arXiv subjects

Marco Baiesi

Publications and source records attributed to Marco Baiesi.

At least 73 records · Page 4Linked to original sources

arXiv2009

Nonequilibrium Linear Response for Markov Dynamics, II: Inertial Dynamics

We continue our study of the linear response of a nonequilibrium system. This Part II concentrates on models of open and driven inertial dynamics but the structure and the interpretation of the result remain unchanged: the response can be expressed as a sum of two temporal correlations in the unperturbed system, one entropic, the other frenetic. The decomposition arises from the (anti)symmetry under time-reversal on the level of the nonequilibrium action. The response formula involves a statistical averaging over explicitly known observables but, in contrast with the equilibrium situation, they depend on the model dynamics in terms of an excess in dynamical activity. As an example, the Einstein relation between mobility and diffusion constant is modified by a correlation term between the position and the momentum of the particle.

cond-mat.stat-mech↗

arXiv2009

Interplay between writhe and knotting for swollen and compact polymers

The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo methods to investigate the interplay between writhe and knotting of ring polymers in good and poor solvents. The model that we consider is interacting self-avoiding polygons on the simple cubic lattice. For polygons with fixed knot type we find a writhe distribution whose average depends on the knot type but is insensitive to the length $N$ of the polygon and to solvent conditions. This "topological contribution" to the writhe distribution has a value that is consistent with that of ideal knots. The standard deviation of the writhe increases approximately as $\sqrt{N}$ in both regimes and this constitutes a geometrical contribution to the writhe. If the sum over all knot types is considered, the scaling of the standard deviation changes, for compact polygons, to $\sim N^{0.6}$. We argue that this difference between the two regimes can be ascribed to the topological contribution to the writhe that, for compact chains, overwhelms the geometrical one thanks to the presence of a large population of complex knots at relatively small values of $N$. For polygons with fixed writhe we find that the knot distribution depends on the chosen writhe, with the occurrence of achiral knots being considerably suppressed for large writhe. In general, the occurrence of a given knot thus depends on a nontrivial interplay between writhe, chain length, and solvent conditions.

cond-mat.stat-mech↗

arXiv2009

A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.

cond-mat.soft↗

arXiv2009

Fluctuations and response of nonequilibrium states

A generalized fluctuation-response relation is found for thermal systems driven out of equilibrium. Its derivation is independent of many details of the dynamics, which is only required to be first-order. The result gives a correction to the equilibrium fluctuation-dissipation theorem, in terms of the correlation between observable and excess in dynamical activity caused by the perturbation. Previous approaches to this problem are recovered and extended in a unifying scheme.

cond-mat.stat-mech↗

arXiv2009

Correlated earthquakes in a self-organized model

Motivated by the fact that empirical time series of earthquakes exhibit long-range correlations in space and time and the Gutenberg-Richter distribution of magnitudes, we propose a simple fault model that can account for these types of scale-invariance. It is an avalanching process that displays power-laws in the event sizes, in the epicenter distances as well as in the waiting-time distributions, and also aftershock rates obeying a generalized Omori law. We thus confirm that there is a relation between temporal and spatial clustering of the activity in this kind of models. The fluctuating boundaries of possible slipping areas show that the size of the largest possible earthquake is not always maximal, and the average correlation length is a fraction of the system size. This suggests that there is a concrete alternative to the extreme interpretation of self-organized criticality as a process in which every small event can cascade to an arbitrary large one: the new picture includes fluctuating domains of coherent stress field as part of the global self-organization. Moreover, this picture can be more easily compared with other scenarios discussing fluctuating correlations lengths in seismicity.

cond-mat.stat-mech↗

arXiv2009

Multiple timescales in a model for DNA denaturation dynamics

The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect this symmetry. Linking dissipation via untwist is allowed only at the two ends of the double strand. The result is a slow denaturation characterized by two time scales that depend on the chain length $L$. In a regime up to a first characteristic time $τ_1\sim L^{2.15}$ the chain embodies an increasing number of small bubbles. Then, in a second regime, bubbles coalesce and form entropic barriers that effectively trap residual double-stranded segments within the chain, slowing down the relaxation to fully molten configurations, which takes place at $τ_2\sim L^3$. This scenario is different from the picture in which the helical constraints are neglected.

