Effective diffusion constant of stochastic processes with spatially periodic noise.

We discuss the effective diffusion constant D_{eff} for stochastic processes with spatially dependent noise. Starting from a stochastic process given by a Langevin equation, different drift-diffusion equations can be derived depending on the choice of the discretization rule 0≤α≤1. We initially study the case of periodic heterogeneous diffusion without drift, and we determine a general result for the effective diffusion coefficient D_{eff}, which is valid for any value of α.

Chromatin remodelers: a concise introduction for biophysicists.

Chromatin remodelers are molecular motors that act on nucleosomes: they move them along DNA or (dis-)assemble them. Despite the fact that they perform essential regulatory functions in cells-their deregulation can contribute to the development of cancers and lead to cell death-chromatin remodelers have only received meager attention in the biophysics community so far. In this short text, we attempt to present the key features of this interesting class of enzymes obtained with different experimental and theoretical methods, thereby providing a concise introduction for biophysicists to further stimulate interest in their properties.

Short-time expansion of one-dimensional Fokker-Planck equations with heterogeneous diffusion.

We formulate a short-time expansion for one-dimensional Fokker-Planck equations with spatially dependent diffusion coefficients, derived from stochastic processes with Gaussian white noise, for general values of the discretization parameter 0≤α≤1 of the stochastic integral. The kernel of the Fokker-Planck equation (the propagator) can be expressed as a product of a singular and a regular term. While the singular term can be given in closed form, the regular term can be computed from a Taylor expansion whose coefficients obey simple ordinary differential equations.

Counterion-controlled phase equilibria in a charge-regulated polymer solution.

We study phase equilibria in a minimal model of charge-regulated polymer solutions. Our model consists of a single polymer species whose charge state arises from protonation-deprotonation processes in the presence of a dissolved acid, whose anions serve as screening counterions. We explicitly account for variability in the polymers' charge states.

Nucleosome Array Deformation in Chromatin is Sustained by Bending, Twisting and Kinking of Linker DNA.

Chromatin in the nucleus undergoes mechanical stresses from different sources during the various stages of cell life. Here a trinucleosome array is used as the minimal model to study the mechanical response to applied stress at the molecular level. By using large-scale, all-atom steered-molecular dynamics simulations, we show that the largest part of mechanical stress in compression is accommodated by the DNA linkers joining pairs of nucleosomes, which store the elastic energy accumulated by the applied force.