arXiv subjects

Davide Vergni

Publications and source records attributed to Davide Vergni.

12 recordsLinked to original sources

arXiv2026

The Critical Patch Size Problem in Random Graphs

The problem of {\it critical patch size} -- a threshold condition for population persistence -- is investigated in the context of discrete habitats, modeled as graphs with a distinguished subset of vertices acting as sinks. These sinks impose boundary-like constraints analogous to Dirichlet conditions in continuous domains. The population proliferates locally at the vertices and diffuse across the network through the graph Laplacian. In the sinks the population cannot survive. The Dirichlet eigenvalue of the habitat is defined as the smallest eigenvalue of the principal submatrix of the Laplacian obtained by removing the rows and columns associated with sink vertices. This spectral parameter governs the habitat's viability: survival occurs when the Dirichlet eigenvalue of the habitat lies below a critical reaction-to-diffusion ratio. We study survival conditions for a sequence of random habitats built on binomial random graphs. We establish a law of large numbers for the corresponding sequence of Dirichlet eigenvalues and prove the emergence of a sharp threshold phenomenon: with high probability, a large random habitat is either viable or non-viable, depending on whether the reaction-to-diffusion ratio lies below or above this threshold. Our results provide the first general spectral theory for critical patch size on graphs, with implications for ecology, synthetic biology, and the modeling of processes on brain connectomes.

math.PR↗

arXiv2021

NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification

Gene-disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated with a disease due to a lack of studies is a challenging task in which prioritization based on prior knowledge is an important element. The computational search for new candidate disease genes may be eased by positive-unlabeled learning, the machine learning setting in which only a subset of instances are labeled as positive while the rest of the data set is unlabeled. In this work, we propose a set of effective network-based features to be used in a novel Markov diffusion-based multi-class labeling strategy for putative disease gene discovery. The performances of the new labeling algorithm and the effectiveness of the proposed features have been tested on ten different disease data sets using three machine learning algorithms. The new features have been compared against classical topological and functional/ontological features and a set of network- and biological-derived features already used in gene discovery tasks. The predictive power of the integrated methodology in searching for new disease genes has been found to be competitive against state-of-the-art algorithms.

cs.LG↗

arXiv2018

Reaction fronts in persistent random walks with demographic stochasticity

Standard Reaction-Diffusion (RD) systems are characterized by infinite velocities and no persistence in the movement of individuals, two conditions that are violated when considering living organisms. Here we consider a discrete particle model in which individuals move following a persistent random walk with finite speed and grow with logistic dynamics. We show that when the number of individuals is very large, the individual-based model is well described by the continuous Reactive Cattaneo Equation (RCE), but for smaller values of the carrying capacity important finite-population effects arise. The effects of fluctuations on the propagation speed are investigated both considering the RCE with a cutoff in the reaction term and by means of numerical simulations of the individual-based model. Finally, a more general Lévy walk process for the transport of individuals is examined and an expression for the front speed of the resulting traveling wave is proposed.

physics.bio-ph↗

arXiv2016

Reaction Spreading in Systems With Anomalous Diffusion

We briefly review some aspects of the anomalous diffusion, and its relevance in reactive systems. In particular we consider {\it strong anomalous} diffusion characterized by the moment behaviour $\langle x(t)^q \rangle \sim t^{q ν(q)}$, where $ν(q)$ is a non constant function, and we discuss its consequences. Even in the apparently simple case $ν(2)=1/2$, strong anomalous diffusion may correspond to non trivial features, such as non Gaussian probability distribution and peculiar scaling of large order moments. When a reactive term is added to a normal diffusion process, one has a propagating front with a constant velocity. The presence of anomalous diffusion by itself does not guarantee a changing in the front propagation scenario; a key factor to select linear in time or faster front propagation has been identified in the shape of the probability distribution tail in absence of reaction. In addition, we discuss the reaction spreading on graphs, underlying the major role of the connectivity properties of these structures, characterized by the {\em connectivity dimension}

cond-mat.stat-mech↗

arXiv2016

Linear and anomalous front propagation in system with non Gaussian diffusion: the importance of tails

We investigate front propagation in systems with diffusive and sub-diffusive behavior. The scaling behavior of moments of the diffusive problem, both in the standard and in the anomalous cases, is not enough to determine the features of the reactive front. In fact, the shape of the bulk of the probability distribution of the transport process, which determines the diffusive properties, is important just for pre-asymptotic behavior of front propagation, while the precise shape of the tails of the probability distribution determines asymptotic behavior of front propagation.

