Computational simulation of DNA origami with plasmonics nanoparticle.

Self-assembled DNA systems provide low-cost, programmable control over matter at the nanoscale. One of the most promising frontiers involves coupling self-assembled DNA nanostructures, such as DNA origami, to plasmonic nanoparticles, which exhibit resonant response to excitation in the visible spectrum that may be useful for both molecular sensings and force transduction applications. To decrease the experimental cost, computational simulations are often desired. However, few simulations combining DNA origami and nanoparticles with plasmonic effects have been made. Here, we present a method to simulate the dynamics of DNA origami combined with gold nanoparticles. Our method works by iteratively evaluating the optical properties of nanoparticles using the finite element method and then coupling the result to atomic resolution Brownian dynamics (ARBD) simulations that capture the fluctuations of the DNA nanostructure using a particle-based coarse-grained MD description. Hence, the developed workflow can be used to model dynamic DNA origami nanostructures where light is used to power and direct nanoscale motion.