arXiv subjects

A. Fiasconaro

Publications and source records attributed to A. Fiasconaro.

At least 19 recordsLinked to original sources

arXiv2022

End-pulled polymer translocation through a many-body flexible pore

This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body recall interaction. In order to guarantee the stability of the system, the membrane is compounded by a lipid bilayer structure having hydrophobic body (internal), while the pore is hydrophilic in both edges. The polymer is end-pulled from the cis-side to the trans-side by a cantilever, to which is connected through a spring able to measure the force acting on the polymer during the translocation. All the structure reacts to the impacts of the monomers of the polymer with vibrations generated by the movement of its constituent bodies. In these conditions, the work done by the cantilever shows a nonmonotonic behavior with the elastic constant, revealing a resonant-like behavior in a parameter region. Moreover, the force spectroscopy registered as a function of time, is able to record the main kinetics of the polymer progression inside the pore.

cond-mat.soft↗

arXiv2017

Mesoscopic model for DNA G-quadruplex unfolding

Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead. In this framework we are able to simulate loading rates similar to the experimental ones, which are not reachable in simulations with atomistic resolution. In this regard, we present single-molecule force-induced unfolding experiments by a high-resolution optical tweezers on a DNA telomeric sequence capable of forming a G-quadruplex conformation. Fitting the parameters of the model to the experiments we find a correct prediction of the rupture-force kinetics and a good agreement with previous near equilibrium measurements. Since G-quadruplex unfolding dynamics is halfway in complexity between secondary nucleic acids and tertiary protein structures, our model entails a nanoscale paradigm for non-equilibrium processes in the cell.

physics.bio-ph↗

arXiv2017

Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor

In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule binding and triggering the impulse, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at fixed temperature. The resulting dynamics shows a Michaelis-Menten translocation velocity that depends on the chain flexibility. The scaling behavior of the mean translocation time with the polymer length for different bending values is also investigated.

cond-mat.soft↗

arXiv2014

Hybrid recommendation methods in complex networks

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 careful choice of the most suitable method is highly relevant for an effective recommendation on a given system. Finally, we studied how an increasing presence of random links in the network affects the recommendation scores, and we found that one of the two recommendation algorithms introduced here can systematically outperform the others in noisy data sets.

physics.soc-ph↗

arXiv2013

Modeling the mechano-chemistry of the ϕ29 DNA translocation motor

We present a study of the DNA translocation of the bacteriophage ϕ29 packaging molecular motor. From the experimental available information we present a model system based in an stochastic fashing potential, which reproduces the experimental observations such as: detailed trajectories, steps and substeps, spatial correlation, and velocity. Moreover the model allows the evaluation of power and efficiency of this motor. We have found that the maximum power regime does not correspond with that of the maximum efficiency. These informations can stimulate further experiments.

physics.bio-ph↗

arXiv2011

Environmental Noise and Nonlinear Relaxation in Biological Systems

We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of \emph{Nezara viridula} (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative Lévy noise.

physics.bio-ph↗

arXiv2011

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

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 of insects which react to the sub-threshold signal, shows a non-monotonic behavior, characterized by the presence of a maximum, for increasing levels of the noise intensity. This constructive interplay between external noise and calling signal is the signature of the non-dynamical stochastic resonance phenomenon. Finally, we describe the behavioral activation statistics by a soft threshold model which shows stochastic resonance. We find that the maximum of the ensemble average of the input-output cross-correlation occurs at a value of the noise intensity very close to that for which the behavioral response has a maximum.

physics.bio-ph↗

arXiv2008

Noise driven translocation of short polymers in crowded solutions

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 translocation time, of the polymer centre of inertia, as a function of the polymer length at low noise intensity. We show how thermal fluctuations influence the motion of short polymers, by inducing two different regimes of translocation in the molecule transport dynamics. In this context, the role played by the length of the molecule in the translocation time is investigated.

cond-mat.stat-mech↗

arXiv2008

Noise effects in polymer dynamics

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.

cond-mat.stat-mech↗

arXiv2008

Lifetime of metastable states and suppression of noise in Interdisciplinary Physical Models

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.

cond-mat.stat-mech↗

arXiv2007

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

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 phenomena in a given regime of noise parameters. We discuss the statistics of first passage times in this regime and the role of different pseudo-potential profiles on the RA and NES phenomena. The RA/NES coexistence region brings an interesting interpretation for the growth kinetics of cancer cells population, as the NES effect enhancing the stability of the tumoral state becomes strongly reduced by the RA phenomenon.

q-bio.PE↗

arXiv2007

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

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 can be observed together.

q-bio.PE↗

arXiv2005

Asymptotic regime in N random interacting species

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.

physics.soc-ph↗

arXiv2005

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

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.

cond-mat.stat-mech↗

arXiv2005

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

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, the "noise signal" and the intrinsic nonlinearity of the ecologic system produces strong glacial or interglacial period according to the stochastic resonance phenomenon.

q-bio.PE↗

arXiv2005

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

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.

cond-mat.stat-mech↗

arXiv2005

Signatures of Noise Enhanced Stability in Metastable States

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.

cond-mat.stat-mech↗

arXiv2004

Transient behavior of a population dynamical model

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.

cond-mat.stat-mech↗