DNA denaturation and wetting in the presence of disorder

We present a precise equivalence of the Lifson-Poland-Scheraga model with wetting models. Making use of a representation of the former model in terms of random matrices, we obtain, in the limit of weak disorder, a mean--field approximation, that shows a change of the critical behavior due to disorder.Comment: 4 page

Manipulating energy and spin currents in nonequilibrium systems of interacting qubits

We consider generic interacting chain of qubits, which are coupled at the edges to baths of fixed polarizations. We can determine the nonequilibrium steady states, described by the fixed point of the Lindblad Master Equation. Under rather general assumptions about local pumping and interactions, symmetries of the reduced density matrix are revealed. The symmetries drastically restrict the form of the steady density matrices in such a way that an exponentially large subset of one--point and many--point correlation functions are found to vanish. As an example we show how in a Heisenberg spin chain a suitable choice of the baths can completely switch off either the spin or the energy current, or both of them, despite the presence of large boundary gradients.Comment: 8 pages, 3 Figure

Thermal conduction in classical low-dimensional lattices

Deriving macroscopic phenomenological laws of irreversible thermodynamics from simple microscopic models is one of the tasks of non-equilibrium statistical mechanics. We consider stationary energy transport in crystals with reference to simple mathematical models consisting of coupled oscillators on a lattice. The role of lattice dimensionality on the breakdown of the Fourier's law is discussed and some universal quantitative aspects are emphasized: the divergence of the finite-size thermal conductivity is characterized by universal laws in one and two dimensions. Equilibrium and non-equilibrium molecular dynamics methods are presented along with a critical survey of previous numerical results. Analytical results for the non-equilibrium dynamics can be obtained in the harmonic chain where the role of disorder and localization can be also understood. The traditional kinetic approach, based on the Boltzmann-Peierls equation is also briefly sketched with reference to one-dimensional chains. Simple toy models can be defined in which the conductivity is finite. Anomalous transport in integrable nonlinear systems is briefly discussed. Finally, possible future research themes are outlined.Comment: 90 pages, revised versio

Computational analysis of folding and mutation properties of C5 domain from Myosin binding protein C

Thermal folding Molecular Dynamics simulations of the domain C5 from Myosin Binding Protein C were performed using a native-centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA' beta-sheet featuring the highest Phi-values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause a little change in the folding temperature and they reside in the low Phi-value BDE beta-sheet, so that their pathologic role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destabilizing CD-loop with respect to the other Ig-like domains we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD-loop as a natively unfolded sequence with a likely coupling between folding and ligand binding.Comment: RevTeX, 10 pages, 9 eps-figure

Stability of the splay state in pulse--coupled networks

The stability of the dynamical states characterized by a uniform firing rate ({\it splay states}) is analyzed in a network of globally coupled leaky integrate-and-fire neurons. This is done by reducing the set of differential equations to a map that is investigated in the limit of large network size. We show that the stability of the splay state depends crucially on the ratio between the pulse--width and the inter-spike interval. More precisely, the spectrum of Floquet exponents turns out to consist of three components: (i) one that coincides with the predictions of the mean-field analysis [Abbott-van Vreesvijk, 1993]; (ii) a component measuring the instability of "finite-frequency" modes; (iii) a number of "isolated" eigenvalues that are connected to the characteristics of the single pulse and may give rise to strong instabilities (the Floquet exponent being proportional to the network size). Finally, as a side result, we find that the splay state can be stable even for inhibitory coupling.Comment: 13 pages, 10 figures, submitted for pubblication to Physical Review

Studies of thermal conductivity in Fermi-Pasta-Ulam like lattices

The pioneering computer simulations of the energy relaxation mechanisms performed by Fermi, Pasta and Ulam can be considered as the first attempt of understanding energy relaxation and thus heat conduction in lattices of nonlinear oscillators. In this paper we describe the most recent achievements about the divergence of heat conductivity with the system size in 1d and 2d FPU-like lattices. The anomalous behavior is particularly evident at low energies, where it is enhanced by the quasi-harmonic character of the lattice dynamics. Remakably, anomalies persist also in the strongly chaotic region where long--time tails develop in the current autocorrelation function. A modal analysis of the 1d case is also presented in order to gain further insight about the role played by boundary conditions.Comment: Invited article to appear in the Chaos focus issue on "Studies of Nonlinear Problems. I" by Enrico Fermi, John Pasta, and Stanislaw Ulam

Boundary-induced instabilities in coupled oscillators

Published version, minor changesPeer reviewedPublisher PD

Intertangled stochastic motifs in networks of excitatory-inhibitory units

We have benefited from discussions with A. Politi. The authors acknowledge financial support from H2020- MSCA-ITN-2015 project COSMOS 642563.Peer reviewedPostprin

Covariant Lyapunov vectors

The recent years have witnessed a growing interest for covariant Lyapunov vectors (CLVs) which span local intrinsic directions in the phase space of chaotic systems. Here we review the basic results of ergodic theory, with a specific reference to the implications of Oseledets' theorem for the properties of the CLVs. We then present a detailed description of a "dynamical" algorithm to compute the CLVs and show that it generically converges exponentially in time. We also discuss its numerical performance and compare it with other algorithms presented in literature. We finally illustrate how CLVs can be used to quantify deviations from hyperbolicity with reference to a dissipative system (a chain of H\'enon maps) and a Hamiltonian model (a Fermi-Pasta-Ulam chain)