Related papers: Crowding competes with trapping to enhance interfa…
We use molecular dynamics simulations to investigate the tracer diffusion in a sea of polymers with specific binding zones for the tracer. These binding zones act as traps. Our simulations show that the tracer can undergo normal yet…
We propose a general model to study the interplay between spatial dispersal and environment spatiotemporal fluctuations in metapopulation dynamics. An ecological landscape of favorable patches is generated like a L\'{e}vy dust, which allows…
Behavior of the mixture of particles and dimers moving with different jump rates at reconstructed surfaces is described. Collective diffusion coefficient is calculated by the variational approach. Anisotropy of the collective particle…
Volume-filling cross-diffusion equations for the components of a tissue structure are formally derived from mass conservation laws and force balances for the interphase pressures and viscous drag forces in a multiphase approach. The…
Rod-shaped particles embedded in certain matrices have been reported to exhibit an increase in their center of mass diffusivity upon increasing the matrix density. This increase has been considered to be caused by a kinetic constraint in…
We study theoretically situations where competition arises between an interdiffusion process and a cross-linking chemical reaction at interfaces between pieces of the same polymer material. An example of such a situation is observable in…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
We study the influence of the boundary conditions at the solid liquid interface on diffusion in a confined fluid. Using an hydrodynamic approach, we compute numerical estimates for the diffusion of a particle confined between two planes.…
An anisotropic random barrier model is presented, in which the transition probabilities in different directions have different probability density functions. At low temperatures, the anisotropic long--time diffusion coefficients, obtained…
Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous…
We consider a one-dimensional Brownian motion with diffusion coefficient $D$ in the presence of $n$ partially absorbing traps with intensity $\beta$, separated by a distance $L$ and evenly spaced around the initial position of the particle.…
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with…
This study investigates the complex dynamic interactions between two typed populations coexisting within a shared space. We propose both theoretical and numerical study to analyze scenarios where one population (population $1$) must…
We consider a stochastic many-body system where a source refills uniformly the empty sites of a hypercubic lattice, on which each particle is allowed to jump (symmetrically) onto neighboring vacant sites. In addition, there is a local {\it…
The influence of crowding on the diffusion of tagged particles in a dense medium is investigated in the framework of a mean-field model, derived in the continuum limit from a microscopic stochastic process with exclusion. The probability…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
Transport in crowded, complex environments occurs across many spatial scales. Geometric restrictions can hinder the motion of individuals and, combined with crowding between individuals, can have drastic effects on global transport…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
The migration of active particles in slowly moving, crowded, and heterogeneous media is fundamental to various biological processes and technological applications, such as cargo transport. In this study, we numerically investigate the…
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics…