Confined dynamics of a single DNA molecule.

The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (R(g,bulk)/h)(1/4) scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.

Tilting angle and water slippage over hydrophobic coatings.

Hydrophobic coatings, such as octadecyltrichlorosilane or n-alkyl monolayers, enhance the slippage of liquids on solid walls. For a given alkyl chain length, the main structural parameter for homogeneous coatings is the tilt angle between coating molecules and the surface normal. In this paper, ab initio calculations are used to calculate the equilibrium configuration of coating molecules, showing that the tilt angle easily changes from 0° to 30° depending on the specific head group binding the solid substrate. These values are used to set up classical molecular dynamics of water slippage over the coatings using different water models (Transferable Intermolecular Potential 3 point (TIP3P), Transferable Intermolecular Potential 4 point (TIP4P) and TIP4P/2005). The slippage is found to be robust with respect to the coating tilting, while a slight dependence on the water model is observed.

Molecular dynamics simulation of ratchet motion in an asymmetric nanochannel.

The persistence of ratchet effects, i.e., nonzero mass flux under a zero-mean time-dependent drive, when many-body interactions are present, is studied via molecular dynamics (MD) simulations of a simple liquid flowing in an asymmetric nanopore. The results show that (i) ratchet effects persist under many-body density correlations induced by the forcing; (ii) two distinct linear responses (flux proportional to the drive amplitude) appear under strong loads. One regime has the same conductivity of linear response theory up to a forcing of about 10 kT, while the second displays a smaller conductivity, the difference in responses is due to geometric effects alone. (iii) Langevin simulations based on a naive mapping of the many-body equilibrium bulk diffusivity, D, onto the damping rate, gamma are also found to yield two distinct linear responses. However, in both regimes, the flux is significantly smaller than the one of MD simulations.

Thin front propagation in random shear flows.

Front propagation in time-dependent laminar flows is investigated in the limit of very fast reaction and very thin fronts--i.e., the so-called geometrical optics limit. In particular, we consider fronts stirred by random shear flows, whose time evolution is modeled in terms of Ornstein-Uhlembeck processes. We show that the ratio between the time correlation of the flow and an intrinsic time scale of the reaction dynamics (the wrinkling time tw) is crucial in determining both the front propagation speed and the front spatial patterns. The relevance of time correlation in realistic flows is briefly discussed in light of the bending phenomenon--i.e., the decrease of propagation speed observed at high flow intensities.