Models and average properties of scale-free directed networks

We extend the merging model for undirected networks by Kim et al. [Eur. Phys. J. B 43, 369 (2004)] to directed networks and investigate the emerging scale-free networks. Two versions of the directed merging model, friendly and hostile merging, give rise to two distinct network types. We uncover that some non-trivial features of these two network types resemble two levels of a certain randomization/non-specificity in the link reshuffling during network evolution. Furthermore the same features show up, respectively, in metabolic networks and transcriptional networks. We introduce measures that single out the distinguishing features between the two prototype networks, as well as point out features which are beyond the prototypes.Comment: 7 pages, 8 figure

One Hub-One Process: A Tool Based View on Regulatory Network Topology

The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces Cerevisiae. We find that the topology of the regulatory network show weak remnants of its history of network reorganizations, but strong features of co-regulated proteins associated to similar tasks. This suggests that local topological features of regulatory networks, including broad degree distributions, emerge as an implicit result of matching a number of needed processes to a finite toolbox of proteins.Comment: 18 pages, 3 figures, 5 supplementary figure

Equilibrium strategy and population-size effects in lowest unique bid auctions

In lowest unique bid auctions, $N$ players bid for an item. The winner is whoever places the \emph{lowest} bid, provided that it is also unique. We use a grand canonical approach to derive an analytical expression for the equilibrium distribution of strategies. We then study the properties of the solution as a function of the mean number of players, and compare them with a large dataset of internet auctions. The theory agrees with the data with striking accuracy for small population size $N$, while for larger $N$ a qualitatively different distribution is observed. We interpret this result as the emergence of two different regimes, one in which adaptation is feasible and one in which it is not. Our results question the actual possibility of a large population to adapt and find the optimal strategy when participating in a collective game.Comment: 6 pag. - 7 figs - added Supplementary Material. Changed affiliations. Published versio

Replicator dynamics with turnover of players

We study adaptive dynamics in games where players abandon the population at a given rate, and are replaced by naive players characterized by a prior distribution over the admitted strategies. We demonstrate how such process leads macroscopically to a variant of the replicator equation, with an additional term accounting for player turnover. We study how Nash equilibria and the dynamics of the system are modified by this additional term, for prototypical examples such as the rock-scissor-paper game and different classes of two-action games played between two distinct populations. We conclude by showing how player turnover can account for non-trivial departures from Nash equilibria observed in data from lowest unique bid auctions.Comment: 14 pages, 7 figure

Size dependent word frequencies and translational invariance of books

It is shown that a real novel shares many characteristic features with a null model in which the words are randomly distributed throughout the text. Such a common feature is a certain translational invariance of the text. Another is that the functional form of the word-frequency distribution of a novel depends on the length of the text in the same way as the null model. This means that an approximate power-law tail ascribed to the data will have an exponent which changes with the size of the text-section which is analyzed. A further consequence is that a novel cannot be described by text-evolution models like the Simon model. The size-transformation of a novel is found to be well described by a specific Random Book Transformation. This size transformation in addition enables a more precise determination of the functional form of the word-frequency distribution. The implications of the results are discussed.Comment: 10 pages, 2 appendices (6 pages), 5 figure

Degree Landscapes in Scale-Free Networks

We generalize the degree-organizational view of real-world networks with broad degree-distributions in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). For example, correlated degrees between adjacent nodes corresponds to smooth landscapes (social networks), hierarchical networks to one-mountain landscapes (the Internet), and degree-disassortative networks without hierarchical features to rough landscapes with several mountains. We also generate ridge landscapes to model networks organized under constraints imposed by the space the networks are embedded in, associated to spatial or, in molecular networks, to functional localization. To quantify the topology, we here measure the widths of the mountains and the separation between different mountains.Comment: 4 pages, 5 figure

Neutral theory of chemical reaction networks

To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However, specific features may sometimes be neutral and uncorrelated with any system-specific purpose, function or causal chain. Such neutral features are caused by chance and randomness. Here we compare two classes of chemical networks: one that has been subjected to biological evolution (the chemical reaction network of metabolism in living cells) and one that has not (the atmospheric planetary chemical reaction networks). Their degree distributions are shown to share the very same neutral system-independent features. The shape of the broad distributions is to a large extent controlled by a single parameter, the network size. From this perspective, there is little difference between atmospheric and metabolic networks; they are just different sizes of the same random assembling network. In other words, the shape of the degree distribution is a neutral characteristic feature and has no functional or evolutionary implications in itself; it is not a matter of life and death.Comment: 13 pages, 8 figure

Symmetry-allowed phase transitions realized by the two-dimensional fully frustrated XY class

A 2D Fully Frustrated XY(FFXY) class of models is shown to contain a new groundstate in addition to the checkerboard groundstates of the standard 2D FFXY model. The spin configuration of this additional groundstate is obtained. Associated with this groundstate there are additional phase transitions. An order parameter accounting for these new transitions is proposed. The transitions associated with the new order parameter are suggested to be similar to a 2D liquid-gas transition which implies Z_2-Ising like transitions. This suggests that the class of 2D FFXY models belongs within a U(1) x Z_2 x Z_2-designation of possible transitions, which implies that there are seven different possible single and combined transitions. MC-simulations for the generalized fully frustrated XY (GFFXY) model on a square lattice are used to investigate which of these possibilities can be realized in practice: five of the seven are encountered. Four critical points are deduced from the MC-simulations, three consistent with central charge c=3/2 and one with c=1. The implications for the standard 2D FFXY-model are discussed in particular with respect to the long standing controversy concerning the characteristics of its phase transitions.Comment: 8 pages, 8 figure