Related papers: Diffusion of Tracer Particles in Early Growing Bio…
The dynamics of a tracer molecule near a fluid membrane is investigated, with particular emphasis given to the interplay between the instantaneous position of the particle and membrane fluctuations. It is found that hydrodynamic…
We study analytically the dynamics and the micro-structural changes of a host medium caused by a driven tracer particle moving in a confined, quiescent molecular crowding environment. Imitating typical settings of active micro-rheology…
We consider the diffusion-advection problem in two simple cellular flow models (often invoked as examples for subdiffusive tracer's motion) and concentrate on the intermediate time range, in which the tracer's motion indeed may show…
This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…
We study the effect of spatially-varying potential and diffusivity on the dispersion of a tracer particle in single-file diffusion. Non-interacting particles in such a system exhibit normal diffusion at late times, which is characterised by…
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed…
Macromolecular diffusion in strongly confined geometries and crowded environments is still to a large extent an open subject in soft matter physics and biology. In this paper, we employ large-scale Langevin dynamics simulations to…
Experiments have shown that self-propelled particles can slide along the surface of a circular obstacle without becoming trapped over long times. Using simulations and theory, we study the impact of boundary conditions on the diffusive…
In this work we address a novel feature of spreading dynamics of tiny liquid droplets on solid surfaces, namely the case where the ends of the molecules feel different interactions to the surface. We consider a simple model of dimers and…
In this study, inspired by the work of K. Nakazato and K. Kitahara [Prog. Theor. Phys. 64, 2261 (1980)], we consider the theoretical problem of tracer particle diffusion in an environment of diffusing hardcore interacting crowder particles.…
Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during…
Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes…
Diffusion of impenetrable particles in a crowded one-dimensional channel is referred as the single file diffusion. The particles do not pass each other and the displacement of each individual particle is sub-diffusive. We analyse a simple…
We apply macroscopic fluctuation theory to study the diffusion of a tracer in a one-dimensional interacting particle system with excluded mutual passage, known as single-file diffusion. In the case of Brownian point particles with hard-core…
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…
The diffusive transport of biased Brownian particles in a two-dimensional symmetric channel is investigated numerically considering both the no-flow and the reflection boundary conditions at the channel boundaries. Here, the geometrical…
The transport of self-propelled particles such as bacteria and phoretic swimmers through crowded heterogeneous environments is relevant to many natural and engineering processes, from biofilm formation and contamination processes to…
Various bacterial strains (e.g. strains belonging to the genera Bacillus, Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns during growth on poor semi-solid substrates. These patterns reflect the bacterial…
We study the diffusivity of a tagged particle in a binary mixture of Brownian particles with non-reciprocal interactions. Numerical simulations reveal that, for a broad class of interaction potentials, non-reciprocity can significantly…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…