Layer-by-layer unsupervised clustering of statistically relevant fluctuations in noisy time-series data of complex dynamical systems.

Complex systems are typically characterized by intricate internal dynamics that are often hard to elucidate. Ideally, this requires methods that allow to detect and classify in an unsupervised way the microscopic dynamical events occurring in the system. However, decoupling statistically relevant fluctuations from the internal noise remains most often nontrivial.

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.

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.

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.