A generalized version of the Rouse-Zimm model is applied to the calculation of the intrinsic viscosity of DNA. Some approximations of the model are examined, and some corrections are introduced in the evaluation of the eigenvalues from which the intrinsic viscosity is calculated. The theoretical results are compared with experimental data to obtain the molecular parameters of the model. The sta...

The organization of chromosomes into territories plays an important role in a wide range of cellular processes, including gene expression, transcription, and DNA repair. Current understanding has largely excluded the spatiotemporal dynamic fluctuations of the chromatin polymer. We combine in vivo chromatin motion analysis with mathematical modeling to elucidate the physical properties that unde...

We study the equilibrium morphologies of a single supramolecular magnetic filament in a three-dimensional system as a function of the effective strength of the magnetic dipolar interactions. The study is performed by means of Langevin dynamics simulations with a bead-spring chain model of freely rotating dipoles. We demonstrate the existence of three structural regimes as the value of the dipol...

It has long been known that some microswimmers seem to swim counter-intuitively faster when the viscosity of the surrounding fluid is increased, whereas others slow down. This conflicting dependence of the swimming velocity on the viscosity is poorly understood theoretically. Here we explain that any mechanical microswimmer with an elastic degree of freedom in a simple Newtonian fluid can exhib...

The apparent analogy between the self-diffusion of linear oligomers, 2 up to 64 monomers, and their trace diffusion in an entangled polymer host of length 256 was investigated by molecular dynamics at constant pressure. Oligomers and polymers were represented by a same generic coarse-grained (bead-spring) model. The scaling relationships of the self-diffusion coefficient, D, and trace diffusion...

A unifying theoretical framework for analyzing stochastic data from single-particle tracking (SPT) in viscoelastic materials is presented. A generalization of the bead-spring model for linear polymers is developed from a molecular point of view and from the standpoint of phenomenological linear viscoelasticity. The hydrodynamic interaction in the former is identified as the dashpots in the latt...

A classical model used in the study of dynamics of polymeric liquids is the beadspring chain representation of polymer molecules. The chain typically consists of a large number of beads and thus the state space V of its configuration, which is essentially the position of all the constituent beads, turns out to be high dimensional. The distribution function governing the configuration of a bead-...

In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong that the particles’ velocities are damped much faster than the duration of an integration timestep. Here we show that this conceptual limit can be dropped wi...

The conformation and drift properties of a telechelic chain moving through a porous host of randomly distributed static obstacles are studied using Brownian dynamics simulation for a Grest–Kremer bead-spring model of polymer. Static chain conformations exhibit non-monotonic behaviour as a function of the impurity density ρimp at zero bias. The chain initially shrinks due to an entropic barrier ...