Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes

Dynamical transitions in correlated driven diffusion in a periodic potential

The diffusion of a two-dimensional array of particles driven by a constant force in the presence of a periodic external potential exhibits a hierarchy of dynamical phase transitions when the driving force is varied. This behavior can be explained by a simple phenomenological approach which reduces the system of strongly interacting particles to weakly interacting quasi-particles (kinks). The richness of the strongly coupled system is however not lost because, contrary to a single-Brownian particle, the array shows an hysteretic behavior even at non-zero temperature. The present investigation can be viewed as a first step toward understanding nanotribology.Comment: 4 pages, 3 pictures, revtex to appear in Phys Rev. Let

Dynamical phase diagram of the dc-driven underdamped Frenkel-Kontorova chain

Multistep dynamical phase transition from the locked to the running state of atoms in response to a dc external force is studied by MD simulations of the generalized Frenkel-Kontorova model in the underdamped limit. We show that the hierarchy of transition recently reported [Braun et al, Phys. Rev. Lett. 78, 1295 (1997)] strongly depends on the value of the friction constant. A simple phenomenological explanation for the friction dependence of the various critical forces separating intermediate regimes is given.Comment: 12 Revtex Pages, 4 EPS figure

When droplets become stars: charged dielectric droplets beyond the Rayleigh limit

When a nano-drop comprising a single spherical central ion and dielectric solvent is charged above a well-defined threshold, it acquires a stable star morphology. These shapes are found by atomistic molecular dynamics and are compared with continuum modelling.</p