Related papers: Multibody simulation of adhesion pili
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
We study a multi-body finite element model of a packing of hydrogel particles using the Flory-Rehner constitutive law to model the deformation of the swollen polymer network. We show that while the dependence of the pressure, $\Pi$, on the…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…
Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions…
Densely packed, motile bacteria can adopt collective states not seen in conventional, passive materials. These states remain in many ways mysterious, and their physical characterization can aid our understanding of natural bacterial…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…
Precipitation of fine particles into the base material of a metal is a potent strengthening mechanism. This is numerically analyzed within a continuum framework based on a higher order strain gradient plasticity theory and by use of an…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
We elucidate the elastic behavior of a wormlike chain in 3D under compression and provide exact solutions for the experimentally accessible force-extension relation in terms of generalized spheroidal wave functions. In striking contrast to…
We analyse the motion of a flagellated bacterium in a two-fluid medium using slender body theory. The two-fluid model is useful for describing a body moving through a complex fluid with a microstructure whose length scale is comparable to…
The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…
We propose a generic model to describe the mechanical response and failure of systems which undergo a series of stick-slip events when subjected to an external load. We model the system as a bundle of fibers, where single fibers can…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Peritrichously-flagellated bacteria, such as Escherichia coli, self-propel in fluids by using specialised motors to rotate multiple helical filaments. The rotation of each motor is transmitted to a short flexible segment called the hook…
The bending rigidity $k_c$ of bilayer vesicles self-assembled from amphiphilic diblock copolymers has been measured using single and dual-micropipet techniques. These copolymers are nearly a factor of 5 greater in hydrophobic membrane…
Biofilms, bacteria cells surrounded by a self-produced polymeric matrix, are common on medical devices and lead to many hospital infections. The biofilm lifecycle includes disassembly and dispersion, where bacteria clusters detach from the…
We study intact and bulging Escherichia coli cells using atomic force microscopy to separate the contributions of the cell wall and turgor pressure to the overall cell stiffness. We find strong evidence of power-law stress-stiffening in the…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…