Biomedical subjects

Matteo Marsili

Publications and source records attributed to Matteo Marsili.

11 recordsLinked to original sources

PubMed2006

Statistical mechanics of combinatorial auctions.

Combinatorial auctions are formulated as frustrated lattice gases on sparse random graphs, allowing the determination of the optimal revenue by methods of statistical physics. Transitions between computationally easy and hard regimes are found and interpreted in terms of the geometric structure of the space of solutions. We introduce an iterative algorithm to solve intermediate and large instances, and discuss competing states of optimal revenue and maximal number of satisfied bidders. The algorithm can be generalized to the hard phase and to more sophisticated auction protocols.

Algorithms↗

PubMed2006

Phenomenological models of socioeconomic network dynamics.

We study a general set of models of social network evolution and dynamics. The models consist of both a dynamics on the network and evolution of the network. Links are formed preferentially between "similar" nodes, where the similarity is defined by the particular process taking place on the network. The interplay between the two processes produces phase transitions and hysteresis, as seen using numerical simulations for three specific processes. We obtain analytic results using mean-field approximations, and for a particular case we derive an exact solution for the network. In common with real-world social networks, we find coexistence of high and low connectivity phases and history dependence.

Journal Article↗

PubMed2006

Effect of degree correlations on the loop structure of scale-free networks.

In this paper we study the impact of degree correlations in the subgraph statistics of scale-free networks. In particular we consider loops, simple cases of network subgraphs which encode the redundancy of the paths passing through every two nodes of the network. We provide an understanding of the scaling of the clustering coefficient in modular networks in terms of the maximal eigenvector of the average adjacency matrix of the ensemble. Furthermore we show that correlations affect in a relevant way the average number of Hamiltonian paths in a three-core of real world networks. We prove our results in the two-vertex correlated hidden variable ensemble and we check the results with exact counting of small loops in real graphs.

Journal Article↗

PubMed2006

Codon usage domains over bacterial chromosomes.

The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context.

Amino Acids↗

PubMed2006

Scale-free networks with an exponent less than two.

We study scale-free simple graphs with an exponent of the degree distribution gamma less than 2. Generically one expects such extremely skewed networks--which occur very frequently in systems of virtually or logically connected units--to have different properties than those of scale free networks with gamma>2: The number of links grows faster than the number of nodes and they naturally possess the small world property, because the diameter increases by the logarithm of the size of the network and the clustering coefficient is finite. We discuss a simple prototype model of such networks, inspired by real world phenomena, which exhibits these properties and allows for a detailed analytical investigation.

Journal Article↗

PubMed2005

Species lifetime distribution for simple models of ecologies.

Interpretation of empirical results based on a taxa's lifetime distribution shows apparently conflicting results. Species' lifetime is reported to be exponentially distributed, whereas higher-order taxa, such as families or genera, follow a broader distribution, compatible with power-law decay. We show that both forms of evidence are consistent with a simple evolutionary model that does not require specific assumptions on species interaction. The model provides a zero-order description of the dynamics of ecological communities, and its species lifetime distribution can be computed exactly. Different behaviors are found as follows: an initial t(-3/2) power law, emerging from a random walk type of dynamics, which crosses over to a steeper t(-2) branching process-like regime and finally is cut off by an exponential decay that becomes weaker and weaker as the total population increases. Sampling effects also can be taken into account and shown to be relevant. If species in the fossil record were sampled according to the Fisher log-series distribution, lifetime should be distributed according to a t(-1) power law. Such variability of behaviors in a simple model, combined with the scarcity of data available, casts serious doubt on the possibility of validating theories of evolution on the basis of species lifetime data.

Animals↗

PubMed2005

Statistical mechanics model for the emergence of consensus.

The statistical properties of pairwise majority voting over S alternatives are analyzed in an infinite random population. We first compute the probability that the majority is transitive (i.e., that if it prefers A to B to C , then it prefers A to C) and then study the case of an interacting population. This is described by a constrained multicomponent random field Ising model whose ferromagnetic phase describes the emergence of a strong transitive majority. We derive the phase diagram, which is characterized by a tricritical point and show that, contrary to intuition, it may be more likely for an interacting population to reach consensus on a number S of alternatives when S increases. This effect is due to the constraint imposed by transitivity on voting behavior. Indeed if agents are allowed to express nontransitive votes, the agents' interaction may decrease considerably the probability of a transitive majority.

Journal Article↗

PubMed2004

Clogging and self-organized criticality in complex networks.

We propose a simple model that aims at describing, in a stylized manner, how local breakdowns due to imbalances or congestion propagate in real dynamical networks. The model converges to a self-organized critical stationary state in which the network shapes itself as a consequence of avalanches of rewiring processes. Depending on the model's specification, we obtain either single-scale or scale-free networks. We characterize in detail the relation between the statistical properties of the network and the nature of the critical state, by computing the critical exponents. The model also displays a nontrivial, sudden collapse to a complete network.

Journal Article↗

PubMed2004

The rise and fall of a networked society: a formal model.

In a well networked community, there is intense social interaction, and information disseminates briskly and broadly. This is important if the environment is volatile (i.e., keeps changing) and individuals never stop searching for fresh opportunities. Here, we present a simple model that attributes the rise of a dynamic society to the emergence of some key features in its social network. We also explain the apparently paradoxical observation that although such features do not necessarily materialize even under favorable conditions they display a significant resilience to deteriorating conditions. We interpret these findings as a discontinuous phase transition in the network formation process.

Journal Article↗

PubMed2003

Criticality and market efficiency in a simple realistic model of the stock market.

We discuss a simple model based on the minority game which reproduces the main stylized facts of anomalous fluctuations in finance. We present the analytic solution of the model in the thermodynamic limit. Stylized facts arise only close to a line of critical points with nontrivial properties, marking the transition to an unpredictable market. We show that the emergence of critical fluctuations close to the phase transition is governed by the interplay between the signal to noise ratio and the system size. These results provide a clear and consistent picture of financial markets, where stylized facts and verge of unpredictability are intimately related aspects of the same critical systems.

Journal Article↗

PubMed2002

Diffusion, peer pressure, and tailed distributions.

We present a general, physically motivated nonlinear and nonlocal advection equation in which the diffusion of interacting random walkers competes with a local drift arising from a kind of peer pressure. We show, using a mapping to an integrable dynamical system, that on varying a parameter the steady-state behavior undergoes a transition from the standard diffusive behavior to a localized stationary state characterized by a tailed distribution. Finally, we show that recent empirical laws on economic growth can be explained as a collective phenomenon due to peer pressure interaction.

Economics↗