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

Facile One-Step Photolithographic Method for Engineering Hierarchically Nano/Microstructured Transparent Superamphiphobic Surfaces

It is of great value to develop a simple, controllable, and scalable method of making superamphiphobic surfaces. Here we present a facile one-step photolithographic method to engineer superamphiphobic surfaces consisting of photoresist micropillars decorated with nanoparticles of the same photoresist. The surface or coating is optically transparent and versatile, and can be fabricated on a broad range of substrates including stretchable elastomers. During the development of the micropillar array, photoresist nanoparticles are spontaneously grown on the micropillars by a well-controlled emulsification process of the un-cross-linked residual photoresist. This creates a hierarchical structure with a re-entrant and convex morphology which is the key for superoleophobicity. The chemical bonding between the nanoparticles and the micropillars is strong producing a robust and durable coating. This facile method is scalable and industry-applicable for a variety of applications such as self-cleaning, antifouling, and deicing/antifrosting

Cleaving C-H bonds with hyperthermal H2: Facile chemistry to cross-link organic molecules under low chemical- and energy-loads

A facile method for cross-linking organic molecules has been developed by computational modeling, instrumentation design, and experimental research. Briefly, organic molecules are hit by H2 with controllable kinetic energy in our novel apparatus where a high flux of hyperthermal H2 is generated. When a C-H bond of the organic molecule is hit by H2 at about 20 eV, efficient kinematic energy-transfer in the H2→H collision facilitates the C-H dissociation with nearly 100% reaction probability. When H2 hits other atoms which are by nature much heavier than H2, mass disparity bars effective energy transfer and this both blocks undesirable bond dissociation and reduces unnecessary energy wastage. The recombination of the carbon radicals generated by the C-H cleavage efficiently completes the production of C-C cross-links at room temperature with no additional energy/chemicals requirements. In addition to these green chemistry merits, this new method is better than other cross-linking techniques which rely on prerequisite reactions to add cross-linkers to the organic molecules or additional reactants and additives. These promising features are validated by several cross-linking trials which demonstrate desirable mechanical, electrical, chemical, and biochemical changes while inducing no undesirable damage of chemical functionalities in the original molecules. © 2014 The Royal Society of Chemistry