arXiv subjects

Massimo Cencini

Publications and source records attributed to Massimo Cencini.

At least 55 records · Page 3Linked to original sources

arXiv2015

The role of the number of degrees of freedom and chaos in macroscopic irreversibility

This article aims at revisiting, with the aid of simple and neat numerical examples, some of the basic features of macroscopic irreversibility, and, thus, of the mechanical foundation of the second principle of thermodynamics as drawn by Boltzmann. Emphasis will be put on the fact that, in systems characterized by a very large number of degrees of freedom, irreversibility is already manifest at a single-trajectory level for the vast majority of the far-from-equilibrium initial conditions - a property often referred to as typicality. We also discuss the importance of the interaction among the microscopic constituents of the system and the irrelevance of chaos to irreversibility, showing that the same irreversible behaviours can be observed both in chaotic and non-chaotic systems.

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↗

arXiv2014

Gyrotactic trapping in laminar and turbulent Kolmogorov flow

Phytoplankton patchiness, namely the heterogeneous distribution of microalgae over multiple spatial scales, dramatically impacts marine ecology. A spectacular example of such heterogeneity occurs in thin phytoplankton layers (TPLs), where large numbers of photosynthetic microorganisms are found within a small depth interval. Some species of motile phytoplankton can form TPLs by gyrotactic trapping due to the interplay of their particular swimming style (directed motion biased against gravity) and the transport by a flow with shear along the direction of gravity. Here we consider gyrotactic swimmers in numerical simulations of the Kolmogorov shear flow, both in laminar and turbulent regimes. In the laminar case, we show that the swimmer motion is integrable and the formation of TPLs can be fully characterized by means of dynamical systems tools. We then study the effects of rotational Brownian motion or turbulent fluctuations (appearing when the Reynolds number is large enough) on TPLs. In both cases we show that TPLs become transient, and we characterize their persistence.

physics.flu-dyn↗

arXiv2014

Coarse-grained modeling of protein unspecifically bound to DNA

There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in solution (jumps), 1D-diffusion along DNA (sliding), and small jumps (hopping) achieving association rates higher than for 3D-diffusion only. We investigate the FD phenomenology through Molecular Dynamics simulations in the framework of coarse-grained modeling. Despite the crude approximations, we show that the model generates, upon varying equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, by focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix leading to a coupling of translation along the DNA-axis with rotation around it. The 1D-diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument able to quantitatively reproduce the measured values.

q-bio.BM↗

arXiv2013

Turbulent fluid acceleration generates clusters of gyrotactic microorganisms

The motility of microorganisms is often biased by gradients in physical and chemical properties of their environment, with myriad implications on their ecology. Here we show that fluid acceleration reorients gyrotactic plankton, triggering small-scale clustering. We experimentally demonstrate this phenomenon by studying the distribution of the phytoplankton Chlamydomonas augustae within a rotating tank and find it to be in good agreement with a new, generalized model of gyrotaxis. When this model is implemented in a direct numerical simulation of turbulent flow, we find that fluid acceleration generates multi-fractal plankton clustering, with faster and more stable cells producing stronger clustering. By producing accumulations in high-vorticity regions, this process is fundamen- tally different from clustering by gravitational acceleration, expanding the range of mechanisms by which turbulent flows can impact the spatial distribution of active suspensions.

physics.flu-dyn↗

arXiv2013

Species abundances and lifetimes: from neutral to niche-stabilized communities

We study a stochastic community model able to interpolate from a neutral regime to a niche partitioned regime upon varying a single parameter tuning the intensity of niche stabilization, namely the difference between intraspecific and interspecific competition. By means of a self-consistent approach, we obtain an analytical expression for the species abundance distribution, in excellent agreement with stochastic simulations of the model. In the neutral limit, the Fisher log-series is recovered, while upon increasing the stabilization strength the species abundance distribution develops a maximum for species at intermediate abundances, corresponding to the emergence of a carrying capacity. Numerical studies of species extinction-time distribution show that niche-stabilization strongly affects also the dynamical properties of the system by increasing the average species lifetimes, while suppressing their fluctuations. The results are discussed in view of the niche-neutral debate and of their potential relevance to field data.

q-bio.PE↗

arXiv2013

Effective rates in dilute reaction-advection systems for the annihilation process $A + A \to \varnothing$

