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In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
We present a new efficient method for Monte Carlo simulations of diffusion-reaction processes. First introduced by us in [Phys. Rev. Lett., 97:230602, 2006], the new algorithm skips the traditional small diffusion hops and propagates the…
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
Most of the research concerting crack propagation in discrete media is concerned with specific types of external loading: displacements on the boundaries, or constant energy fluxes or feeding waves originating from infinity. In this paper…
We consider a tracer particle on a lattice in the presence of immobile obstacles. Starting from equilibrium, a force pulling on the particle is switched on, driving the system to a new stationary state. We solve for the complete transient…
We study the diffusion of a tracer particle driven out-of-equilibrium by an external force and traveling in a dense environment of arbitrary density. The system evolves on a discrete lattice and its stochastic dynamics is described by a…
In this article, we study a type of a one dimensional percolation model whose basic features include a sequential dropping of particles on a substrate followed by their transport via a pushing mechanism (see [S. N. Majumdar and D. S. Dean,…
We analyse diffusion dynamics on weakly-coupled networks (interconnected networks) by means of separation of time scales. Using an adiabatic approximation we reduced the system dynamics to a Markov chain with aggregated variables and…
In this paper we present a computer simulation of a random walk (RW) for diffusion on a rearranging lattice. The lattice consists of two types of sites -- one good conducting (type 1) and the other poor conducting (type 2), distributed at…
We have numerically studied the trapping problem in a two-dimensional lattice where particles are continuously generated. We have introduced interaction between particles and directionality of their movement. This model presents a critical…
By means of Brownian dynamics simulations we study the steady-state dynamic properties of a flexible active polymer in a poor solvent condition. Our results show that the effective diffusion constant of the polymer $D_{\rm eff}$ gets…
We show that the injection of polymer chains into nanochannels becomes easier as the channel becomes narrower. This counter intuitive result arises because of a decrease in the diffusive time scale of the chains with increasing confinement.…
We consider a discrete time particle model for kinetic transport on the two dimensional integer lattice. The particle can move due to advection in the $x$-direction and due to dispersion. This happens when the particle is free, but it can…
We present an analytical and numerical study of a nonlinear diffusion model which describes density relaxation of loosely packed particles under gravity and weak random (thermal) vibration, and compare the results with Monte Carlo…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
We consider random networks whose dynamics is described by a rate equation, with transition rates $w_{nm}$ that form a symmetric matrix. The long time evolution of the system is characterized by a diffusion coefficient $D$. In one dimension…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
We demonstrate that a completely integrable classical mechanical model, namely the lattice Landau-Lifshitz classical spin chain, supports diffusive spin transport with a finite diffusion constant in the easy-axis regime, while in the…
Monte Carlo (MC) simulations of transport in random porous networks indicate that for high variances of the log-normal permeability distribution, the transport of a passive tracer is non-Fickian. Here we model this non-Fickian dispersion in…