cond-mat.stat-mech↗

arXiv2015

Extinction dynamics of a discrete population in an oasis

Understanding the conditions ensuring the persistence of a population is an issue of primary importance in population biology. The first theoretical approach to the problem dates back to the 50's with the KiSS (after Kierstead, Slobodkin and Skellam) model, namely a continuous reaction-diffusion equation for a population growing on a patch of finite size $L$ surrounded by a deadly environment with infinite mortality -- i.e. an oasis in a desert. The main outcome of the model is that only patches above a critical size allow for population persistence. Here, we introduce an individual-based analogue of the KiSS model to investigate the effects of discreteness and demographic stochasticity. In particular, we study the average time to extinction both above and below the critical patch size of the continuous model and investigate the quasi-stationary distribution of the number of individuals for patch sizes above the critical threshold.

q-bio.PE↗

arXiv2013

Reaction spreading on percolating clusters

Reaction-diffusion processes in two-dimensional percolating structures are investigated. Two different problems are addressed: reaction spreading on a percolating cluster and front propagation through a percolating channel. For reaction spreading, numerical data and analytical estimates show a power-law behavior of the reaction product as M(t) \sim t^dl, where dl is the connectivity dimension. In a percolating channel, a statistically stationary traveling wave develops. The speed and the width of the traveling wave are numerically computed. While the front speed is a low-fluctuating quantity and its behavior can be understood using a simple theoretical argument, the front width is a high-fluctuating quantity showing a power-law behavior as a function of the size of the channel

cond-mat.stat-mech↗

arXiv2013

Front speed in reactive compressible stirred media

We investigated a nonlinear advection-diffusion-reaction equation for a passive scalar field. The purpose is to understand how the compressibility can affect the front dynamics and the bulk burning rate. We study two classes of flows: periodic shear flow and cellular flow both in the case of fast advection regime, analysing the system at varying the extent of compressibility and the reaction rate. We find that the bulk burning rate in a shear flow increases with compressibility intensity. Furthermore, the faster the reaction the more important the difference with respect to the laminar case. The effect has been quantitatively measured and it turns out to be generally little. For the cellular flow, the two extreme cases have been investigated, with the whole perturbation situated either in the centre of the vortex or in the periphery. The dependence in this case does not show a monotonic scaling with different behaviour in the two cases. The enhancing remains modest and always less than 20%

physics.bio-ph↗

arXiv2012

Invasions in heterogeneous habitats in the presence of advection

We investigate invasions from a biological reservoir to an initially empty, heterogeneous habitat in the presence of advection. The habitat consists of a periodic alternation of favorable and unfavorable patches. In the latter the population dies at fixed rate. In the former it grows either with the logistic or with an Allee effect type dynamics, where the population has to overcome a threshold to grow. We study the conditions for successful invasions and the speed of the invasion process, which is numerically and analytically investigated in several limits. Generically advection enhances the downstream invasion speed but decreases the population size of the invading species, and can even inhibit the invasion process. Remarkably, however, the rate of population increase, which quantifies the invasion efficiency, is maximized by an optimal advection velocity. In models with Allee effect, differently from the logistic case, above a critical unfavorable patch size the population localizes in a favorable patch, being unable to invade the habitat. However, we show that advection, when intense enough, may activate the invasion process.

q-bio.PE↗

arXiv2007

Discreteness effects in a reacting system of particles with finite interaction radius

An autocatalytic reacting system with particles interacting at a finite distance is studied. We investigate the effects of the discrete-particle character of the model on properties like reaction rate, quenching phenomenon and front propagation, focusing on differences with respect to the continuous case. We introduce a renormalized reaction rate depending both on the interaction radius and the particle density, and we relate it to macroscopic observables (e.g., front speed and front thickness) of the system.

cond-mat.stat-mech↗

arXiv2002

Superfast front propagation in reactive systems with anomalous diffusion

We study a reaction diffusion system where we consider a non-gaussian process instead of a standard diffusion. If the process increments follow a probability distribution with tails approaching to zero faster than a power law, the usual qualitative behaviours of the standard reaction diffusion system, i.e., exponential tails for the reacting field and a constant front speed, are recovered. On the contrary if the process has power law tails, also the reacting field shows power law tail and the front speed increases exponentially with time. The comparison with other reaction-transport systems which exhibit anomalous diffusion shows that, not only the presence of anomalous diffusion, but also the detailed mechanism, is relevant for the front propagation.

nlin.CG↗

arXiv2002

Efficiency of a stirred chemical reaction in a closed vessel

We perform a numerical study of the reaction efficiency in a closed vessel. Starting with a little spot of product, we compute the time needed to complete the reaction in the container following an advection-reaction-diffusion process. Inside the vessel it is present a cellular velocity field that transports the reactants. If the size of the container is not very large compared with the typical length of the velocity field one has a plateau of the reaction time as a function of the strength of the velocity field, $U$. This plateau appears both in the stationary and in the time-dependent flow. A comparison of the results for the finite system with the infinite case (for which the front speed, $v_f$, gives a simple estimate of the reacting time) shows the dramatic effect of the finite size.

nlin.CD↗