Related papers: Excluded volume effects in on- and off-lattice rea…
We introduce a simplified technique for incorporating diffusive phenomena into lattice-gas molecular dynamics models. In this method, spatial interactions take place one dimension at a time, with a separate fractional timestep devoted to…
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While…
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we…
Several models based on the diffusion-limited aggregation (DLA) model were proposed and their scaling properties explored by computational and theoretical approaches. In this paper, we consider a new extension of the on-lattice DLA model in…
Discontinuous transitions into absorbing states require an effective mechanism that prevents the stabilization of low density states. They can be found in different systems, such as lattice models or stochastic differential equations (e.g.…
We present results on the modeling of on- and off-ramps in cellular automata for traffic flow, especially the Nagel-Schreckenberg model. We study two different types of on-ramps that cause qualitatively the same effects. In a certain…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
We studied through Monte Carlo simulations, the kinetics of the two-species diffusion-limited reaction model with same species excluded volume interaction in substrates embedded on a square lattice ranging in occupancy from a fractal…
Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets,…
Discrete element method simulations of confined bidisperse granular shear flows elucidate the balance between diffusion and segregation that can lead to either mixed or segregated states, depending on confining pressure. Results indicate…
Lattice Boltzmann simulations of liquid-gas systems are believed to be restricted to modest density ratios of less than 10. In this article we show that reducing the speed of sound and, just as importantly, the interfacial contributions to…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
The sensitivity of anomalous transport in crowded media to the form of the inter-particle interactions is investigated through computer simulations. We extend the highly simplified Lorentz model towards realistic natural systems by modeling…
Agent-based (AB) or Cellular Automata (CA) models are rule based and are a relatively simple discrete method that can be used to simulate complex interactions of many agents or cells. The relative ease of implementing the computational…
A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…
In this paper, we study a numerical approximation for a class of stationary states for reaction-diffusion system with m densities having disjoint support, which are governed by a minimization problem. We use quantitative properties of both…
Reaction-diffusion systems, which consist of the reacting particles subject to diffusion process, constitute one of the common examples of non-linear statistical systems. In low space dimensions $d \leq 2$ the usual description by means of…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…