arXiv subjects

Alessandro Fiasconaro

Publications and source records attributed to Alessandro Fiasconaro.

18 recordsLinked to original sources

arXiv2024

Hippocampal synchronization in a realistic CA1 neuron model

This work delves into studying the synchronization in two realistic neuron models using Hodgkin-Huxley dynamics. Unlike simplistic point-like models, excitatory synapses are here randomly distributed along the dendrites, introducing strong stochastic contributions into their signal propagation. To focus on the role of different excitatory positions, we use two copies of the same neuron whose synapses are located at different distances from the soma and are exposed to identical Poissonian distributed current pulses. The synchronization is investigated through a specifically defined spiking correlation function, and its behavior is analyzed as a function of several parameters: inhibition weight, distance from the soma of one synaptic group, excitatory inactivation delay, and weight of the excitatory synapses.

q-bio.NC↗

arXiv2024

Effects of synapse location, delay and background stochastic activity on synchronising hippocampal CA1 neurons

We study the synchronisation of neurons in a realistic model under the Hodgkin-Huxley dynamics. To focus on the role of the different locations of the excitatory synapses, we use two identical neurons where the set of input signals is grouped at two different distances from the soma. The system is intended to represent a CA1 hippocampal neuron in which the synapses arriving from the CA3 neurons of the trisynaptic pathway appear to be localised in the apical dendritic region and are, in principle, either proximal or distal to the soma. Synchronisation is studied using a specifically defined spiking correlation function as a function of various parameters such as the distance from the soma of one of the synaptic groups, the inhibition weight and the associated activation delay. We found that the neurons' spiking activity depends nonmonotonically on the relative dendritic location of the synapses and their inhibitory weight, whereas the synchronisation measure always decreases with inhibition, and strongly depends on its activation time delay. The background activity on the somas results essentially independent on the fluctuation intensity and strongly support the importance of the balance between inhibition and excitation for neuronal synchronization.

q-bio.NC↗

arXiv2023

Polymer translocation driven by longitudinal and transversal time-dependent end-pulling forces

Polymer translocation has long been a topic of interest in the field of biological physics given its relevance in both biological (protein and DNA/RNA translocation through nuclear and cell membranes) and technological processes (nanopore DNA sequencing, drug delivery). In this work, we simulate the translocation of a semiflexible homopolymer through an extended pore, driven by both a constant and a time-dependent end-pulled force, employing a model introduced in previous studies. The time dependence is simplistically modeled as a cosine function, and we distinguish between two scenarios for the driving -- longitudinal force and transversal force -- depending on the relative orientation of the force, parallel or perpendicular respectively, with respect to the pore axis. Beside some key differences between the two drivings, the mean translocation times present a large minimum region as function of the frequency of the force that is typical of the Resonant Activation effect. The presence of the minimum is independent on the elastic characteristics of the polymeric chains and reveals a linear relation between the optimum mean translocation time and the corresponding period of the driving. The mean translocation times show different scaling exponent with the polymer length for different flexibilities. Lastly, we derive an analytical expression of the mean translocation time for low driving frequency, which clearly agrees with the simulations.

cond-mat.soft↗

arXiv2023

Elastic traits of the extensible discrete wormlike chain model

Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete worm-like chain polymer as a function of the applied force has been calculated both numerically and analytically, the latter as an effective approximation. The numerical evaluation uses the Transfer Matrix formalism to obtain an exact calculation of the partition function, while the analytic derivations generalize the simple phenomenological formulas largely used up to now. The obtained formulas are simple enough to be implemented in the fit analysis of experimental data of semi-flexible extensible polymers, with the result that the elastic parameters obtained are compatible with previous measurements, and more, their accuracy strongly improves in a large range of chain extensibility.

cond-mat.soft↗

arXiv2021

Analytical results of the extensible freely jointed chain model

Based on classical statistical mechanics, we calculate analytically the length extension and the fluctuations, under a pulling force, of a polymer modelled as a freely jointed chain with extensible bonds, the latter considered as harmonic springs. We obtain an analytical formula for the partition function, and derive both the extension curve of the chain and the fluctuations as a function of the force. An independent high force approximation has been also evaluated. The analytical formulas have been validated by analysing the exactness of their fit on data obtained from Langevin simulations, and compared with the phenomenological expressions largely used in the past literature.

