Related papers: Multibody simulation of adhesion pili
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a…
Peritrichous bacteria such as Escherichia coli swim in viscous fluids by forming a helical bundle of flagellar filaments. The filaments are spatially distributed around the cell body to which they are connected via a flexible hook. To…
Optical tweezers are a technique in which microscopic-sized particles, including living cells and bacteria, can be non-intrusively trapped with high accuracy solely using focused light. The technique has therefore become a powerful tool in…
A new kinetic model for the dynamics of myxobacteria colonies on flat surfaces is derived formally, and first analytical and numerical results are presented. The model is based on the assumption of hard binary collisions of two different…
In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers. These models serve as valuable frameworks for…
Run-and-tumble motility is widely used by swimming microorganisms including numerous prokaryotic eukaryotic organisms. Here, we experimentally investigate the run-and-tumble dynamics of the bacterium E. coli in polymeric solutions. We find…
To model the morphogenesis of rod-shaped bacterial micro-colony, several individual-based models have been proposed in the biophysical literature. When studying the shape of micro-colonies, most models present interaction forces such as…
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 investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
The wear volume is known to keep increasing during frictional processes, and Archard notably proposed a model to describe the probability of wear particle formation upon asperity collision in a two-body contact configuration. While this…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Two-dimensional (2D) mechanical models of confluent tissues have related the mechanical state of a monolayer of cells to the average perimeter length of the cell cross sections, predicting floppiness or rigidity of the material. For the…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
In some conditions, bacteria self-organise into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed on polysaccharides, DNA, proteins and lipids. It is known that bacteria change their colony/matrix…
The presence of bacterial biofilms in clinical and industrial settings is a major issue worldwide. A biofilm is a viscoelastic matrix, composed of bacteria producing a network of Extracellular Polymeric Substances (EPS) to which bacteria…
In Part I of this two part series, we presented a multi-neighbor dependent contact model for adhesive elastic-plastic particles built upon the method of dimensionality reduction that is valid for the elastic and fully-plastic contact…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…