Condensed Matter Theory

Abstract:

We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement.

Abstract:

We investigate the capillary filling of three-dimensional microchannels with surfaces patterned by posts of square cross section. We show that pinning on the edges of the posts suppresses and can halt capillary filling. We stress the importance of the channel walls in controlling whether filling can occur. In particular for channels higher than the distance between adjacent posts, filling occurs for contact angles less than a threshold angle of approximately 55 degrees , independent of the height of the channel.