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We study numerically domain growth and interface fluctuations in one- and two-dimensional lattice systems composed of four species that interact in a cyclic way. Particle mobility is implemented through exchanges of particles located on…
In the present work, we study random walks on complex networks subject to stochastic resetting when the resetting probability is node-dependent. Using a renewal approach, we derive the exact expressions of the stationary occupation…
Two known distinct examples of one-dimensional systems which are known to exhibit a phase transition are critically examined: (A) a lattice model with harmonic nearest-neighbor elastic interactions and an on-site Morse potential, and (B)…
One-dimensional non-equilibrium models of particles subjected to a coagulation-diffusion process are important in understanding non-equilibrium dynamics, and fluctuation-dissipation relation. We consider in this paper transport properties…
We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between…
Many insects like ants communicate chemically via chemotaxis. This allows them to build large trail systems which in many respects are similar to human-build highway networks. Using a recently proposed stochastic cellular automaton model we…
Diverse complex dynamical systems are known to exhibit abrupt regime shifts at bifurcation points of the saddle-node type. The dynamics of most of these systems, however, have a stochastic component resulting in noise driven regime shifts…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
A two-dimensional half-filled lattice gas model with nearest-neighbor attractive interaction is studied where particles are coupled to two thermal baths at different temperatures $T_1$ and $T_2$. The hopping of particles is governed by the…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
We consider the Activated Random Walk model in any dimension with any sleep rate and jump distribution and ergodic initial state. We show that the stabilization properties depend only on the average density of particles, regardless of how…
Monte Carlo simulation is used to study the dynamical crossover from single file diffusion to normal diffusion in fluids confined to narrow channels. We show that the long time diffusion coefficients for a series of systems involving hard…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
Using the framework of generalized exclusion processes we study mixtures of passive and active particles interacting by steric repulsion. The particles move in a pore with periodically modulated aperture, which is modeled by a…
We analyze ecological systems that are influenced by random environmental fluctuations. We first provide general conditions which ensure that the species coexist and the system converges to a unique invariant probability measure (stationary…
We study a model of bacterial dynamics where two interacting random walkers perform run-and-tumble motion on a one-dimensional lattice under mutual exclusion and find an exact expression for the probability distribution in the steady state.…
We examine a system of interacting random walks with leftward drift on $\mathbb{Z}$, which begins with a single active particle at the origin and some distribution of inactive particles on the positive integers. Inactive particles become…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…