Related papers: Network representations of non-equilibrium steady …
A procedure is introduced which allows to represent the dynamics of a non-equilibrium system violating detailed balance by its steady state loop fluxes. It is shown that detailed balance is restored in this representation, such that the…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
A driven stochastic system in a constant temperature heat bath relaxes into a steady state which is characterized by the steady state probability distribution. We investigate the relationship between the driving force and the steady state…
The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional dynamics of interacting particles on a $1$D-lattice that is much used in systems biology and statistical physics. Its master equation…
We describe a large family of nonequilibrium steady states (NESS) corresponding to forced flows over obstacles. The spatial structure at large distances from the obstacle is shown to be universal, and can be quantitatively characterised in…
Entropy is a central concept in physics, but can be challenging to calculate even for systems that are easily simulated. This is exacerbated out of equilibrium, where generally little is known about the distribution characterizing simulated…
Closely related to the laws of thermodynamics, the detection and quantification of disequilibria are crucial in unraveling the complexities of nature, particularly those beneath observable layers. Theoretical developments in nonequilibrium…
We study the generic non-equilibrium steady states in asymmetric exclusion processes on a closed network with bottlenecks. To this end we proposes and study closed simple networks with multiply-connected non-identical junctions. Depending…
Transition rates in continuously driven steady states were derived in [Evans R M L, 2005 J. Phys. A: Math. Gen. 38, 293] by demanding that no information other than the microscopic laws of motion and the macroscopic observables of the…
Diverse equilibrium systems with heterogeneous interactions lie at the edge of stability. Such marginally stable states are dynamically selected as the most abundant ones or as those with the largest basins of attraction. On the other hand,…
We consider an open one dimensional lattice gas on sites $i=1,...,N$, with particles jumping independently with rate 1 to neighboring interior empty sites, the {\it simple symmetric exclusion process}. The particle fluxes at the left and…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally…
In this paper we investigate equilibria of continuous differential equation models of network dynamics. The motivation comes from gene regulatory networks where each directed edge represents either down- or up-regulation, and is modeled by…
We propose a housekeeping/excess decomposition of entropy production for general nonlinear dynamics in a discrete space, including chemical reaction networks and discrete stochastic systems. We exploit the geometric structure of…
Model reduction of Markov processes is a basic problem in modeling state-transition systems. Motivated by the state aggregation approach rooted in control theory, we study the statistical state compression of a discrete-state Markov chain…
Network topology plays an important role in governing the collective dynamics. Partial synchronization (PaS) on regular networks with a few non-local links is explored. Different PaS patterns out of the symmetry breaking are observed for…
An equivalence between non equilibrium steady states (NESS) driven by a time-independent force and stochastic pumps (SP) stirred by a time-varying conservative force is studied for general many-body diffusive systems. When the particle…
This paper analyzes stochastic networks consisting of a set of finite capacity sites where different classes of individuals move according to some routing policy. The associated Markov jump processes are analyzed under a thermodynamic limit…
Motivated by fundamental issues in non-equilibrium statistical mechanics (NESM), we study the venerable susceptible-infected (SIS) model of disease spreading in an idealized, simple setting. Using Monte Carlo and analytic techniques, we…