cond-mat.stat-mech↗

arXiv2018

Force spectroscopy analysis in polymer translocation

This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the potential barrier generated by the reaction of the membrane walls. The polymer is modeled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment described by a Langevin dynamics at fixed temperature. The force trajectories recorded at different velocities reveal two unexplored exponential regimes: the force increases when the first part of the chain enters the pore, and then decreases when the first monomer reaches the trans region. The spectroscopy analysis of the force values permit the estimation of the free energy barrier as well as the limit force to permit the translocation. The stall force to maintain the polymer fixed has been also calculated independently, and its value confirms the force spectroscopy outcomes.

cond-mat.soft↗

arXiv2016

Spatio-temporal analysis of micro economic activities in Rome reveals patterns of mixed-use urban evolution

Understanding urban growth is one with understanding how society evolves to satisfy the needs of its individuals in sharing a common space and adapting to the territory. We propose here a quantitative analysis of the historical development of a large urban area by investigating the spatial distribution and the age of commercial activities in the whole city of Rome. We find that the age of activities of various categories presents a very interesting double exponential trend, with a transition possibly related to the long-term economical effects determined by the oil crisis of the Seventies. The diversification of commercial categories, studied through various measures of entropy, shows, among other interesting features, a saturating behaviour with the density of activities. Moreover, different couples of commercial categories exhibit over the years a tendency to attract in space. Our results demonstrate that the spatio-temporal distribution of commercial activities can provide important insights on the urbanisation processes at work, revealing specific and not trivial socio-economical dynamics, as the presence of crisis periods and expansion trends, and contributing to the characterisation of the maturity of urban areas.

physics.soc-ph↗

arXiv2013

Analysis of Remote Synchronization in Complex Networks

A novel regime of synchronization, called remote synchronization, where the peripheral nodes form a phase synchronized cluster not including the hub, was recently observed in star motifs. We show the existence of a more general dynamical state of remote synchronization in arbitrary networks of coupled oscillators. This state is characterized by the synchronization of pairs of nodes that are not directly connected via a physical link or any sequence of synchronized nodes. This phenomenon is almost negligible in networks of phase oscillators as its underlying mechanism is the modulation of the amplitude of those intermediary nodes between the remotely synchronized units. Our findings thus show the ubiquity and robustness of these states and bridge the gap from their recent observation in simple toy graphs to complex networks.

physics.soc-ph↗

arXiv2012

Directional motion of forced polymer chains with hydrodynamic interaction

We study the propulsion of a one-dimensional (1D) polymer chain under sinusoidal external forces in the overdamped (low Reynolds number) regime. We show that, when hydrodynamical interactions are included, the polymer presents directional motion which depends on the phase differences of the external force applied along the chain. Moreover, the velocity shows a maximum as a function of the frequency. We discuss the relevance of all these results in light of recent nanotechnology experiments.

cond-mat.soft↗

arXiv2012

Dynamical model for the full stretching curve of DNA

We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications, which properly describes the elongation features at low and intermediate forces. The dynamics is developed under a double-well potential with a linear term, which, at high forces, accounts for the narrow transition present in the DNA elongation (overstretching). A quite good agreement between simulation and experiment is obtained.

physics.bio-ph↗

arXiv2012

Translocation of a polymer chain driven by a dichotomous noise

We consider the translocation of a one-dimensional polymer through a pore channel helped by a motor driven by a dichotomous noise with time exponential correlation. We are interested in the study of the translocation time, mean velocity and stall force of the system as a function of the mean driving frequency. We find a monotonous translocation time, in contrast with the mean velocity which shows a pronounced maximum at a given frequency. Interestingly, the stall force shows a nonmonotonic behavior with the presence of a minimum. The influence of the spring elastic constant to the mean translocation times and velocities is also presented.

cond-mat.soft↗

arXiv2012

Michaelis-Menten dynamics of a polymer chain out of a dichotomous ATP-based motor

