Related papers: Chain reconfiguration in active noise
We study the effects of noise on the dynamics of a system of coupled self-propelling particles in the case where the coupling is time-delayed, and the delays are discrete and randomly generated. Previous work has demonstrated that the…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical…
The dynamical organization in the presence of noise of a Boolean neural network with random connections is analyzed. For low levels of noise, the system reaches a stationary state in which the majority of its elements acquire the same…
Using computer simulations, we study the dynamics of colloidal particles with time-delayed feedback interactions. In particular, here we consider "feedback-pullers", i.e.~colloidal particles that are pulled away from their current position…
Foam is a canonical example of disordered soft matter where local force balance leads to the competition of many metastable configurations. Here we present an experimental and theoretical framework for "active foam" where an individual…
The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to…
We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the…
We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
The most conspicuous property of a semiflexible polymer is its persistence length, defined as the decay length of tangent correlations along its contour. Using an efficient stochastic growth algorithm to sample polymers embedded in a…
Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer chain is usually assumed to occur via the Forster mechanism which predicts a 1/R^6 distance dependence of the transfer rate, where R is the…
The Kaczmarz algorithm is an iterative method to reconstruct an unknown vector $f$ from inner products $\langle f , \varphi_{n} \rangle $. We consider the problem of how additive noise affects the reconstruction under the assumption that…
The constituents in a class of active matter systems change their directions of motion by being influenced by the velocities of the neighbors. Such systems may undergo phase transitions, with respect to ordering in the velocity field, as…
Active polymer translocation through confined spaces is a key biological process underlying DNA transport through nuclear pores and actin filament dynamics in cell migration. Here, we use living polymer-like Tubifex tubifex worms as a model…
We study how the temporal behaviours of p53 and MDM2 are affected by stress inducing bioactive molecules NO (Nitric Oxide) in the p53-MDM2-NO regulatory network. We also study synchronization among a group of identical stress systems…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…