NOISE EFFECTS IN POLYMER DYNAMICS

2008

The study of the noise induced effects on the dynamics of a chain molecule crossing a potential barrier, in the presence of a metastable state, is presented. A two-dimensional stochastic version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics and to take into account the interactions between adjacent monomers. We obtain a nonmonotonic behavior of the mean first passage time and its standard deviation, of the polymer centre of inertia, with the noise intensity. These findings reveal a noise induced effect on the mean crossing time. The role of the polymer length is also investigated.

Signatures of noise-enhanced stability in metastable state

2005

The lifetime of a metastable state in the transient dynamics of an overdamped Brownian particle is analyzed, both in terms of the mean first passage time and by means of the mean growth rate coefficient. Both quantities feature non monotonic behaviors as a function of the noise intensity, and are independent signatures of the noise enhanced stability effect. They can therefore be alternatively used to evaluate and estimate the presence of this phenomenon, which characterizes metastability in nonlinear physical systems.

Resonant activation in polymer translocation: new insights into the escape dynamics of molecules driven by an oscillating field

2010

The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics, by taking into account the harmonic interactions between adjacent monomers and the excluded-volume effect by introducing a Lennard–Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by num…

Nonmonotonic Pattern Formation in Three Species Lotka-Volterra System with Colored Noise

2005

A coupled map lattice of generalized Lotka-Volterra equations in the presence of colored multiplicative noise is used to analyze the spatiotemporal evolution of three interacting species: one predator and two preys symmetrically competing each other. The correlation of the species concentration over the grid as a function of time and of the noise intensity is investigated. The presence of noise induces pattern formation, whose dimensions show a nonmonotonic behavior as a function of the noise intensity. The colored noise induces a greater dimension of the patterns with respect to the white noise case and a shift of the maximum of its area towards higher values of the noise intensity.

Tuning active Brownian motion with shot noise energy pulses

2009

The main aim of this work is to explore the possibility of modeling the biological energy support mediated by absorption of ATP (adenosine triphosphate) as an energetic shot noise. We develop a general model with discrete input of energy pulses and study shot-noise-driven ratchets. We consider these ratchets as prototypes of Brownian motors driven by energy-rich ATP molecules. Our model is a stochastic machine able to acquire energy from the environment and convert it into kinetic energy of motion. We present characteristic features and demonstrate the possibility of tuning these motors by adapting the mean frequency of the discrete energy inputs, which are described as a special shot noise…

Noise-induced enhancement of stability in a metastable system with damping

2010

5 páginas, 5 figuras.-- PACS number(s): 05.40.-a, 02.50.-r

Asymptotic regime in N random interacting species

2005

The asymptotic regime of a complex ecosystem with \emph{N}random interacting species and in the presence of an external multiplicative noise is analyzed. We find the role of the external noise on the long time probability distribution of the i-th density species, the extinction of species and the local field acting on the i-th population. We analyze in detail the transient dynamics of this field and the cavity field, which is the field acting on the $i^{th}$ species when this is absent. We find that the presence or the absence of some population give different asymptotic distributions of these fields.

Co-occurrence of resonant activation and noise-enhanced stability in the Michaelis-Menten model

2006

Noise in ecosystems: a short review

2004

Noise, through its interaction with the nonlinearity of the living systems, can give rise to counter-intuitive phenomena such as stochastic resonance, noise-delayed extinction, temporal oscillations, and spatial patterns. In this paper we briefly review the noise-induced effects in three different ecosystems: (i) two competing species; (ii) three interacting species, one predator and two preys, and (iii) N-interacting species. The transient dynamics of these ecosystems are analyzed through generalized Lotka-Volterra equations in the presence of multiplicative noise, which models the interaction between the species and the environment. The interaction parameter between the species is random …

Active Brownian Motion Models and Applications to Ratchets

2008

We give an overview over recent studies on the model of Active Brownian Motion (ABM) coupled to reservoirs providing free energy which may be converted into kinetic energy of motion. First, we present an introduction to a general concept of active Brownian particles which are capable to take up energy from the source and transform part of it in order to perform various activities. In the second part of our presentation we consider applications of ABM to ratchet systems with different forms of differentiable potentials. Both analytical and numerical evaluations are discussed for three cases of sinusoidal, staircase-like and Mateos ratchet potentials, also with the additional loads modeled by…

