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.Comment: Proceedings of the "YKIS 2009 : Frontiers in Nonequilibrium Physics" conference in Kyoto, August 2009. To appear in Progress of Theoretical Physics Supplemen

Collective chaos in pulse-coupled neural networks

We study the dynamics of two symmetrically coupled populations of identical leaky integrate-and-fire neurons characterized by an excitatory coupling. Upon varying the coupling strength, we find symmetry-breaking transitions that lead to the onset of various chimera states as well as to a new regime, where the two populations are characterized by a different degree of synchronization. Symmetric collective states of increasing dynamical complexity are also observed. The computation of the the finite-amplitude Lyapunov exponent allows us to establish the chaoticity of the (collective) dynamics in a finite region of the phase plane. The further numerical study of the standard Lyapunov spectrum reveals the presence of several positive exponents, indicating that the microscopic dynamics is high-dimensional.Comment: 6 pages, 5 eps figures, to appear on Europhysics Letters in 201

Ensemble inequivalence: A formal approach

Ensemble inequivalence has been observed in several systems. In particular it has been recently shown that negative specific heat can arise in the microcanonical ensemble in the thermodynamic limit for systems with long-range interactions. We display a connection between such behaviour and a mean-field like structure of the partition function. Since short-range models cannot display this kind of behaviour, this strongly suggests that such systems are necessarily non-mean field in the sense indicated here. We further show that a broad class of systems with non-integrable interactions are indeed of mean-field type in the sense specified, so that they are expected to display ensemble inequivalence as well as the peculiar behaviour described above in the microcanonical ensemble.Comment: 4 pages, no figures, given at the NEXT2001 conference on non-extensive thermodynamic

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

Pattern formation often occurs in spatially extended physical, biological and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular revealing for the Swift-Hohenberg equations a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of an weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.Comment: 9 pages, 10 figures, submitted to Chao

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.Comment: 11 pages, 13 figures, submitted to Phys. Rev.

Low frequency fluctuations in a Vertical Cavity Lasers: experiments versus Lang-Kobayashi dynamics

The limits of applicability of the Lang-Kobayashi (LK) model for a semiconductor laser with optical feedback are analyzed. The model equations, equipped with realistic values of the parameters, are investigated below solitary laser threshold where Low Frequency Fluctuations (LFF) are usually observed. The numerical findings are compared with experimental data obtained for the selected polarization mode from a Vertical Cavity Surface Laser (VCSEL) subject to polarization selective external feedback. The comparison reveals the bounds within which the dynamics of the LK can be considered as realistic. In particular, it clearly demonstrates that the deterministic LK, for realistic values of the linewidth enhancement factor $\alpha$, reproduces the LFF only as a transient dynamics towards one of the stationary modes with maximal gain. A reasonable reproduction of real data from VCSEL can be obtained only by considering noisy LK or alternatively deterministic LK for extremely high $\alpha$-values

Discrete synaptic events induce global oscillations in balanced neural networks

Neural dynamics is triggered by discrete synaptic inputs of finite amplitude. However, the neural response is usually obtained within the diffusion approximation (DA) representing the synaptic inputs as Gaussian noise. We derive a mean-field formalism encompassing synaptic shot-noise for sparse balanced networks of spiking neurons. For low (high) external drives (synaptic strengths) irregular global oscillations emerge via continuous and hysteretic transitions, correctly predicted by our approach, but not from the DA. These oscillations display frequencies in biologically relevant bands.Comment: 6 pages, 3 figure

A reduction methodology for fluctuation driven population dynamics

Lorentzian distributions have been largely employed in statistical mechanics to obtain exact results for heterogeneous systems. Analytic continuation of these results is impossible even for slightly deformed Lorentzian distributions, due to the divergence of all the moments (cumulants). We have solved this problem by introducing a `pseudo-cumulants' expansion. This allows us to develop a reduction methodology for heterogeneous spiking neural networks subject to extrinsinc and endogenous noise sources, thus generalizing the mean-field formulation introduced in [E. Montbri\'o et al., Phys. Rev. X 5, 021028 (2015)].Comment: 10 pages (with supplementary materials), 3 figure

Entropy potential and Lyapunov exponents

According to a previous conjecture, spatial and temporal Lyapunov exponents of chaotic extended systems can be obtained from derivatives of a suitable function: the entropy potential. The validity and the consequences of this hypothesis are explored in detail. The numerical investigation of a continuous-time model provides a further confirmation to the existence of the entropy potential. Furthermore, it is shown that the knowledge of the entropy potential allows determining also Lyapunov spectra in general reference frames where the time-like and space-like axes point along generic directions in the space-time plane. Finally, the existence of an entropy potential implies that the integrated density of positive exponents (Kolmogorov-Sinai entropy) is independent of the chosen reference frame.Comment: 20 pages, latex, 8 figures, submitted to CHAO