A dilute system of reacting particles transported by fluid flows is considered. The particles react as $A + A \to \varnothing$ with a given rate when they are within a finite radius of interaction. The system is described in terms of the joint n-point number spatial density that it is shown to obey a hierarchy of transport equations. An analytic solution is obtained in either the dilute or the long-time limit by using a Lagrangian approach where statistical averages are performed along non- reacting trajectories. In this limit, it is shown that the moments of the number of particles have an exponential decay rather than the algebraic prediction of standard mean-field approaches. The effective reaction rate is then related to Lagrangian pair statistics by a large-deviation principle. A phenomenological model is introduced to study the qualitative behavior of the effective rate as a function of the interaction length, the degree of chaoticity of the dynamics and the compressibility of the carrier flow. Exact computations, obtained via a Feynman-Kac approach, in a smooth, compressible, random delta-correlated-in-time Gaussian velocity field support the proposed heuristic approach.

nlin.CD↗

arXiv2013

Geotropic tracers in turbulent flows: a proxy for fluid acceleration

We investigate the statistics of orientation of small, neutrally buoyant, spherical tracers whose center of mass is displaced from the geometrical center. If appropriate-sized particles are considered, a linear relation can be derived between the horizontal components of the orientation vector and the same components of acceleration. Direct numerical simulations are carried out, showing that such relation can be used to reconstruct the statistics of acceleration fluctuations up to the order of the gravitational acceleration. Based on such results, we suggest a novel method for the local experimental measurement of accelerations in turbulent flows.

physics.flu-dyn↗

arXiv2012

Clustering of gyrotactic microorganisms in turbulent flows

We study the spatial distribution of gyrotactic microorganisms transported by a three-dimensional turbulent flow generated by direct numerical simulations. We find that gyrotaxis combines with turbulent fluctuations to produce small scales (multi-)fractal clustering. We explain this result by showing that gyrotactic swimming cells behave like tracers in a compressible flow. The effective compressibility is derived in the limits of fluid acceleration much larger and smaller than the gravity.

nlin.CD↗

arXiv2012

What ecological factors shape species-area curves in neutral models?

Understanding factors that shape biodiversity and species coexistence across scales is of utmost importance in ecology, both theoretically and for conservation policies. Species-area relationships (SARs), measuring how the number of observed species increases upon enlarging the sampled area, constitute a convenient tool for quantifying the spatial structure of biodiversity. While general features of species-area curves are quite universal across ecosystems, some quantitative aspects can change significantly. Several attempts have been made to link these variations to ecological forces. Within the framework of spatially explicit neutral models, here we scrutinize the effect of varying the local population size (i.e. the number of individuals per site) and the level of habitat saturation (allowing for empty sites). We conclude that species-area curves become shallower when the local population size increases, while habitat saturation, unless strongly violated, plays a marginal role. Our findings provide a plausible explanation of why SARs for microorganisms are flatter than those for larger organisms.

q-bio.PE↗

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↗

arXiv2011

Nonlinear superposition of direct and inverse cascades in two-dimensional turbulence forced at large and small scales

We inquire about the properties of 2d Navier-Stokes turbulence simultaneously forced at small and large scales. The background motivation comes by observational results on atmospheric turbulence. We show that the velocity field is amenable to the sum of two auxiliary velocity fields forced at large and small scale and exhibiting a direct-enstrophy and an inverse-energy cascade, respectively. Remarkably, the two auxiliary fields reconcile universal properties of fluxes with positive statistical correlation in the inertial range.

physics.flu-dyn↗

arXiv2010

Coexistence and invasibility in a two-species competition model with habitat-preference

The outcome of competition among species is influenced by the spatial distribution of species and effects such as demographic stochasticity, immigration fluxes, and the existence of preferred habitats. We introduce an individual-based model describing the competition of two species and incorporating all the above ingredients. We find that the presence of habitat preference --- generating spatial niches --- strongly stabilizes the coexistence of the two species. Eliminating habitat preference --- neutral dynamics --- the model generates patterns, such as distribution of population sizes, practically identical to those obtained in the presence of habitat preference, provided an higher immigration rate is considered. Notwithstanding the similarity in the population distribution, we show that invasibility properties depend on habitat preference in a non-trivial way. In particular, the neutral model results results more invasible or less invasible depending on whether the comparison is made at equal immigration rate or at equal distribution of population size, respectively. We discuss the relevance of these results for the interpretation of invasibility experiments and the species occupancy of preferred habitats.

