Biomedical subjects

Petter Holme

Publications and source records attributed to Petter Holme.

7 recordsLinked to original sources

PubMed2003

Dynamic critical behavior of the XY model in small-world networks.

The critical behavior of the XY model on small-world network is investigated by means of dynamic Monte Carlo simulations. We use the short-time relaxation scheme, i.e., the critical behavior is studied from the nonequilibrium relaxation to equilibrium. Static and dynamic critical exponents are extracted through the use of the dynamic finite-size scaling analysis. It is concluded that the dynamic universality class at the transition is of the mean-field nature. We also confirm numerically that the value of dynamic critical exponent is independent of the rewiring probability P for P greater, similar 0.03.

Journal Article↗

PubMed2003

Subnetwork hierarchies of biochemical pathways.

MOTIVATION: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied. RESULTS: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks. AVAILABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/

Algorithms↗

PubMed2002

Edge overload breakdown in evolving networks.

We investigate growing networks based on Barabási and Albert's algorithm for generating scale-free networks, but with edges sensitive to overload breakdown. The load is defined through edge betweenness centrality. We focus on the situation where the average number of connections per vertex is, like the number of vertices, linearly increasing in time. After an initial stage of growth, the network undergoes avalanching breakdowns to a fragmented state from which it never recovers. This breakdown is much less violent if the growth is by random rather than by preferential attachment (as defines the Barabási and Albert model). We briefly discuss the case where the average number of connections per vertex is constant. In this case no breakdown avalanches occur. Implications to the growth of real-world communication networks are discussed.

Journal Article↗

PubMed2002

Dynamic instabilities induced by asymmetric influence: prisoners' dilemma game in small-world networks.

A two-dimensional small-world-type network, subject to spatial prisoners' dilemma dynamics and containing an influential node defined as a special node, with a finite density of directed random links to the other nodes in the network, is numerically investigated. It is shown that the degree of cooperation does not remain at a steady state level but displays a punctuated equilibrium-type behavior manifested by the existence of sudden breakdowns of cooperation. The breakdown of cooperation is linked to an imitation of a successful selfish strategy of the influential node. It is also found that while the breakdown of cooperation occurs suddenly, its recovery requires longer time. This recovery time may, depending on the degree of steady state cooperation, either increase or decrease with an increasing number of long-range connections.

Behavior↗

PubMed2002

Vertex overload breakdown in evolving networks.

We study evolving networks based on the Barabási-Albert scale-free network model with vertices sensitive to overload breakdown. The load of a vertex is defined as the betweenness centrality of the vertex. Two cases of load limitation are considered, corresponding to the fact that the average number of connections per vertex is increasing with the network's size ("extrinsic communication activity"), or that it is constant ("intrinsic communication activity"). Avalanchelike breakdowns for both load limitations are observed. In order to avoid such avalanches we argue that the capacity of the vertices has to grow with the size of the system. An interesting irregular dynamics of the formation of the giant component (for the intrinsic communication activity case) is also studied. Implications on the growth of the Internet are discussed.

Journal Article↗

PubMed2002

Attack vulnerability of complex networks.

We study the response of complex networks subject to attacks on vertices and edges. Several existing complex network models as well as real-world networks of scientific collaborations and Internet traffic are numerically investigated, and the network performance is quantitatively measured by the average inverse geodesic length and the size of the largest connected subgraph. For each case of attacks on vertices and edges, four different attacking strategies are used: removals by the descending order of the degree and the betweenness centrality, calculated for either the initial network or the current network during the removal procedure. It is found that the removals by the recalculated degrees and betweenness centralities are often more harmful than the attack strategies based on the initial network, suggesting that the network structure changes as important vertices or edges are removed. Furthermore, the correlation between the betweenness centrality and the degree in complex networks is studied.

Journal Article↗

PubMed2002

Growing scale-free networks with tunable clustering.

We extend the standard scale-free network model to include a "triad formation step." We analyze the geometric properties of networks generated by this algorithm both analytically and by numerical calculations, and find that our model possesses the same characteristics as the standard scale-free networks such as the power-law degree distribution and the small average geodesic length, but with the high clustering at the same time. In our model, the clustering coefficient is also shown to be tunable simply by changing a control parameter---the average number of triad formation trials per time step.

Journal Article↗