257919 Nanocubes and Nucleosomes: One Story of Assembly and Another of Disassembly [Invited]
I will discuss the role of computational methods in providing new insights into the assembly and disassembly of nanoscale systems. First, I will discuss Monte Carlo simulations of polymer-grafted Silver nanoparticles that helped design strategies to assemble them, within a polymer thin film, into 1D plasmonic strings possessing tunable orientation and electromagnetic properties . We demonstrate the critical role played by the grafted polymer chain length in modulating the relative strengths of van der Waals attraction and steric repulsion and thereby dictating interparticle orientations. Second, I will discuss the development of a mesoscale model of the nucleosome and its Brownian dynamics simulations that helped elucidate the dynamics of force-induced unraveling of DNA from histone octamers . We demonstrate the role of non-uniform DNA/histone interactions in stabilizing the second turn of DNA relative to the first turn and reveal the complex flipping and rocking motions of the octamer during unraveling.
 B. Gao, G. Arya, & A. R. Tao, “Self-orienting nanocubes for the assembly of plasmonic nanojunctions,” Nat. Nano., in press (2012).
 I. V. Dobrovolskaia & G. Arya, “Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions,” submitted (2012).