arXiv subjects

Franco Bagnoli

Publications and source records attributed to Franco Bagnoli.

At least 91 records · Page 5Linked to original sources

arXiv2007

Dynamical affinity in opinion dynamics modelling

We here propose a model to simulate the process of opinion formation, which accounts for the mutual affinity between interacting agents. Opinion and affinity evolve self-consistently, manifesting a highly non trivial interplay. A continuous transition is found between single and multiple opinion states. Fractal dimension and signature of critical behaviour are also reported. A rich phenomenology is presented and discussed with reference to corresponding psychological implications.

physics.soc-ph↗

arXiv2006

A toy model of polymer stretching

We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the cantilever) and long-range interactions terms inside each domain. Exact equilibrium computations and Monte Carlo simulations qualitatively reproduce the experimental saw-tooth pattern of force-extension profiles, corresponding (in our model) to first-order phase transitions. We study the influence of the coupling induced by the cantilever and the pulling speed on the relative heights of the force peaks. The results suggest that the increasing height of the critical force for subsequent unfolding events is an out-of-equilibrium effect due to a finite pulling speed. The dependence of the average unfolding force on the pulling speed is shown to reproduce the experimental logarithmic law.

q-bio.BM↗

arXiv2006

The influence of risk perception in epidemics: a cellular agent model

Our work stems from the consideration that the spreading of a disease is modulated by the individual's perception of the infected neighborhood and his/her strategy to avoid being infected as well. We introduced a general ``cellular agent'' model that accounts for a hetereogeneous and variable network of connections. The probability of infection is assumed to depend on the perception that an individual has about the spreading of the disease in her local neighborhood and on broadcasting media. In the one-dimensional homogeneous case the model reduces to the DK one, while for long-range coupling the dynamics exhibits large fluctuations that may lead to the complete extinction of the disease.

q-bio.PE↗

arXiv2006

Mathematical Model of HIV superinfection dynamics and R5 to X4 switch

During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been correlated with a faster progression of the disease to the AIDS phase. As several pharmaceutical companies are starting large phase III trials for R5 and X4 drugs, models are needed to predict the co-evolutionary and competitive dynamics of virus strains. We present a model of HIV early infection which describes the dynamics of R5 quasispecies and a model of HIV late infection which describes the R5 to X4 switch. We report the following findings: after superinfection or coinfection, quasispecies dynamics has time scales of several months and becomes even slower at low number of CD4+ T cells. The curve of CD4+ T cells decreases, during AIDS late stage, and can be described taking into account the X4 related Tumor Necrosis Factor dynamics. Phylogenetic inference of chemokine receptors suggests that viral mutational pathway may generate R5 variants able to interact with chemokine receptors different from CXCR4. This may explain the massive signaling disruptions in the immune system observed during AIDS late stages and may have relevance for vaccination and therapy.

q-bio.PE↗

arXiv2006

A discrete statistical mechanics approach to aeolian ripple dynamics

The interaction between a fluid and a granular material plays a crucial role in a large class of phenomena such as landscape morphology and transport of sediments, aeolian sand dunes formation and ripples dynamics. Standard models involve deterministic continuum equations or, alternatively, Lattice Boltzmann and Lattice Gas Cellular Automata. We here introduce a toy-model to address the issue of aeolian ripple formation and evolution. Our simplified approach accounts for the basic physical mechanisms and enables to reproduce the observed phenomenology in the framework of an innovative statistical mechanics formulation.

cond-mat.stat-mech↗

arXiv2005

Synchronization universality classes and stability of smooth, coupled map lattices

We study two problems related to spatially extended systems: the dynamical stability and the universality classes of the replica synchronization transition. We use a simple model of one dimensional coupled map lattices and show that chaotic behavior implies that the synchronization transition belongs to the multiplicative noise universality class, while stable chaos implies that the synchronization transition belongs to the directed percolation universality class.

cond-mat.stat-mech↗

arXiv2005

Opinion formation and phase transitions in a probabilistic cellular automaton with two absorbing states