We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The machine activation rate can be put in relationship with the available ATP concentration in the solution, which gives the necessary energy supply. The translocation time shows a monotonic behavior as a function of the activation frequency and the velocity follows a Michaelis-Menten law that arises naturally in this description. The estimation of the stall force of the motor follows a corrected Michaelis-Menten law which still is to be checked in experimental investigation. The results presented agree with recent biological experimental findings.

cond-mat.soft↗

arXiv2010

Translocation time of periodically forced polymer chains

We show the presence of both a minimum and clear oscillations in the frequency dependence of the translocation time of a polymer described as a unidimensional Rouse chain driven by a spatially localized oscillating linear potential. The observed oscillations of the mean translocation time arise from the synchronization between the very mean translocation time and the period of the external force. We have checked the robustness of the frequency value for the minimum translocation time by changing the damping parameter, finding a very simple relationship between this frequency and the correspondent translocation time. The translocation time as a function of the polymer length has been also evaluated, finding a precise $L^2$ scaling. Furthermore, the role played by the thermal fluctuations described as a Gaussian uncorrelated noise has been also investigated, and the analogies with the resonant activation phenomenon are commented.

cond-mat.soft↗

arXiv2009

Stability measures in metastable states with Gaussian colored noise

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 $τ_c$ investigated. We can distinguish two dynamical regimes characterized by weak and strong correlated noise respectively, depending on the value of $τ_c$ with respect to the relaxation time of the system.

cond-mat.stat-mech↗

arXiv2008

Resonant Activation in Asymmetric Potentials

The resonant activation effect (RA) has been well studied in different ways during the last two decades. It consists in the presence of a minimum in the mean time spent by a Brownian particle to exit from a potential well in the presence of a fluctuating external force, as a function of the mean frequency (or the correlation time) of the latter. This work studies the role played by the asymmetry of a piecewise linear potential in the RA effect, and, in general, the behavior of the mean first passage time and the mean velocity of the particle crossing through the potential barrier. A strong dependence on the asymmetry of the potential has been found which can be put in relationship with the current in the ratchet whose the potential here used is an elementary module. In this case a current reversal as a function of the frequency of the switching potential occurs. Comparison of the calculations with the Doering-Gadua model have been performed, as well as comparison with smooth symmetrical potentials, by checking for the robustness of the resonant correlation time. The calculations have been done by solving numerically the Langevin equation in the presence of an uncorrelated Gaussian noise. The resonant mean first passage times show an unexpected behavior as a function of the thermal noise intensity. The related curves present for the different symmetries an unexpected inversion of their relative behavior beyond a certain threshold value of the noise. This means that the current reversal can only occur for weak noise intensities, lower than that threshold value.

cond-mat.stat-mech↗

arXiv2008

Extinction statistics in N random interacting species

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.

cond-mat.stat-mech↗

arXiv2008

Active Brownian Motion Models and Applications to Ratchets

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 tilted potential structure. In addition, stochastic character of the kinetics is investigated by considering perturbation by Gaussian white noise which is shown to be responsible for driving the directionality of the asymptotic flux in the ratchet. This \textit{stochastically driven directionality} effect is visualized as a strong nonmonotonic dependence of the statistics of the right versus left trajectories of motion leading to a net current of particles. Possible applications of the ratchet systems to molecular motors are also briefly discussed

physics.data-an↗

arXiv2008

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

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 dynamics in the external quasi-potential represented by a double well. We analyze properties of the system within the range of parameters for which the potential wells are of the same depth and when the additional perturbation, modeling a periodic treatment, is insufficient to overcome the barrier height and to cause cancer extinction. In this case the presence of a small amount of noise can positively enhance the treatment, driving the system to a state of tumor extinction. On the other hand, however, the same noise can give rise to return effects up to a stochastic resonance behavior. This observation provides a quantitative analysis of mechanisms responsible for optimization of periodic tumor therapy in the presence of spontaneous external noise. Studying the behavior of the extinction time as a function of the treatment frequency, we have also found the typical resonant activation effect: For a certain frequency of the treatment, there exists a minimum extinction time.

physics.bio-ph↗