q-bio.PE↗

arXiv2009

Speciation-rate dependence in species-area relationships

The general tendency for species number (S) to increase with sampled area (A) constitutes one of the most robust empirical laws of ecology, quantified by species-area relationships (SAR). In many ecosystems, SAR curves display a power-law dependence, $S\propto A^z$. The exponent $z$ is always less than one but shows significant variation in different ecosystems. We study the multitype voter model as one of the simplest models able to reproduce SAR similar to those observed in real ecosystems in terms of basic ecological processes such as birth, dispersal and speciation. Within the model, the species-area exponent $z$ depends on the dimensionless speciation rate $ν$, even though the detailed dependence is still matter of controversy. We present extensive numerical simulations in a broad range of speciation rates from $ν=10^{-3}$ down to $ν= 10^{-11}$, where the model reproduces values of the exponent observed in nature. In particular, we show that the inverse of the species-area exponent linearly depends on the logarithm of $ν$. Further, we compare the model outcomes with field data collected from previous studies, for which we separate the effect of the speciation rate from that of the different species lifespans. We find a good linear relationship between inverse exponents and logarithm of species lifespans. However, the slope sets bounds on the speciation rates that can hardly be justified on evolutionary basis, suggesting that additional effects should be taken into account to consistently interpret the observed exponents.

q-bio.PE↗

arXiv2008

Quantifying turbulence induced segregation of inertial particles

Particles with density different from that of the advecting turbulent fluid cluster due to the different response of light/heavy particles to turbulent fluctuations. This study focuses on the quantitative characterization of the segregation of dilute poly-disperse inertial particles evolving in turbulent flow, as obtained from Direct Numerical Simulation of the Navier-Stokes equations. We introduce an indicator of segregation amongst particles of different inertia and/or size, from which a length scale r_{seg} quantifying the degree of segregation of two different types of particles is deduced.

nlin.CD↗

arXiv2008

Role of chaos for the validity of statistical mechanics laws: diffusion and conduction

Several years after the pioneering work by Fermi Pasta and Ulam, fundamental questions about the link between dynamical and statistical properties remain still open in modern statistical mechanics. Particularly controversial is the role of deterministic chaos for the validity and consistency of statistical approaches. This contribution reexamines such a debated issue taking inspiration from the problem of diffusion and heat conduction in deterministic systems. Is microscopic chaos a necessary ingredient to observe such macroscopic phenomena?

nlin.CD↗

arXiv2007

Transport properties in chaotic and non-chaotic many particles systems

Two deterministic models for Brownian motion are investigated by means of numerical simulations and kinetic theory arguments. The first model consists of a heavy hard disk immersed in a rarefied gas of smaller and lighter hard disks acting as a thermal bath. The second is the same except for the shape of the particles, which is now square. The basic difference of these two systems lies in the interaction: hard core elastic collisions make the dynamics of the disks chaotic whereas that of squares is not. Remarkably, this difference is not reflected in the transport properties of the two systems: simulations show that the diffusion coefficients, velocity correlations and response functions of the heavy impurity are in agreement with kinetic theory for both the chaotic and the non-chaotic model. The relaxation to equilibrium, however, is very sensitive to the kind of interaction. These observations are used to reconsider and discuss some issues connected to chaos, statistical mechanics and diffusion.

nlin.CD↗

arXiv2007

Stochastic suspensions of heavy particles

Turbulent suspensions of heavy particles in incompressible flows have gained much attention in recent years. A large amount of work focused on the impact that the inertia and the dissipative dynamics of the particles have on their dynamical and statistical properties. Substantial progress followed from the study of suspensions in model flows which, although much simpler, reproduce most of the important mechanisms observed in real turbulence. This paper presents recent developments made on the relative motion of a pair of particles suspended in time-uncorrelated and spatially self-similar Gaussian flows. This review is complemented by new results. By introducing a time-dependent Stokes number, it is demonstrated that inertial particle relative dispersion recovers asymptotically Richardson's diffusion associated to simple tracers. A perturbative (homogeneization) technique is used in the small-Stokes-number asymptotics and leads to interpreting first-order corrections to tracer dynamics in terms of an effective drift. This expansion implies that the correlation dimension deficit behaves linearly as a function of the Stokes number. The validity and the accuracy of this prediction is confirmed by numerical simulations.

nlin.CD↗