cond-mat.stat-mech↗

arXiv2008

Exact computation of current cumulants in small Markovian systems

We describe an algorithm computing the exact value of the mean current, its variance, and higher order cumulants for stochastic driven systems. The method uses a Rayleigh-Schrodinger perturbation expansion of the generating function of the current, and can be extended to compute covariances of multiple currents. As an example of application of the method, we give numerical evidence for a simple relation [Eq.(5)] between the second and the fourth cumulants of the current in a symmetric exclusion process.

cond-mat.stat-mech↗

arXiv2008

Computation of current cumulants for small nonequilibrium systems

We analyze a systematic algorithm for the exact computation of the current cumulants in stochastic nonequilibrium systems, recently discussed in the framework of full counting statistics for mesoscopic systems. This method is based on identifying the current cumulants from a Rayleigh-Schrodinger perturbation expansion for the generating function. Here it is derived from a simple path-distribution identity and extended to the joint statistics of multiple currents. For a possible thermodynamical interpretation, we compare this approach to a generalized Onsager-Machlup formalism. We present calculations for a boundary driven Kawasaki dynamics on a one-dimensional chain, both for attractive and repulsive particle interactions.

cond-mat.stat-mech↗

arXiv2006

Realistic time correlations in sandpiles

A ``sandpile'' cellular automaton achieves complex temporal correlations, like a $1/f$ spectrum, if the position where it is perturbed diffuses slowly rather than changing completely at random, showing that the spatial correlations of the driving are deeply related to the intermittent activity. Hence, recent arguments excluding the relevance of self-organized criticality in seismicity and in other contexts are inaccurate. As a toy model of single fault evolution, and despite of its simplicity, our automaton uniquely reproduces the scaling form of the broad distributions of waiting times between earthquakes.

cond-mat.stat-mech↗

arXiv2006

A Self-Organized-Criticality model consistent with statistical properties of edge turbulence in a fusion plasma

The statistical properties of the intermittent signal generated by a recent model for self-organized-criticality (SOC) are examined. A successful comparison is made with previously published results of the equivalent quantities measured in the electrostatic turbulence at the edge of a fusion plasma. This result re-establishes SOC as a potential paradigm for transport in magnetic fusion devices, overriding shortcomings pointed out in earlier works [E. Spada, et al, Phys. Rev. Lett. 86, 3032 (2001); V. Antoni, et al, Phys. Rev. Lett. 87, 045001 (2001)].

cond-mat.stat-mech↗

arXiv2006

Fluctuation symmetries for work and heat

We consider a particle dragged through a medium at constant temperature as described by a Langevin equation with a time-dependent potential. The time-dependence is specified by an external protocol. We give conditions on potential and protocol under which the dissipative work satisfies an exact symmetry in its fluctuations for all times. We also present counter examples to that exact fluctuation symmetry when our conditions are not satisfied. Finally, we consider the dissipated heat which differs from the work by a temporal boundary term. We explain when and why there can be a correction to the standard fluctuation theorem due to the unboundedness of that temporal boundary. However, the corrected fluctuation symmetry has again a general validity.

cond-mat.stat-mech↗

arXiv2005

Enstrophy dissipation in two-dimensional turbulence

Insight into the problem of two-dimensional turbulence can be obtained by an analogy with a heat conduction network. It allows the identification of an entropy function associated to the enstrophy dissipation and that fluctuates around a positive (mean) value. While the corresponding enstrophy network is highly nonlocal, the direction of the enstrophy current follows from the Second Law of Thermodynamics. An essential parameter is the ratio $T_k = γ_k /(νk^2)$ of the intensity of driving $γ_k>0$ as a function of wavenumber $k$, to the dissipation strength $νk^2$, where $ν$ is the viscosity. The enstrophy current flows from higher to lower values of $T_k$, similar to a heat current from higher to lower temperature. Our probabilistic analysis of the enstrophy dissipation and the analogy with heat conduction thus complements and visualizes the more traditional spectral arguments for the direct enstrophy cascade. We also show a fluctuation symmetry in the distribution of the total entropy production which relates the probabilities of direct and inverse enstrophy cascades.

cond-mat.stat-mech↗

arXiv2005

Intensity Thresholds and the Statistics of the Temporal Occurrence of Solar Flares

Introducing thresholds to analyze time series of emission from the Sun enables a new and simple definition of solar flare events, and their interoccurrence times. Rescaling time by the rate of events, the waiting and quiet time distributions both conform to scaling functions that are independent of the intensity threshold over a wide range. The scaling functions are well described by a two parameter function, with parameters that depend on the phase of the solar cycle. For flares identified according to the current, standard definition, similar behavior is found.

cond-mat.stat-mech↗

arXiv2005

Scaling of a collapsed polymer globule in 2D

Extensive Monte Carlo data analysis gives clear evidence that collapsed linear polymers in two dimensions fall in the universality class of athermal, dense self-avoiding walks, as conjectured by B.Duplantier [Phys.Rev.Lett. 71, 4274 (1993)]. However, the boundary of the globule has self affine roughness and does not determine the anticipated nonzero topological boundary contribution to entropic exponents. Scaling corrections are due to subleading contributions to the partition function corresponding to polymer configurations with one end located on the globule-solvent interface.

cond-mat.stat-mech↗

arXiv2005

Inter-occurrence Times in the Bak-Tang-Wiesenfeld Sandpile Model: A Comparison with the Turbulent Statistics of Solar Flares

A sequence of bursts observed in an intermittent time series may be caused by a single avalanche, even though these bursts appear as distinct events when noise and/or instrument resolution impose a detection threshold. In the Bak-Tang-Wiesenfeld sandpile, the statistics of quiet times between bursts switches from Poissonian to scale invariant on raising the threshold for detecting instantaneous activity, since each zero-threshold avalanche breaks into a hierarchy of correlated bursts. Calibrating the model with the time resolution of GOES data, qualitative agreement with the inter-occurrence time statistics of solar flares at different intensity thresholds is found.

astro-ph↗

arXiv2004

Complex networks of earthquakes and aftershocks

We invoke a metric to quantify the correlation between any two earthquakes. This provides a simple and straightforward alternative to using space-time windows to detect aftershock sequences and obviates the need to distinguish main shocks from aftershocks. Directed networks of earthquakes are constructed by placing a link, directed from the past to the future, between pairs of events that are strongly correlated. Each link has a weight giving the relative strength of correlation such that the sum over the incoming links to any node equals unity for aftershocks, or zero if the event had no correlated predecessors. A correlation threshold is set to drastically reduce the size of the data set without losing significant information. Events can be aftershocks of many previous events, and also generate many aftershocks. The probability distribution for the number of incoming and outgoing links are both scale free, and the networks are highly clustered. The Omori law holds for aftershock rates up to a decorrelation time that scales with the magnitude, $m$, of the initiating shock as $t_{\rm cutoff} \sim 10^{βm}$ with $β\simeq 3/4$. Another scaling law relates distances between earthquakes and their aftershocks to the magnitude of the initiating shock. Our results are inconsistent with the hypothesis of finite aftershock zones. We also find evidence that seismicity is dominantly triggered by small earthquakes. Our approach, using concepts from the modern theory of complex networks, together with a metric to estimate correlations, opens up new avenues of research, as well as new tools to understand seismicity.

physics.geo-ph↗

arXiv2004

Scaling and precursor motifs in earthquake networks

A measure of the correlation between two earthquakes is used to link events to their aftershocks, generating a growing network structure. In this framework one can quantify whether an aftershock is close or far, from main shocks of all magnitudes. We find that simple network motifs involving links to far aftershocks appear frequently before the three biggest earthquakes of the last 16 years in Southern California. Hence, networks could be useful to detect symptoms typically preceding major events.

cond-mat.stat-mech↗

arXiv2004

Unbinding of mutually avoiding random walks and two dimensional quantum gravity

We analyze the unbinding transition for a two dimensional lattice polymer in which the constituent strands are mutually avoiding random walks. At low temperatures the strands are bound and form a single self-avoiding walk. We show that unbinding in this model is a strong first order transition. The entropic exponents associated to denaturated loops and end-segments distributions show sharp differences at the transition point and in the high temperature phase. Their values can be deduced from some exact arguments relying on a conformal mapping of copolymer networks into a fluctuating geometry, i.e. in the presence of quantum gravity. An excellent agreement between analytical and numerical estimates is observed for all cases analized.

cond-mat.stat-mech↗