Stability measures in metastable states with Gaussian colored noise

2009

We present a study of the escape time from a metastable state of an overdamped Brownian particle, in the presence of colored noise generated by Ornstein-Uhlenbeck process. We analyze the role of the correlation time on the enhancement of the mean first passage time through a potential barrier and on the behavior of the mean growth rate coefficient as a function of the noise intensity. We observe the noise enhanced stability effect for all the initial unstable states used, and for all values of the correlation time $\tau_c$ investigated. We can distinguish two dynamical regimes characterized by weak and strong correlated noise respectively, depending on the value of $\tau_c$ with respect to …

Hybrid recommendation methods in complex networks

2015

We propose here two new recommendation methods, based on the appropriate normalization of already existing similarity measures, and on the convex combination of the recommendation scores derived from similarity between users and between objects. We validate the proposed measures on three relevant data sets, and we compare their performance with several recommendation systems recently proposed in the literature. We show that the proposed similarity measures allow to attain an improvement of performances of up to 20\% with respect to existing non-parametric methods, and that the accuracy of a recommendation can vary widely from one specific bipartite network to another, which suggests that a …

Co-occurrence of resonant activation and noise-enhanced stability in a model of cancer growth in the presence of immune response.

2006

We investigate a stochastic version of a simple enzymatic reaction which follows the generic Michaelis-Menten kinetics. At sufficiently high concentrations of reacting species, the molecular fluctuations can be approximated as a realization of a Brownian dynamics for which the model reaction kinetics takes on the form of a stochastic differential equation. After eliminating a fast kinetics, the model can be rephrased into a form of a one-dimensional overdamped Langevin equation. We discuss physical aspects of environmental noises acting in such a reduced system, pointing out the possibility of coexistence of dynamical regimes where noise-enhanced stability and resonant activation phenomena …

The bistable potential: An archetype for classical and quantum systems

2012

In this work we analyze the transient dynamics of three different classical and quantum systems. First, we consider a classical Brownian particle moving in an asymmetric bistable potential, subject to a multiplicative and additive noise source. We investigate the role of these two noise sources on the life time of the metastable state. A nonmonotonic behavior of the lifetime as a function of both additive and multiplicative noise intensities is found, revealing the phenomenon of noise enhanced stability. Afterward, by using a LotkaVolterra model, the dynamics of two competing species in the presence of Lévy noise sources is analyzed. Quasiperiodic oscillations and stochastic resonance pheno…

Noise stabilization effects in models of interdisciplinary physics

2009

Metastability is a generic feature of many nonlinear systems, and the problem of the lifetime of metastable states involves fundamental aspects of nonequilibrium statistical mechanics. The investigation of noise-induced phenomena in far from equilibrium systems is one of the approaches used to understand the behaviour of physical and biological complex systems. The enhancement of the lifetime of metastable states through the noise enhanced stability effect and the role played by the resonant activation phenomenon will be discussed in models of interdisciplinary physics: (i) polymer translocation dynamics; (ii) transient regime of FitzHugh-Nagumo model; (iii) market stability in a nonlinear …

Lifetime of metastable states and suppression of noise in interdisciplinary physical models

2008

Transient properties of different physical systems with metastable states perturbed by external white noise have been investigated. Two noise-induced phenomena, namely the noise enhanced stability and the resonant activation, are theoretically predicted in a piece-wise linear fluctuating potential with a metastable state. The enhancement of the lifetime of metastable states due to the noise, and the suppression of noise through resonant activation phenomenon will be reviewed in models of interdisciplinary physics: (i) dynamics of an overdamped Josephson junction; (ii) transient regime of the noisy FitzHugh-Nagumo model; (iii) population dynamics.

Transient behavior of a population dynamical model

2005

The transient behavior of an ecosystem with N random interacting species in the presence of a multiplicative noise is analyzed. The multiplicative noise mimics the interaction with the environment. We investigate different asymptotic dynamical regimes and the role of the external noise on the probability distribution of the local field.

Resonant activation in piecewise linear asymmetric potentials

2011

7 páginas, 8 figuras.-- PACS number(s): 05.40.−a, 05.45.−a, 02.50.Ey

Translocation time of periodically forced polymer chains.

2010

6 páginas, 11 figuras.-- PACS number(s): 36.20.-r, 05.40.-a, 87.15.A-, 87.10.-e

Extinction statistics in N random interacting species

2008

A randomly interacting N-species Lotka-Volterra system in the presence of a Gaussian multiplicative noise is analyzed. The investigation is focused on the role of this external noise into the statistical properties of the extinction times of the populations. The distributions show a Gaussian shape for each noise intensity value investigated. A monotonic behavior of the mean extinction time as a function of the noise intensity is found, while a nonmonotonic behavior of the width of the extinction time probability distribution characterizes the dynamical evolution.

