10,377 research outputs found
Evolution of the Protein Interaction Network of Budding Yeast: Role of the Protein Family Compatibility Constraint
Understanding of how protein interaction networks (PIN) of living organisms
have evolved or are organized can be the first stepping stone in unveiling how
life works on a fundamental ground. Here we introduce a hybrid network model
composed of the yeast PIN and the protein family interaction network. The
essential ingredient of the model includes the protein family identity and its
robustness under evolution, as well as the three previously proposed ones: gene
duplication, divergence, and mutation. We investigate diverse structural
properties of our model with parameter values relevant to yeast, finding that
the model successfully reproduces the empirical data.Comment: 5 pages, 5 figures, 1 table. Title changed. Final version published
in JKP
Betweenness centrality correlation in social networks
Scale-free (SF) networks exhibiting a power-law degree distribution can be
grouped into the assortative, dissortative and neutral networks according to
the behavior of the degree-degree correlation coefficient. Here we investigate
the betweenness centrality (BC) correlation for each type of SF networks. While
the BC-BC correlation coefficients behave similarly to the degree-degree
correlation coefficients for the dissortative and neutral networks, the BC
correlation is nontrivial for the assortative ones found mainly in social
networks. The mean BC of neighbors of a vertex with BC is almost
independent of , implying that each person is surrounded by almost the
same influential environments of people no matter how influential the person
is.Comment: 4 pages, 4 figures, 1 tabl
Branching process approach for Boolean bipartite networks of metabolic reactions
The branching process (BP) approach has been successful in explaining the
avalanche dynamics in complex networks. However, its applications are mainly
focused on unipartite networks, in which all nodes are of the same type. Here,
motivated by a need to understand avalanche dynamics in metabolic networks, we
extend the BP approach to a particular bipartite network composed of Boolean
AND and OR logic gates. We reduce the bipartite network into a unipartite
network by integrating out OR gates, and obtain the effective branching ratio
for the remaining AND gates. Then the standard BP approach is applied to the
reduced network, and the avalanche size distribution is obtained. We test the
BP results with simulations on the model networks and two microbial metabolic
networks, demonstrating the usefulness of the BP approach
Coarsening Dynamics of Granular Heaplets in Tapped Granular Layers
A semi-continuum model is introduced to study the dynamics of the formation
of granular heaplets in tapped granular layers. By taking into account the
energy dissipation of collisions and screening effects due to avalanches, this
model is able to reproduce qualitatively the pattern of these heaplets. Our
simulations show that the granular heaplets are characterised by an effective
surface tension which depends on the magnitude of the tapping intensity. Also,
we observe that there is a coarsening effect in that the average size of the
heaplets, V grows as the number of taps k increases. The growth law at
intermediate times can be fitted by a scaling function V ~ k^z but the range of
validity of the power law is limited by size effects. The growth exponent z
appears to diverge as the tapping intensity is increased.Comment: 4 pages, 4 figure
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