arXiv subjects

A. Torcini

Publications and source records attributed to A. Torcini.

16 recordsLinked to original sources

arXiv2017

Functional Cliques in Developmentally Correlated Neural Networks

We consider a sparse random network of excitatory leaky integrate-and-fire neurons with short-term synaptic depression. Furthermore to mimic the dynamics of a brain circuit in its first stages of development we introduce for each neuron correlations among in-degree and out-degree as well as among excitability and the corresponding total degree, We analyze the influence of single neuron stimulation and deletion on the collective dynamics of the network. We show the existence of a small group of neurons capable of controlling and even silencing the bursting activity of the network. These neurons form a functional clique since only their activation in a precise order and within specific time windows is capable to ignite population bursts.

q-bio.NC↗

arXiv2014

Stochastic mean field formulation of the dynamics of diluted neural networks

We consider pulse-coupled Leaky Integrate-and-Fire neural networks with randomly distributed synaptic couplings. This random dilution induces fluctuations in the evolution of the macroscopic variables and deterministic chaos at the microscopic level. Our main aim is to mimic the effect of the dilution as a noise source acting on the dynamics of a globally coupled non-chaotic system. Indeed, the evolution of a diluted neural network can be well approximated as a fully pulse coupled network, where each neuron is driven by a mean synaptic current plus additive noise. These terms represent the average and the fluctuations of the synaptic currents acting on the single neurons in the diluted system. The main microscopic and macroscopic dynamical features can be retrieved with this stochastic approximation. Furthermore, the microscopic stability of the diluted network can be also reproduced, as demonstrated from the almost coincidence of the measured Lyapunov exponents in the deterministic and stochastic cases for an ample range of system sizes. Our results strongly suggest that the fluctuations in the synaptic currents are responsible for the emergence of chaos in this class of pulse coupled networks.

nlin.CD↗

arXiv2011

Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $β$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.

cond-mat.dis-nn↗

arXiv2009

Out-of-equilibrium versus dynamical and thermodynamical transitions for a model protein

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.

cond-mat.soft↗

arXiv2009

Synchronization of spatio-temporal chaos as an absorbing phase transition: a study in 2+1 dimensions

The synchronization transition between two coupled replicas of spatio-temporal chaotic systems in 2+1 dimensions is studied as a phase transition into an absorbing state - the synchronized state. Confirming the scenario drawn in 1+1 dimensional systems, the transition is found to belong to two different universality classes - Multiplicative Noise (MN) and Directed Percolation (DP) - depending on the linear or nonlinear character of damage spreading occurring in the coupled systems. By comparing coupled map lattice with two different stochastic models, accurate numerical estimates for MN in 2+1 dimensions are obtained. Finally, aiming to pave the way for future experimental studies, slightly non-identical replicas have been considered. It is shown that the presence of small differences between the dynamics of the two replicas acts as an external field in the context of absorbing phase transitions, and can be characterized in terms of a suitable critical exponent.

cond-mat.stat-mech↗

arXiv2008

Stochastic dynamics of model proteins on a directed graph

A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical features are shown to yield an effective estimate of the time scales associated with the folding and with the equilibration processes. This conclusion is drawn by comparing molecular dynamics simulations at constant temperature with the dynamics on the graph, defined by a temperature dependent Markov process. The main advantage of the graph representation is that its dynamics can be naturally renormalized by collecting nodes into "hubs", while redefining their connectivity. We show that both topological and dynamical properties are preserved by the renormalization procedure. Moreover, we obtain clear indications that the heteropolymers exhibit common topological properties, at variance with the homopolymer, whose peculiar graph structure stems from its spatial homogeneity. In order to obtain a clear distinction between a "fast folder" and a "slow folder" in the heteropolymers one has to look at kinetic features of the directed graph. We find that the average time needed to the fast folder for reaching its native configuration is two orders of magnitude smaller than its equilibration time, while for the bad folder these time scales are comparable. Accordingly, we can conclude that the strategy described in this paper can be successfully applied also to more realistic models, by studying their renormalized dynamics on the directed graph, rather than performing lengthy molecular dynamics simulations.

cond-mat.soft↗

arXiv2008

Chaotic synchronizations of spatially extended systems as non-equilibrium phase transitions

Two replicas of spatially extended chaotic systems synchronize to a common spatio-temporal chaotic state when coupled above a critical strength. As a prototype of each single spatio-temporal chaotic system a lattice of maps interacting via power-law coupling is considered. The synchronization transition is studied as a non-equilibrium phase transition, and its critical properties are analyzed at varying the spatial interaction range as well as the nonlinearity of the dynamical units composing each system. In particular, continuous and discontinuous local maps are considered. In both cases the transitions are of the second order with critical indexes varying with the exponent characterizing the interaction range. For discontinuous maps it is numerically shown that the transition belongs to the {\it anomalous directed percolation} (ADP) family of universality classes, previously identified for L{é}vy-flight spreading of epidemic processes. For continuous maps, the critical exponents are different from those characterizing ADP, but apart from the nearest-neighbor case, the identification of the corresponding universality classes remains an open problem. Finally, to test the influence of deterministic correlations for the studied synchronization transitions, the chaotic dynamical evolutions are substituted by suitable stochastic models. In this framework and for the discontinuous case, it is possible to derive an effective Langevin description that corresponds to that proposed for ADP.

nlin.CD↗

arXiv2006

Contact processes with long-range interactions

A class of non-local contact processes is introduced and studied using mean-field approximation and numerical simulations. In these processes particles are created at a rate which decays algebraically with the distance from the nearest particle. It is found that the transition into the absorbing state is continuous and is characterized by continuously varying critical exponents. This model differs from the previously studied non-local directed percolation model, where particles are created by unrestricted Levy flights. It is motivated by recent studies of non-equilibrium wetting indicating that this type of non-local processes play a role in the unbinding transition. Other non-local processes which have been suggested to exist within the context of wetting are considered as well.

