Related papers: Multibody simulation of adhesion pili
We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
We discuss the implementation of a multiscale biophysico-chemical model able to cope with the main mechanisms underlying cumulative exocytosis in cells. The model is based on a diffusion equation in the presence of external forces that…
We extend classical Flory-Rehner theory for the expansion and compression of porous materials such as cross-linked polymer networks. The theory includes volume exclusion, affinity with the solvent, and finite stretching of the polymer…
Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new,…
As the development of new classes of antibiotics slows, bacterial resistance to existing antibiotics is becoming an increasing problem. A potential solution is to develop treatment strategies with an alternative mode of action. We consider…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We propose a nonlinear extension of the standard tube model for semidilute solutions of freely-sliding semiflexible polymers. Non-affine filament deformations at the entanglement scale, the renormalisation of direct interactions by thermal…
Bacteria can adjust the structure of colonies and biofilms to enhance their survival rate under external stress. Here, we explore the link between bacterial interaction forces and colony structure. We show that the activity of extracellular…
We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…
The adhesive and frictional response of an AFM tip connected to a substrate through supramolecular host-guest complexes is investigated by dynamic Monte Carlo simulations. The variation of the pull-off force with the unloading rate recently…
The near-surface swimming patterns of bacteria are strongly determined by the hydrodynamic interactions between bacteria and the surface, which trap bacteria in smooth circular trajectories that lead to inefficient surface exploration.…
We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ~25 nm^2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic…
We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility…
Growing living cultures of Escherichia coli bacteria were investigated using real-time in situ rheology and rheo-imaging measurements. In the early stages of growth (lag phase), and when subjected to a constant stationary shear, the…
The evolutionary success of bacteria lies in their ability to form complex surface-associated communities in diverse biophysical settings. However, it remains poorly understood how compliance of soft surfaces, measured in terms of their…