Condensed Matter Theory

Abstract:

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately and allows strand displacement to occur.

Abstract:

These lecture notes are intended to provide a simple overview of the physics of geometrically frustrated magnets. The emphasis is on classical and semiclassical treatments of the statistical mechanics and dynamics of frustrated Heisenberg models, and on the ways in which the results provide an understanding of some of the main observed properties of these systems.