We discuss the process of opinion formation in a completely homogeneous, democratic population using a class of probabilistic cellular automata models with two absorbing states. Each individual can have one of two opinions that can change according to that of his neighbors. It is dominated by an overwhelming majority and can disagree against a marginal one. We present the phase diagram in the mean field approximation and from numerical experiments for the simplest nontrivial case. For arbitrarily large neighborhoods we discuss the mean field results for a non-conformist society, where each individual adheres to the overwhelming majority of its neighbors and choses an opposite opinion in other cases. Mean field results and preliminary lattice simulations with long-range connections among individuals show the presence of coherent temporal oscillations of the population.

nlin.AO↗

arXiv2005

Chaos in a simple cellular automata model of a uniform society

In this work we study the collective behaviors arising in a model of a simplified homogeneous society. Each agent is modeled as a binary ``perceptron'', receiving neighbors' opinions as inputs and outputting one of two possible opinions, according to the conformist attitude and to the external pressure of mass media. For a neighborhood size greater than three, the system shows a very complex phase diagram, including a disordered phase and chaotic behavior. We present analytic calculations, mean fields approximation and numeric simulations for different values of the parameters.

nlin.AO↗

arXiv2005

Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics

The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have not yet been understood. We present a model of HIV quasispecies competition, that describes the conditions of viral quasispecies coexistence under different immune system conditions. Our model incorporates both T and B cells responses, and we show that the role of B cells is important and additive to that of T cells. Simulations of coinfection (simultaneous infection) and superinfection (delayed secondary infection) scenarios in the early stages (days) and in the late stages of the infection (years) are in agreement with emerging molecular biology findings. The immune response induces a competition among similar phenotypes, leading to differentiation (quasi-speciation), escape dynamics and complex oscillations of viral strain abundance. We found that the quasispecies dynamics after superinfection or coinfection has time scales of several months and becomes even slower when the immune system response is weak. Our model represents a general framework to study the speed and distribution of HIV quasispecies during disease progression, vaccination and therapy.

q-bio.PE↗

arXiv2004

A microscopic model of evolution of recombination

We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not related to the population itself, and a dynamic one that accounts for interactions between organisms e.g. competition. We focus on the dynamics of colonization of an empty niche. As competition is a function of the population, selection pressure rapidly changes in time. The simulations show that both in the case of flat and steep static fitness landscapes, recombination provides a high velocity of movement in the phenotypic space thus allowing recombinants to colonize the highest fitness regions earlier than non recombinants that are often driven to extinction. The stabilizing effects of competition and assortativity are also discussed. Finally, the analysis of phase diagrams shows that competition is the key factor for the evolution of recombination, while assortativity plays a significant role only in small populations.

q-bio.PE↗

arXiv2004

A model of sympatric speciation through assortative mating

A microscopic model is developed, within the frame of the theory of quantitative traits, to study both numerically and analytically the combined effect of competition and assortativity on the sympatric speciation process, i.e. speciation in the absence of geographical barriers. Two components of fitness are considered: a static one that describes adaptation to environmental factors not related to the population itself, and a dynamic one that accounts for interactions between organisms, e.g. competition. The effects of finiteness of population size on survival of coexisting species are also accounted for. The simulations show that both in the case of flat and ripid static fitness landscapes, competition and assortativity do exert a synergistic effect on speciation. We also show that competition acts as a stabilizing force against extinction due to random sampling in a finite population. Finally, evidence is shown that speciation can be seen as a phase transition.

q-bio.PE↗

arXiv2003

WebTeach in practice: the entrance test to the Engineering faculty in Florence

We present the WebTeach project, formed by a web interface to database for test management, a wiki site for the diffusion of teaching material and student forums, and a suite for the generation of multiple-choice mathematical quiz with automatic elaboration of forms. This system has been massively tested for the entrance test to the Engineering Faculty of the University of Florence, Italy

cs.HC↗

arXiv2003

Short period attractors and non-ergodic behavior in the deterministic fixed energy sandpile model

