Condensed Matter Theory

Abstract:

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.

Abstract:

The lateral Casimir force is employed to propose a nanoscale mechanical device composed of one rack and N pinions. A coupling between the pinions via torsional springs is shown to coordinate their motion through a synchronization transition. The system can work against loads that are greater than the lateral Casimir force for each device. The existence of a stable synchronized state ensures that the system could operate in full coordination without the need of delicate fine tuning of all the characteristics such as the spring constants, the corrugation amplitudes, and the distances between the rack and the pinions. © 2012 American Institute of Physics.