Role of the Colored Noise in Spatio-Temporal Behavior of Two Competing Species

2005

We study the spatial distributions of two randomly interacting species, in the presence of an external multiplicative colored noise. The dynamics of the ecosystem is described by a coupled map lattice model. We find a nonmonotonic behavior in the formation of large scale spatial correlations as a function of the multiplicative colored noise intensity. This behavior is shifted towards higher values of the noise intensity for increasing correlation time of the noise.

Evidence of stochastic resonance in the mating behavior of Nezara viridula (L.)

2008

We investigate the role of the noise in the mating behavior between individuals of Nezara viridula (L.), by analyzing the temporal and spectral features of the non-pulsed type female calling song emitted by single individuals. We have measured the threshold level for the signal detection, by performing experiments with the calling signal at different intensities and analyzing the insect response by directionality tests performed on a group of male individuals. By using a sub-threshold signal and an acoustic Gaussian noise source, we have investigated the insect response for different levels of noise, finding behavioral activation for suitable noise intensities. In particular, the percentage…

Coexistence of resonant activation and noise enhanced stability in a model of tumor-host interaction: Statistics of extinction times

2006

We study a Langevin equation derived from the Michaelis-Menten (MM) phenomenological scheme for catalysis accompanying a spontaneous replication of molecules, which may serve as a simple model of cell-mediated immune surveillance against cancer. We examine how two different and statistically independent sources of noise - dichotomous multiplicative noise and additive Gaussian white noise - influence the population's extinction time. This quantity is identified as the mean first passage time of the system across the zero population state. We observe the effects of resonant activation (RA) and noise-enhanced stability (NES) and we report the evidence for competitive co-occurrence of both phen…

Cyclic fluctuations, climatic changes and role of noise in planktonic foraminifera in the Mediterranean Sea

2005

The study of Planktonic Foraminifera abundances permits to obtain climatic curves on the basis of percentage ratio between tropical and temperate/polar forms. Climatic changes were controlled by several phenomena as: (i) Milankovitch's cycles, produced by variations of astronomical parameters such as precession, obliquity and eccentricity; (ii) continental geodynamic evolution and orogenic belt; (iii) variations of atmospheric and oceanic currents; (iv) volcanic eruptions; (v) meteor impacts. But while astronomical parameters have a quasi-regular periodicity, the other phenomena can be considered as "noise signal" in natural systems. The interplay between cyclical astronomical variations, t…

Monitoring noise-resonant effects in cancer growth influenced by external fluctuations and periodic treatment

2007

In the paper we investigate a mathematical model describing the growth of tumor in the presence of immune response of a host organism. The dynamics of tumor and immune cells is based on the generic Michaelis-Menten kinetics depicting interaction and competition between the tumor and the immune system. The appropriate phenomenological equation modeling cell-mediated immune surveillance against cancer is of the predator-prey form and exhibits bistability within a given choice of the immune response-related parameters. Under the influence of weak external fluctuations, the model may be analyzed in terms of a stochastic differential equation bearing the form of an overdamped Langevin-like dynam…

2012

classical and quantum systems are investigated. First, the role of multiplicative and additive noise in a classical metastable system is analyzed. The mean lifetime of the metastable state shows a nonmonotonic behavior with a maximum as a function of both the additive and multiplicative noise intensities. In the second system, the simultaneous action of thermal and non-Gaussian noise on the dynamics of an overdamped point Josephson junction is studied. The eect of a Levy noise generated by a Cauchy‐Lorentz distribution on the mean lifetime of the superconductive metastable state, in the presence of a periodic driving, is investigated. We find resonant activation and noise enhanced stability…

Noise driven translocation of short polymers in crowded solutions

2008

In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable tran…

Stochastic resonance and noise delayed extinction in a model of two competing species

2003

We study the role of the noise in the dynamics of two competing species. We consider generalized Lotka-Volterra equations in the presence of a multiplicative noise, which models the interaction between the species and the environment. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence of a periodic driving term, which accounts for the environment temperature variation. We find noise-induced periodic oscillations of the species concentrations and stochastic resonance phenomenon. We find also a nonmonotonic behavior of the mean extinction time of one of the two competing species…

