Density-tunable pathway complexity in a minimalistic self-assembly model.

An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.

RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration.

We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation.

Molecular layers in thin supported films exhibit the same scaling as the bulk between slow relaxation and vibrational dynamics.

We perform molecular-dynamics simulations of a supported molecular thin film. By varying thickness and temperature, we observe anisotropic mobility as well as strong gradients of both the vibrational motion and the structural relaxation through film layers with monomer-size thickness. We show that the gradients of the fast and the slow dynamics across the layers (except the adherent layer to the substrate) comply, without any adjustment, with the same scaling between the structural relaxation time and the Debye-Waller factor originally observed in the bulk [Larini et al., Nat. Phys., 2008, 4, 42]. The scaling is not observed if the average dynamics of the film is inspected. Our results suggest that the solidification process of each layer may be tracked by knowing solely the vibrational properties of the layer and the bulk.