We study the asymptotic behaviour of the Bak, Tang, Wiesenfeld sandpile automata as a closed system with fixed energy. We explore the full range of energies characterizing the active phase. The model exhibits strong non-ergodic features by settling into limit-cycles whose period depends on the energy and initial conditions. The asymptotic activity $ρ_a$ (topplings density) shows, as a function of energy density $ζ$, a devil's staircase behaviour defining a symmetric energy interval-set over which also the period lengths remain constant. The properties of $ζ$-$ρ_a$ phase diagram can be traced back to the basic symmetries underlying the model's dynamics.

cond-mat.stat-mech↗

arXiv2003

De Gustibus Disputandum

We propose a simple method to predict individuals' expectations about products using a knowledge network. As a complementary result, we show that the method is able, under certain conditions, to extract hidden information at neural level from a customers' choices database.

cond-mat.stat-mech↗

arXiv2001

Small world effects in evolution

For asexual organisms point mutations correspond to local displacements in the genotypic space, while other genotypic rearrangements represent long-range jumps. We investigate the spreading properties of an initially homogeneous population in a flat fitness landscape, and the equilibrium properties on a smooth fitness landscape. We show that a small-world effect is present: even a small fraction of quenched long-range jumps makes the results indistinguishable from those obtained by assuming all mutations equiprobable. Moreover, we find that the equilibrium distribution is a Boltzmann one, in which the fitness plays the role of an energy, and mutations that of a temperature.

cond-mat.stat-mech↗

arXiv2000

Nature of phase transitions in a probabilistic cellular automaton with two absorbing states

We present a probabilistic cellular automaton with two absorbing states, which can be considered a natural extension of the Domany-Kinzel model. Despite its simplicity, it shows a very rich phase diagram, with two second-order and one first-order transition lines that meet at a tricritical point. We study the phase transitions and the critical behavior of the model using mean field approximations, direct numerical simulations and field theory. A closed form for the dynamics of the kinks between the two absorbing phases near the tricritical point is obtained, providing an exact correspondence between the presence of conserved quantities and the symmetry of absorbing states. The second-order critical curves and the kink critical dynamics are found to be in the directed percolation and parity conservation universality classes, respectively. The first order phase transition is put in evidence by examining the hysteresis cycle. We also study the "chaotic" phase, in which two replicas evolving with the same noise diverge, using mean field and numerical techniques. Finally, we show how the shape of the potential of the field-theoretic formulation of the problem can be obtained by direct numerical simulations.

cond-mat.stat-mech↗

arXiv2000

Boolean derivatives and computation of cellular automata

The derivatives of a Boolean function are defined up to any order. The Taylor and MacLaurin expansions of a Boolean function are thus obtained. The last corresponds to the ring sum expansion (RSE) of a Boolean function, and is a more compact form than the usual canonical disjunctive form. For totalistic functions the RSE allows the saving of a large number of Boolean operations. The algorithm has natural applications to the simulations of cellular automata using the multi site coding technique. Several already published algorithms are analized, and expressions with fewer terms are generally found.

cond-mat↗

arXiv1999

An evolutionary model for simple ecosystems

In this review some simple models of asexual populations evolving on smooth landscapes are studied. The basic model is based on a cellular automaton, which is analyzed here in the spatial mean-field limit. Firstly, the evolution on a fixed fitness landscape is considered. The correspondence between the time evolution of the population and equilibrium properties of a statistical mechanics system is investigated, finding the limits for which this mapping holds. The mutational meltdown, Eigen's error threshold and Muller's ratchet phenomena are studied in the framework of a simplified model. Finally, the shape of a quasi-species and the condition of coexistence of multiple species in a static fitness landscape are analyzed. In the second part, these results are applied to the study of the coexistence of quasi-species in the presence of competition, obtaining the conditions for a robust speciation effect in asexual populations.

cond-mat.stat-mech↗