cond-mat.stat-mech↗

arXiv2006

Desynchronization in diluted neural networks

The dynamical behaviour of a weakly diluted fully-inhibitory network of pulse-coupled spiking neurons is investigated. Upon increasing the coupling strength, a transition from regular to stochastic-like regime is observed. In the weak-coupling phase, a periodic dynamics is rapidly approached, with all neurons firing with the same rate and mutually phase-locked. The strong-coupling phase is characterized by an irregular pattern, even though the maximum Lyapunov exponent is negative. The paradox is solved by drawing an analogy with the phenomenon of ``stable chaos'', i.e. by observing that the stochastic-like behaviour is "limited" to a an exponentially long (with the system size) transient. Remarkably, the transient dynamics turns out to be stationary.

cond-mat.dis-nn↗

arXiv2003

From multiplicative noise to directed percolation in wetting transitions

A simple one-dimensional microscopic model of the depinning transition of an interface from an attractive hard wall is introduced and investigated. Upon varying a control parameter, the critical behaviour observed along the transition line changes from a directed-percolation to a multiplicative-noise type. Numerical simulations allow for a quantitative study of the multicritical point separating the two regions, Mean-field arguments and the mapping on a yet simpler model provide some further insight on the overall scenario.

cond-mat.stat-mech↗

arXiv2002

On the relationship between directed percolation and the synchronization transition in spatially extended systems

We study the nature of the synchronization transition in spatially extended systems by discussing a simple stochastic model. An analytic argument is put forward showing that, in the limit of discontinuous processes, the transition belongs to the directed percolation (DP) universality class. The analysis is complemented by a detailed investigation of the dependence of the first passage time for the amplitude of the difference field on the adopted threshold. We find the existence of a critical threshold separating the regime controlled by linear mechanisms from that controlled by collective phenomena. As a result of this analysis we conclude that the synchronization transition belongs to the DP class also in continuous models. The conclusions are supported by numerical checks on coupled map lattices too.

cond-mat.stat-mech↗

arXiv2002

Thin front propagation in steady and unsteady cellular flows

Front propagation in two dimensional steady and unsteady cellular flows is investigated in the limit of very fast reaction and sharp front, i.e., in the geometrical optics limit. In the steady case, by means of a simplified model, we provide an analytical approximation for the front speed, $v_{\scriptsize{f}}$, as a function of the stirring intensity, $U$, in good agreement with the numerical results and, for large $U$, the behavior $v_{\scriptsize{f}}\sim U/\log(U)$ is predicted. The large scale of the velocity field mainly rules the front speed behavior even in the presence of smaller scales. In the unsteady (time-periodic) case, the front speed displays a phase-locking on the flow frequency and, albeit the Lagrangian dynamics is chaotic, chaos in front dynamics only survives for a transient. Asymptotically the front evolves periodically and chaos manifests only in the spatially wrinkled structure of the front.

nlin.PS↗

arXiv1999

Noise-driven Synchronization in Coupled Map Lattices

Synchronization is shown to occur in spatially extended systems under the effect of additive spatio-temporal noise. In analogy to low dimensional systems, synchronized states are observable only if the maximum Lyapunov exponent $Λ$ is negative. However, a sufficiently high noise level can lead, in map with finite domain of definition, to nonlinear propagation of information, even in non chaotic systems. In this latter case the transition to synchronization is ruled by a new ingredient : the propagation velocity of information $V_F$. As a general statement, we can affirm that if $V_F$ is finite the time needed to achieve a synchronized trajectory grows exponentially with the system size $L$, while it increases logarithmically with $L$ when, for sufficiently large noise amplitude, $V_F = 0$ .

chao-dyn↗

arXiv1999

An integration scheme for reaction-diffusion models

A detailed description and validation of a recently developed integration scheme is here reported for one- and two-dimensional reaction-diffusion models. As paradigmatic examples of this class of partial differential equations the complex Ginzburg-Landau and the Fitzhugh-Nagumo equations have been analyzed. The novel algorithm has precision and stability comparable to those of pseudo-spectral codes, but it is more convenient to employ for systems with quite large linear extention $L$. As for finite-difference methods, the implementation of the present scheme requires only information about the local enviroment and this allows to treat also system with very complicated boundary conditions.

cond-mat.stat-mech↗

arXiv1999

Comment on ``Lyapunov Exponent of a Many Body System and Its Transport Coefficients''

In a recent Letter, Barnett, Tajima, Nishihara, Ueshima and Furukawa obtained a theoretical expression for the maximum Lyapunov exponent $λ_1$ of a dilute gas. They conclude that $λ_1$ is proportional to the cube root of the self-diffusion coefficient $D$, independent of the range of the interaction potential. They validate their conjecture with numerical data for a dense one-component plasma, a system with long-range forces. We claim that their result is highly non-generic. We show in the following that it does not apply to a gas of hard spheres, neither in the dilute nor in the dense phase.

cond-mat.stat-mech↗

arXiv1995

ERROR PROPAGATION IN EXTENDED CHAOTIC SYSTEMS

A strong analogy is found between the evolution of localized disturbances in extended chaotic systems and the propagation of fronts separating different phases. A condition for the evolution to be controlled by nonlinear mechanisms is derived on the basis of this relationship. An approximate expression for the nonlinear velocity is also determined by extending the concept of Lyapunov exponent to growth rate of finite perturbations.

chao-dyn↗