Here, we demonstrate that EtpA interacts with glycans presented by transmembrane and secreted intestinal mucins at epithelial surfaces to facilitate pathogen-host interactions that culminate in toxin delivery. Moreover, we found that a major effector molecule of ETEC, the heat-labile enterotoxin (LT), may enhance these interactions by stimulating the production of the gel-forming mucin MUC2. Our studies suggest, however, that EtpA participates in complex and dynamic interactions between ETEC and the gastrointestinal mucosae in which host glycoproteins promote bacterial attachment while simultaneously limiting the epithelial engagement required for effective toxin delivery. Collectively, these data provide additional insight into the intricate nature of ETEC interactions with the intestinal epithelium that have potential implications for rational approaches to vaccine design
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