Related papers: Diffusion limited reactions in confined environmen…
Living systems at the sub-cellular, cellular, and multi-cellular level are often crowded systems that contain active particles. The active motion of these particles can also propel passive particles, which typically results in enhanced…
We introduce two discrete models of a collection of colliding particles with stored momentum and study the asymptotic growth of the mean-square displacement of an active particle. We prove that the models are superdiffusive in one dimension…
Reaction-diffusion models with nonlocal constraints naturally arise as limiting cases of coupled bulk-surface models of intracellular signalling. In this paper, a minimal, mass-conserving model of cell-polarization on a curved membrane is…
Diffusion-limited reactions (DLR) are usually described within the Smoluchowski theory, which neglects interactions between the diffusing components. We propose a first extension of such frame- work that incorporates excluded-volume…
We study the low-frequency dielectric response of highly charged spheres arranged in a cubic lattice and immersed in an electrolyte solution. We focus on the influence of the out-of-phase current in the regime where the ionic charge is…
We have performed confocal microscopy experiments and computer simulations of colloidal suspensions with moderate volume fraction confined between two quasi-parallel, rough walls [A. Villada-Balbuena et al., Soft Matter, 2022, 18,…
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…
We summarise different results on the diffusion of a tracer particle in lattice gases of hard-core particles with stochastic dynamics, which are confined to narrow channels -- single-files, comb-like structures and quasi-one-dimensional…
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions; one example is the immune system signalling, where infected tissues release chemokines…
We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of…
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
The standard analysis of reaction networks based on deterministic rate equations fails in confined geometries, commonly encountered in fields such as astrochemistry, thin film growth and cell biology. In these systems the small reactant…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
Consider a particle diffusing in a confined volume which is divided into two equal regions. In one region the diffusion coefficient is twice the value of the diffusion coefficient in the other region. Will the particle spend equal…
We investigate the effects of spatial discreteness of molecules in reaction-diffusion systems. It is found that discreteness within the so called Kuramoto length can lead to a localization of molecules, resulting in novel steady states that…
A microscopic model of the effect of unbinding in diffusion limited aggregation based on a cellular automata approach is presented. The geometry resembles electrochemical deposition - ``ions'' diffuse at random from the top of a container…