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The methodology based on the random walk processes is adapted and applied to a comprehensive analysis of the statistical properties of the probability fluxes. To this aim we define a simple model of the Markovian stochastic dynamics on a…
We prove that the flux function of the totally asymmetric simple exclusion process (TASEP) with site disorder exhibits a flat segment for sufficiently dilute disorder. For high dilution, we obtain an accurate description of the flux. The…
We study nonlinear dynamics on complex networks. Each vertex $i$ has a state $x_i$ which evolves according to a networked dynamics to a steady-state $x_i^*$. We develop fundamental tools to learn the true steady-state of a small part of the…
We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport,…
We give an introduction to phase transitions in the steady states of systems that evolve stochastically with equilibrium and nonequilibrium dynamics, the latter defined as those that do not possess a time-reversal symmetry. We try as much…
We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks…
Generalizations of the microcanonical and canonical ensembles for paths of Markov processes have been proposed recently to describe the statistical properties of nonequilibrium systems driven in steady states. Here we propose a theory of…
Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized…
Under many circumstances many soft and hard materials are present in a puzzling wealth of non-equilibrium amorphous states, whose properties are not stationary and depend on preparation. They are often summarized in unconventional "phase…
Symbolic dynamics has proven to be an invaluable tool in analyzing the mechanisms that lead to unpredictability and random behavior in nonlinear dynamical systems. Surprisingly, a discrete partition of continuous state space can produce a…
The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional flow of interacting particles on a 1D-lattice that is much used in systems biology and statistical physics. Its master equation describes…
We derive the representation of the nonequilibrium steady-state distribution function which is expressed in terms of the excess free energy production. This representation resembles the one derived recently by Komatsu and Nakagawa [Phys.…
We formulate a comprehensive theoretical description of excitation harvesting in molecular aggregates photoexcited by weak incoherent radiation. An efficient numerical scheme that respects the continuity equation for excitation fluxes is…
We study a novel alternative approach for the computation of transport coefficients at mesoscales. While standard nonequilibrium molecular dynamics (NEMD) approaches fix the forcing and measure the average induced flux in the system driven…
Asymptotic properties of Markov Processes, such as steady state probabilities or hazard rate for absorbing states can be efficiently calculated by means of linear algebra even for large-scale problems. This paper discusses the methods for…
Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach…
Recent results have shown how to partition the space of Markov systems into dynamical equivalence classes. These equivalence classes structure transport properties in such a way that makes, among other features, their responses fully…
We formulate a dynamical fluctuation theory for stationary non equilibrium states (SNS) which is tested explicitly in stochastic models of interacting particles. In our theory a crucial role is played by the time reversed dynamics. Within…
We adapt the time-evolving block decimation (TEBD) algorithm, originally devised to simulate the dynamics of 1D quantum systems, to simulate the time-evolution of non-equilibrium stochastic systems. We describe this method in detail; a…