Related papers: Diffusion of Tracer Particles in Early Growing Bio…
The behavior of particles driven through a narrow constriction is investigated in experiment and simulation. The system of particles adapts to the confining potentials and the interaction energies by a self-consistent arrangement of the…
Free boundaries of biofilms advancing on surfaces evolve according to conservation laws coupled with systems of partial differential equations for velocities, pressures and chemicals affecting cell behavior. Thin film approximations lead to…
Understanding the spread of infectious diseases requires integrating movement, physical constraints, and spatial configurations into epidemiological models. In this study, we investigate how particle diffusivity, hardcore interactions, and…
It is well known that on long time scales the behaviour of tracer particles diffusing in a cellular flow is effectively that of a Brownian motion. This paper studies the behaviour on "intermediate" time scales before diffusion sets in.…
We analyze diffusion of small particles in a solid polymeric medium taking into account a short range particle-polymer interaction. The system is modeled by a particle diffusion on a ternary lattice where the sites occupied by polymer…
Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex…
We consider one-dimensional systems comprising either active run-and-tumble particles (RTPs) or passive Brownian random walkers. These particles are either noninteracting or have hardcore exclusions. We study the dynamics of a single tracer…
Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by intricate, non-even surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive…
During development, organisms acquire three-dimensional shapes with important physiological consequences. While the basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To…
We propose a computational framework to study the growth and spread of bacterial biofilms on interfaces, as well as the action of antibiotics on them. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard…
We calculate the diffusion coefficient of an active tracer in a schematic crowded environment, represented as a lattice gas of passive particles with hardcore interactions. Starting from the master equation of the problem, we put forward a…
We have studied experimentally transport properties in a slowly driven granular system which recently was shown to display self-organized criticality [Frette {\em et al., Nature} {\bf 379}, 49 (1996)]. Tracer particles were added to a pile…
We consider a particle that is subject to a constant force and scatters inelastically on a vibrating periodically corrugated floor. At small friction and small radius of the circular scatterers the dynamics is dominated by resonances…
Modeling collective motion in non-conservative systems, such as granular materials, is difficult since a general microscopic-to-macroscopic approach is not available: there is no Hamiltonian, no known stationary densities in phase space,…
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…
A model for anomalous transport of tracer particles diffusing in complex media in two dimensions is proposed. The model takes into account the characteristics of persistent motion that active bath transfer to the tracer, thus the model…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
Biofilm growth changes many physical properties of porous media such as porosity, permeability and mass transport parameters. The growth depends on various environmental conditions, and in particular, on flow rates. Modeling the evolution…