Noise effects in two different biological systems

2009

We investigate the role of the colored noise in two biological systems: (i) adults of Nezara viridula (L.) (Heteroptera: Pentatomidae), and (ii) polymer translocation. In the first system we analyze, by directionality tests, the response of N. viridula individuals to subthreshold signals plus noise in their mating behaviour. The percentage of insects that react to the subthreshold signal shows a nonmonotonic behaviour, characterized by the presence of a maximum, as a function of the noise intensity. This is the signature of the non-dynamical stochastic resonance phenomenon. By using a “soft” threshold model we find that the maximum of the input-output cross correlation occurs in the same ra…

Noise Induced Phenomena in Lotka-Volterra Systems

2003

We study the time evolution of two ecosystems in the presence of external noise and climatic periodical forcing by a generalized Lotka-Volterra (LV) model. In the first ecosystem, composed by two competing species, we find noise induced phenomena such as: (i) quasi deterministic oscillations, (ii) stochastic resonance, (iii) noise delayed extinction and (iv) spatial patterns. In the second ecosystem, composed by three interacting species (one predator and two preys), using a discrete model of the LV equations we find that the time evolution of the spatial patterns is strongly dependent on the initial conditions of the three species.

Translocation dynamics of a short polymer driven by an oscillating force

2013

Under the terms of the Creative Commons Attribution 3.0 Unported License.

Probability Density P(x, t) and First Exit Time Distribution for Unstable Initial Positions in Metastable Potential,

2005

Preliminary Analysis on Correlations between Spatial Distribution of Chlorophyll-a and Experimental Data of Biomass in the Strait of Sicily

2010

This study, using both remotely sensed and measured in situ data, is directed to the analysis of the correlations between the chlorophyll-a concentration and the biomass of sardines and anchovies acoustically evaluated in the Strait of Sicily. This work, inter alia, shows the usefulness of remote observation of seas in determining possible relationships between fish stocks and some oceanographic parameters (Sea Surface Temperature, Chlorophyll-a, Zooplankton).

Noise in biological systems: Phenomenology and theoretical models

2005

RELAXATION PHENOMENA IN CLASSICAL AND QUANTUM SYSTEMS

2012

Relaxation phenomena in three different classical and quantum systems are investigated. First, the role of multiplicative and additive noise in a classical metastable system is analyzed. The mean lifetime of the metastable state shows a nonmonotonicbehavior with a maximum as a function of both the additive and multiplicative noise intensities. In the second system, the simultaneous action of thermal and non-Gaussian noise on the dynamics of an overdamped point Josephson junction is studied. The effect of a Lévy noise generated by a Cauchy–Lorentz distribution on the mean lifetime of the superconductive metastable state, in the presence of a periodic driving, is investigated. We find resonan…

Lyapunov Coefficient in the Presence of Noise in Metastable Potential

2004

Cancer growth dynamics: stochastic models and noise induced effects

2009

In the framework of the Michaelis-Menten (MM) reaction kinetics, we analyze the cancer growth dynamics in the presence of the immune response. We found the coexistence of noise enhanced stability (NES) and resonant activation (RA) phenomena which act in an opposite way with respect to the extinction of the tumor The role of the stochastic resonance (SR) in the case of weak cancer therapy has been analyzed. The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a Monte Carlo approach. We analyzed the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. We show how t…

Noise effects in biological systems

2008

Population dynamics in the presence of noise for different systems

2004

Probability Density of Escape Times from a Metastable State

2005

Role of colored noise in the patterns formation of a Lotka-Volterra system

2004

Role of the dichotomous noise in time evolution of two competing species

2004

Lyapunov Coefficient in the Presence of Noise in Metastable Potentials”, 31st Workshop of the International School of Solid State Physics “Complexity…

2004

Cyclic Fluctuations, Climatic Changes and Role of Noise in Planktonic Foraminifera in the Mediterranean Sea

2004

Population Dynamics of N random interacting species with multiplicative noise

2005

Asymptotic Regime and Statistics of Extinction in Random Interacting Species

2005

Stochastic Dynamics in Polymer Translocation

2007

Two-species model for spatial distributions of sardine and anchovy: A comparison with real data

2010

We present a study of pattern formation in a set of two coupled equations modeling two competing species. We consider generalized Lotka-Volterra equations in the presence of a multiplicative noise which models the interaction between the species and the environment. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence of a periodic driving term, which accounts for the environment temperature variation.We find noise-induced spatial patterns with strong anti-correlation between the two species. We compare our theoretical results with the experimental data of the spatial distributi…

Transient behavior of a population dynamical model

2004