How long does it take to pull an ideal polymer into a small hole?

We present scaling estimates for characteristic times taulin and taubr of pulling ideal linear and randomly branched polymers of N monomers into a small hole by a force f. We show that the absorbtion process develops as sequential straightening of folds of the initial polymer configuration. By estimating the typical size of the fold involved into the motion, we arrive at the following predictions, taulin(N) approximately N3/2/f and taubr(N)approximately N5/4/f, and we also confirm them by the molecular dynamics experiment.

How proteins search for their specific sites on DNA: the role of DNA conformation.

It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.

Electrophoresis of a charge-inverted macroion complex: Molecular-dynamics study.

We have performed molecular-dynamics simulations to study the effect of an external electric field on a macroion in the solution of multivalent Z : 1 salt. To obtain plausible hydrodynamics of the medium, we explicitly make the simulation of many neutral particles along with ions. In a weak electric field, the macroion drifts together with the strongly adsorbed multivalent counterions along the electric field, in the direction proving inversion of the charge sign. The reversed mobility of the macroion is insensitive to the external field, and increases with salt ionic strength. The reversed mobility takes a maximal value at intermediate counterion valence. The motion of the macroion complex does not induce any flow of the neutral solvent away from the macroion, which reveals screening of hydrodynamic interactions at short distances in electrolyte solutions. A very large electric field, comparable to the macroion unscreened field, disrupts charge inversion by stripping the adsorbed counterions off the macroion.