(201e) 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 [1]. 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 [2]. 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.

[1] B. Gao, G. Arya, & A. R. Tao, “Self-orienting nanocubes for the assembly of plasmonic nanojunctions,” Nat. Nano., in press (2012).

[2] I. V. Dobrovolskaia & G. Arya, “Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions,” submitted (2012).