No abstract

We investigate the nucleation of ordered phases, their symmetries, and distributions in dense frictional hard sphere packings as a function of particle volume fraction ϕ, by imposing cyclic shear and constant applied pressure conditions. We show, with internal imaging, that the nucleating crystallites in the bulk consist of 10-60 spheres with hexagonal close packed (hcp) order and nonspherical shape, that are oriented preferentially along the shear axis. Above ϕ=0.62±0.005, crystallites with face centered cubic (fcc) order are observed with increasing probability, and ordered domains grow rapidly. A polycrystalline phase with domains of fcc and hcp order is observed after hundreds of thousands of shear cycles.

A novel coarse-grained model is developed to elucidate thermodynamics and kinetic mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to capture key experimental results such as sequence-dependent thermal property and salt-dependent persistence length of ssDNA and dsDNA. Moreover, constant-temperature simulations on two single strands of a homogeneous sequence show two main mechanisms of hybridization: a slow slithering mechanism and a one-order faster zippering mechanism. Furthermore, large-scale simulations at a high DNA strand concentration demonstrate that DNA self-assembly is a robust and enthalpically driven process in which the formation of double helices is deciphered to occur via multiple self-assembly pathways including the strand displacement mechanism. However, sequence plays an important role in shifting the majority of one pathway over the others and controlling size distribution of self-assembled aggregates. This study yields a complex picture on the role of sequence on programmable self-assembly and demonstrates a promising simulation tool that is suitable for studies in DNA nanotechnology.