Related papers: Steady-state MreB helices inside bacteria: dynamic…
We study the partitioning of motile bacteria in an aqueous two-phase mixture of dextran (DEX) and polyethylene glycol (PEG), which can phase separate into DEX-rich and PEG-rich phases. While non-motile bacteria partition exclusively into…
Unlike macroscopic multistable mechanical systems such as snap bracelets or elastic shells that must be physically manipulated into various conformations, microscopic systems can undergo spontaneous conformation switching between…
We use ensemble machine learning algorithms to study the evolution of magnetic fields in magnetohydrodynamic (MHD) turbulence that is helically forced. We perform direct numerical simulations of helically forced turbulence using mean field…
The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, helix has a unique position. Helical structures are ubiquitous in nature and a helical shape…
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing…
We investigate the large population dynamics of a family of stochastic particle systems with three-state cyclic individual behaviour and parameter-dependent transition rates. On short time scales, the dynamics turns out to be approximated…
We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We develop a numerical framework to simulate the locomotion of a flagellated bacterium with a spheroidal head (such as Escherichia coli) in biological fluids like mucus, which are entangled polymer solutions exhibiting elasto-viscoplastic…
The flow of motor proteins on a filamental track is modelled within the the framework of lattice driven diffusive systems. Motors, considered as hopping particles, perform a highly biased asymmetric exclusion process when bound to the…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Engineered bacteria in which motility is reduced by local cell density generate periodic stripes of high and low density when spotted on agar plates. We study theoretically the origin and mechanism of this process in a kinetic model that…
Meso-scale turbulence was originally observed experimentally in various suspensions of swimming bacteria, as well as in the collective motion of active colloids. The corresponding large-scale dynamical patterns were reproduced in a simple…
Freestanding ferroelectric membranes are promising for flexible electronics, nonvolatile memory, photonics, and spintronics, but their synthesis is challenged by the need for reproducibility with precise stoichiometric control. Here, we…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
We study a generic model for the polarisation and motility of self-propelled soft objects, biological cells or biomimetic systems, interacting with a viscous substrate. The active forces generated by the cell on the substrate are modelled…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
We present direct numerical simulations of the equations of compressible magnetohydrodynamics in a wedge-shaped spherical shell, without shear, but with random helical forcing which has negative (positive) helicity in the northern…