(117d) Self-Assembly of Complex DNA Architectures Via Multiscale Simulations for Nanotechnology and Alterative Energy

Elucidation of the molecular-level mechanisms by which DNA units are self-assembled nanostructures might provide new informative tools in the engineering of novel biomaterials. Our studies examine the role of DNA sequences and the environmental conditions on the morphology and mechanical properties of DNA assemblies by performing molecular dynamics simulations. We use a newly-developed coarse-grained model that bridges the gap between detailed atomistic models and extremely simplified models by capturing geometric and energetic details yet it is sufficiently simple to allow simulations of the spontaneous self-assembly of many DNA units simultaneously. We first examine the dependence of persistence length and melting temperature of as a function of ionic strength, composition and chain length. Our results from single-molecule simulations agree qualitatively with experimental data. To examine the kinetic mechanisms involved in DNA self-assembly, we perform constant-temperature simulations to observe the whole process of DNA assembly starting from random configurations of relatively large DNA systems. We also perform replica-exchange simulations to delineate a phase diagram characterizing different types of structure exhibited for each sequence as a function of the condition being examined. The findings of this research will guide experimentalists to identify systems of novel biomaterials with advantageous morphological properties.